Mercurial > octave-nkf
annotate src/ls-hdf5.cc @ 8676:22462fd58e66
require HDF5 v1.6 API
| author | John W. Eaton <jwe@octave.org> |
|---|---|
| date | Thu, 05 Feb 2009 01:19:29 -0500 |
| parents | 712cfdc2e417 |
| children | 354179c24c79 |
| rev | line source |
|---|---|
| 4634 | 1 /* |
| 2 | |
| 7017 | 3 Copyright (C) 1996, 1997, 2003, 2004, 2005, 2006, 2007 John W. Eaton |
| 4634 | 4 |
| 5 This file is part of Octave. | |
| 6 | |
| 7 Octave is free software; you can redistribute it and/or modify it | |
| 8 under the terms of the GNU General Public License as published by the | |
| 7016 | 9 Free Software Foundation; either version 3 of the License, or (at your |
| 10 option) any later version. | |
| 4634 | 11 |
| 12 Octave is distributed in the hope that it will be useful, but WITHOUT | |
| 13 ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or | |
| 14 FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License | |
| 15 for more details. | |
| 16 | |
| 17 You should have received a copy of the GNU General Public License | |
| 7016 | 18 along with Octave; see the file COPYING. If not, see |
| 19 <http://www.gnu.org/licenses/>. | |
| 4634 | 20 |
| 21 */ | |
| 22 | |
| 23 // Author: Steven G. Johnson <stevenj@alum.mit.edu> | |
| 24 | |
| 25 #ifdef HAVE_CONFIG_H | |
| 26 #include <config.h> | |
| 27 #endif | |
| 28 | |
| 29 #if defined (HAVE_HDF5) | |
| 30 | |
| 31 #include <cfloat> | |
| 32 #include <cstring> | |
| 33 #include <cctype> | |
| 34 | |
| 35 #include <fstream> | |
| 36 #include <iomanip> | |
| 37 #include <iostream> | |
| 38 #include <string> | |
| 4726 | 39 #include <vector> |
| 4634 | 40 |
| 41 #include "byte-swap.h" | |
| 42 #include "data-conv.h" | |
| 43 #include "file-ops.h" | |
| 44 #include "glob-match.h" | |
| 45 #include "lo-mappers.h" | |
| 46 #include "mach-info.h" | |
| 47 #include "oct-env.h" | |
| 48 #include "oct-time.h" | |
| 49 #include "quit.h" | |
| 50 #include "str-vec.h" | |
|
8377
25bc2d31e1bf
improve OCTAVE_LOCAL_BUFFER
Jaroslav Hajek <highegg@gmail.com>
parents:
7336
diff
changeset
|
51 #include "oct-locbuf.h" |
| 4634 | 52 |
| 53 #include "Cell.h" | |
| 54 #include "defun.h" | |
| 55 #include "error.h" | |
| 56 #include "gripes.h" | |
| 57 #include "load-save.h" | |
| 58 #include "oct-obj.h" | |
| 59 #include "oct-map.h" | |
| 60 #include "ov-cell.h" | |
| 61 #include "pager.h" | |
| 62 #include "pt-exp.h" | |
| 63 #include "sysdep.h" | |
| 64 #include "unwind-prot.h" | |
| 65 #include "utils.h" | |
| 66 #include "variables.h" | |
| 67 #include "version.h" | |
| 68 #include "dMatrix.h" | |
| 69 | |
| 70 #include "ls-utils.h" | |
| 71 #include "ls-hdf5.h" | |
| 72 | |
| 73 static std::string | |
| 74 make_valid_identifier (const std::string& nm) | |
| 75 { | |
| 76 std::string retval; | |
| 77 | |
| 78 size_t nm_len = nm.length (); | |
| 79 | |
| 80 if (nm_len > 0) | |
| 81 { | |
| 82 if (! isalpha (nm[0])) | |
| 83 retval += '_'; | |
| 84 | |
| 85 for (size_t i = 0; i < nm_len; i++) | |
| 86 { | |
| 87 char c = nm[i]; | |
| 88 retval += (isalnum (c) || c == '_') ? c : '_'; | |
| 89 } | |
| 90 } | |
| 91 | |
| 92 return retval; | |
| 93 } | |
| 94 | |
| 95 // Define this to 1 if/when HDF5 supports automatic conversion between | |
| 96 // integer and floating-point binary data: | |
| 97 #define HAVE_HDF5_INT2FLOAT_CONVERSIONS 0 | |
| 98 | |
| 99 // Given two compound types t1 and t2, determine whether they | |
| 100 // are compatible for reading/writing. This function only | |
| 101 // works for non-nested types composed of simple elements (ints, floats...), | |
| 102 // which is all we need it for | |
| 103 | |
| 104 bool | |
| 105 hdf5_types_compatible (hid_t t1, hid_t t2) | |
| 106 { | |
| 107 int n; | |
| 108 if ((n = H5Tget_nmembers (t1)) != H5Tget_nmembers (t2)) | |
| 109 return false; | |
| 110 | |
| 111 for (int i = 0; i < n; ++i) | |
| 112 { | |
| 113 hid_t mt1 = H5Tget_member_type (t1, i); | |
| 114 hid_t mt2 = H5Tget_member_type (t2, i); | |
| 115 | |
| 116 if (H5Tget_class (mt1) != H5Tget_class (mt2)) | |
| 117 return false; | |
| 118 | |
| 119 H5Tclose (mt2); | |
| 120 H5Tclose (mt1); | |
| 121 } | |
| 122 | |
| 123 return true; | |
| 124 } | |
| 125 | |
| 126 // Return true if loc_id has the attribute named attr_name, and false | |
| 127 // otherwise. | |
| 128 | |
| 129 bool | |
| 130 hdf5_check_attr (hid_t loc_id, const char *attr_name) | |
| 131 { | |
| 132 bool retval = false; | |
| 133 | |
| 134 // we have to pull some shenanigans here to make sure | |
| 135 // HDF5 doesn't print out all sorts of error messages if we | |
| 136 // call H5Aopen for a non-existing attribute | |
| 137 | |
| 138 H5E_auto_t err_func; | |
| 139 void *err_func_data; | |
| 140 | |
| 141 // turn off error reporting temporarily, but save the error | |
| 142 // reporting function: | |
| 143 | |
| 144 H5Eget_auto (&err_func, &err_func_data); | |
| 145 H5Eset_auto (0, 0); | |
| 146 | |
| 147 hid_t attr_id = H5Aopen_name (loc_id, attr_name); | |
| 148 | |
| 149 if (attr_id >= 0) | |
| 150 { | |
| 151 // successful | |
| 152 retval = 1; | |
| 153 H5Aclose (attr_id); | |
| 154 } | |
| 155 | |
| 156 // restore error reporting: | |
| 157 H5Eset_auto (err_func, err_func_data); | |
| 158 | |
| 159 return retval; | |
| 160 } | |
| 161 | |
| 4687 | 162 // The following subroutines creates an HDF5 representations of the way |
| 163 // we will store Octave complex types (pairs of floating-point numbers). | |
| 164 // NUM_TYPE is the HDF5 numeric type to use for storage (e.g. | |
| 165 // H5T_NATIVE_DOUBLE to save as 'double'). Note that any necessary | |
| 166 // conversions are handled automatically by HDF5. | |
| 4634 | 167 |
| 4687 | 168 hid_t |
| 4634 | 169 hdf5_make_complex_type (hid_t num_type) |
| 170 { | |
| 171 hid_t type_id = H5Tcreate (H5T_COMPOUND, sizeof (double) * 2); | |
| 172 | |
| 173 H5Tinsert (type_id, "real", 0 * sizeof (double), num_type); | |
| 174 H5Tinsert (type_id, "imag", 1 * sizeof (double), num_type); | |
| 175 | |
| 176 return type_id; | |
| 177 } | |
| 178 | |
| 179 // This variable, set in read_hdf5_data(), tells whether we are using | |
| 180 // a version of HDF5 with a buggy H5Giterate (i.e. which neglects to | |
| 181 // increment the index parameter to the next unread item). | |
| 182 static bool have_h5giterate_bug = false; | |
| 183 | |
| 184 // This function is designed to be passed to H5Giterate, which calls it | |
| 185 // on each data item in an HDF5 file. For the item whose name is NAME in | |
| 186 // the group GROUP_ID, this function sets dv->tc to an Octave representation | |
| 187 // of that item. (dv must be a pointer to hdf5_callback_data.) (It also | |
| 188 // sets the other fields of dv). | |
| 189 // | |
| 190 // It returns 1 on success (in which case H5Giterate stops and returns), | |
| 191 // -1 on error, and 0 to tell H5Giterate to continue on to the next item | |
| 192 // (e.g. if NAME was a data type we don't recognize). | |
| 193 | |
| 4687 | 194 herr_t |
| 4634 | 195 hdf5_read_next_data (hid_t group_id, const char *name, void *dv) |
| 196 { | |
| 197 hdf5_callback_data *d = static_cast <hdf5_callback_data *> (dv); | |
| 4687 | 198 hid_t type_id = -1, type_class_id = -1, data_id = -1, subgroup_id = -1, |
| 199 space_id = -1; | |
| 4634 | 200 |
| 201 H5G_stat_t info; | |
| 202 herr_t retval = 0; | |
| 203 bool ident_valid = valid_identifier (name); | |
| 204 | |
| 205 std::string vname = name; | |
| 206 | |
| 207 // Allow identifiers as all digits so we can load lists saved by | |
| 208 // earlier versions of Octave. | |
| 209 | |
| 4687 | 210 if (! ident_valid ) |
| 4634 | 211 { |
| 212 // fix the identifier, replacing invalid chars with underscores | |
| 213 vname = make_valid_identifier (vname); | |
| 214 | |
| 215 // check again (in case vname was null, empty, or some such thing): | |
| 216 ident_valid = valid_identifier (vname); | |
| 217 } | |
| 218 | |
| 219 H5Gget_objinfo (group_id, name, 1, &info); | |
| 220 | |
| 4687 | 221 if (info.type == H5G_GROUP && ident_valid) |
| 4634 | 222 { |
| 4687 | 223 subgroup_id = H5Gopen (group_id, name); |
| 4634 | 224 |
| 225 if (subgroup_id < 0) | |
| 226 { | |
| 227 retval = subgroup_id; | |
| 228 goto done; | |
| 229 } | |
| 230 | |
| 4687 | 231 if (hdf5_check_attr (subgroup_id, "OCTAVE_NEW_FORMAT")) |
| 232 { | |
| 233 data_id = H5Dopen (subgroup_id, "type"); | |
| 4634 | 234 |
| 4687 | 235 if (data_id < 0) |
| 4634 | 236 { |
| 4687 | 237 retval = data_id; |
| 238 goto done; | |
| 4634 | 239 } |
| 240 | |
| 4687 | 241 type_id = H5Dget_type (data_id); |
| 242 | |
| 243 type_class_id = H5Tget_class (type_id); | |
| 244 | |
| 245 if (type_class_id != H5T_STRING) | |
| 246 goto done; | |
| 247 | |
| 248 space_id = H5Dget_space (data_id); | |
| 249 hsize_t rank = H5Sget_simple_extent_ndims (space_id); | |
| 250 | |
| 251 if (rank != 0) | |
| 252 goto done; | |
| 253 | |
| 254 int slen = H5Tget_size (type_id); | |
| 255 if (slen < 0) | |
| 256 goto done; | |
| 257 | |
| 258 OCTAVE_LOCAL_BUFFER (char, typ, slen); | |
| 259 | |
| 260 // create datatype for (null-terminated) string to read into: | |
| 261 hid_t st_id = H5Tcopy (H5T_C_S1); | |
| 262 H5Tset_size (st_id, slen); | |
| 263 | |
| 264 if (H5Dread (data_id, st_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, | |
| 5760 | 265 typ) < 0) |
| 4687 | 266 goto done; |
| 267 | |
| 268 H5Tclose (st_id); | |
| 269 H5Dclose (data_id); | |
| 270 | |
| 271 d->tc = octave_value_typeinfo::lookup_type (typ); | |
| 272 | |
| 273 retval = (d->tc.load_hdf5 (subgroup_id, "value", | |
| 274 have_h5giterate_bug) ? 1 : -1); | |
| 275 | |
| 276 // check for OCTAVE_GLOBAL attribute: | |
| 277 d->global = hdf5_check_attr (subgroup_id, "OCTAVE_GLOBAL"); | |
| 278 | |
| 279 H5Gclose (subgroup_id); | |
| 4634 | 280 } |
| 281 else | |
| 282 { | |
| 4687 | 283 // an HDF5 group is treated as an octave structure by |
| 284 // default (since that preserves name information), and an | |
| 285 // octave list otherwise. | |
| 286 | |
| 287 if (hdf5_check_attr (subgroup_id, "OCTAVE_LIST")) | |
| 288 d->tc = octave_value_typeinfo::lookup_type ("list"); | |
| 289 else | |
| 4948 | 290 d->tc = octave_value_typeinfo::lookup_type ("struct"); |
| 4687 | 291 |
| 292 // check for OCTAVE_GLOBAL attribute: | |
| 293 d->global = hdf5_check_attr (subgroup_id, "OCTAVE_GLOBAL"); | |
| 294 | |
| 295 H5Gclose (subgroup_id); | |
| 4634 | 296 |
| 4687 | 297 retval = (d->tc.load_hdf5 (group_id, name, have_h5giterate_bug) |
| 298 ? 1 : -1); | |
| 299 } | |
| 300 | |
| 301 } | |
| 302 else if (info.type == H5G_DATASET && ident_valid) | |
| 303 { | |
| 304 // For backwards compatiability. | |
| 305 data_id = H5Dopen (group_id, name); | |
| 306 | |
| 307 if (data_id < 0) | |
| 308 { | |
| 309 retval = data_id; | |
| 310 goto done; | |
| 4634 | 311 } |
| 312 | |
| 4687 | 313 type_id = H5Dget_type (data_id); |
| 314 | |
| 315 type_class_id = H5Tget_class (type_id); | |
| 316 | |
| 317 if (type_class_id == H5T_FLOAT) | |
| 318 { | |
| 319 space_id = H5Dget_space (data_id); | |
| 320 | |
| 321 hsize_t rank = H5Sget_simple_extent_ndims (space_id); | |
| 322 | |
| 323 if (rank == 0) | |
| 324 d->tc = octave_value_typeinfo::lookup_type ("scalar"); | |
| 325 else | |
| 326 d->tc = octave_value_typeinfo::lookup_type ("matrix"); | |
| 327 | |
| 328 H5Sclose (space_id); | |
| 329 } | |
| 4948 | 330 else if (type_class_id == H5T_INTEGER) |
| 331 { | |
| 332 // What integer type do we really have.. | |
| 333 std::string int_typ; | |
| 334 #ifdef HAVE_H5T_GET_NATIVE_TYPE | |
| 5775 | 335 // FIXME test this code and activated with an autoconf |
| 5351 | 336 // test!! It is also incorrect for 64-bit indexing!! |
| 337 | |
| 4948 | 338 switch (H5Tget_native_type (type_id, H5T_DIR_ASCEND)) |
| 339 { | |
| 340 case H5T_NATIVE_CHAR: | |
| 341 int_typ = "int8 "; | |
| 342 break; | |
| 343 | |
| 344 case H5T_NATIVE_SHORT: | |
| 345 int_typ = "int16 "; | |
| 346 break; | |
| 347 | |
| 348 case H5T_NATIVE_INT: | |
| 349 case H5T_NATIVE_LONG: | |
| 350 int_typ = "int32 "; | |
| 351 break; | |
| 352 | |
| 353 case H5T_NATIVE_LLONG: | |
| 354 int_typ = "int64 "; | |
| 355 break; | |
| 356 | |
| 357 case H5T_NATIVE_UCHAR: | |
| 358 int_typ = "uint8 "; | |
| 359 break; | |
| 360 | |
| 361 case H5T_NATIVE_USHORT: | |
| 362 int_typ = "uint16 "; | |
| 363 break; | |
| 364 | |
| 365 case H5T_NATIVE_UINT: | |
| 366 case H5T_NATIVE_ULONG: | |
| 367 int_typ = "uint32 "; | |
| 368 break; | |
| 369 | |
| 370 case H5T_NATIVE_ULLONG: | |
| 371 int_typ = "uint64 "; | |
| 372 break; | |
| 373 } | |
| 374 #else | |
| 375 hid_t int_sign = H5Tget_sign (type_id); | |
| 376 | |
| 377 if (int_sign == H5T_SGN_ERROR) | |
| 378 warning ("load: can't read `%s' (unknown datatype)", name); | |
| 379 else | |
| 380 { | |
| 381 if (int_sign == H5T_SGN_NONE) | |
| 382 int_typ.append ("u"); | |
| 383 int_typ.append ("int"); | |
| 384 | |
| 385 int slen = H5Tget_size (type_id); | |
| 386 if (slen < 0) | |
| 387 warning ("load: can't read `%s' (unknown datatype)", name); | |
| 388 else | |
| 389 { | |
| 390 switch (slen) | |
| 391 { | |
| 392 case 1: | |
| 393 int_typ.append ("8 "); | |
| 394 break; | |
| 395 | |
| 396 case 2: | |
| 397 int_typ.append ("16 "); | |
| 398 break; | |
| 399 | |
| 400 case 4: | |
| 401 int_typ.append ("32 "); | |
| 402 break; | |
| 403 | |
| 404 case 8: | |
| 405 int_typ.append ("64 "); | |
| 406 break; | |
| 407 | |
| 408 default: | |
| 409 warning ("load: can't read `%s' (unknown datatype)", | |
| 410 name); | |
| 411 int_typ = ""; | |
| 412 break; | |
| 413 } | |
| 414 } | |
| 415 } | |
| 416 #endif | |
| 417 if (int_typ == "") | |
| 418 warning ("load: can't read `%s' (unknown datatype)", name); | |
| 419 else | |
| 420 { | |
| 421 // Matrix or scalar? | |
| 422 space_id = H5Dget_space (data_id); | |
| 423 | |
| 424 hsize_t rank = H5Sget_simple_extent_ndims (space_id); | |
| 425 | |
| 426 if (rank == 0) | |
| 427 int_typ.append ("scalar"); | |
| 428 else | |
| 429 int_typ.append ("matrix"); | |
| 430 | |
| 431 d->tc = octave_value_typeinfo::lookup_type (int_typ); | |
| 432 H5Sclose (space_id); | |
| 433 } | |
| 434 } | |
| 4687 | 435 else if (type_class_id == H5T_STRING) |
| 436 d->tc = octave_value_typeinfo::lookup_type ("string"); | |
| 437 else if (type_class_id == H5T_COMPOUND) | |
| 438 { | |
| 439 hid_t complex_type = hdf5_make_complex_type (H5T_NATIVE_DOUBLE); | |
| 440 | |
| 441 if (hdf5_types_compatible (type_id, complex_type)) | |
| 442 { | |
| 443 // read complex matrix or scalar variable | |
| 444 space_id = H5Dget_space (data_id); | |
| 445 hsize_t rank = H5Sget_simple_extent_ndims (space_id); | |
| 446 | |
| 447 if (rank == 0) | |
| 448 d->tc = octave_value_typeinfo::lookup_type ("complex scalar"); | |
| 449 else | |
| 450 d->tc = octave_value_typeinfo::lookup_type ("complex matrix"); | |
| 451 | |
| 452 H5Sclose (space_id); | |
| 453 } | |
| 454 else | |
| 455 // Assume that if its not complex its a range. If its not | |
| 456 // it'll be rejected later in the range code | |
| 457 d->tc = octave_value_typeinfo::lookup_type ("range"); | |
| 458 | |
| 459 H5Tclose (complex_type); | |
| 460 } | |
| 461 else | |
| 462 { | |
| 463 warning ("load: can't read `%s' (unknown datatype)", name); | |
| 464 retval = 0; // unknown datatype; skip | |
| 465 } | |
| 466 | |
| 467 // check for OCTAVE_GLOBAL attribute: | |
| 468 d->global = hdf5_check_attr (data_id, "OCTAVE_GLOBAL"); | |
| 469 | |
| 470 H5Tclose (type_id); | |
| 471 H5Dclose (data_id); | |
| 472 | |
| 473 retval = (d->tc.load_hdf5 (group_id, name, have_h5giterate_bug) | |
| 474 ? 1 : -1); | |
| 4634 | 475 } |
| 4687 | 476 |
| 477 if (!ident_valid) | |
| 4634 | 478 { |
| 479 // should we attempt to handle invalid identifiers by converting | |
| 480 // bad characters to '_', say? | |
| 481 warning ("load: skipping invalid identifier `%s' in hdf5 file", | |
| 482 name); | |
| 483 } | |
| 484 | |
| 485 done: | |
| 486 if (retval < 0) | |
| 487 error ("load: error while reading hdf5 item %s", name); | |
| 4687 | 488 |
| 4634 | 489 if (retval > 0) |
| 490 { | |
| 491 // get documentation string, if any: | |
| 492 int comment_length = H5Gget_comment (group_id, name, 0, 0); | |
| 493 | |
| 494 if (comment_length > 1) | |
| 495 { | |
| 496 OCTAVE_LOCAL_BUFFER (char, tdoc, comment_length); | |
| 497 H5Gget_comment (group_id, name, comment_length, tdoc); | |
| 498 d->doc = tdoc; | |
| 499 } | |
| 500 else if (vname != name) | |
| 501 { | |
| 4687 | 502 // the name was changed; store the original name |
| 4634 | 503 // as the documentation string: |
| 504 d->doc = name; | |
| 505 } | |
| 506 | |
| 507 // copy name (actually, vname): | |
| 508 d->name = vname; | |
| 509 } | |
| 510 | |
| 511 return retval; | |
| 512 } | |
| 513 | |
| 514 // Read the next Octave variable from the stream IS, which must really be | |
| 515 // an hdf5_ifstream. Return the variable value in tc, its doc string | |
| 516 // in doc, and whether it is global in global. The return value is | |
| 517 // the name of the variable, or NULL if none were found or there was | |
| 4687 | 518 // and error. |
| 4634 | 519 std::string |
| 4687 | 520 read_hdf5_data (std::istream& is, const std::string& /* filename */, |
| 521 bool& global, octave_value& tc, std::string& doc) | |
| 4634 | 522 { |
| 523 std::string retval; | |
| 524 | |
| 525 doc.resize (0); | |
| 526 | |
| 5760 | 527 hdf5_ifstream& hs = dynamic_cast<hdf5_ifstream&> (is); |
| 4634 | 528 hdf5_callback_data d; |
| 529 | |
| 530 // Versions of HDF5 prior to 1.2.2 had a bug in H5Giterate where it | |
| 531 // would return the index of the last item processed instead of the | |
| 532 // next item to be processed, forcing us to increment the index manually. | |
| 533 | |
| 534 unsigned int vers_major, vers_minor, vers_release; | |
| 535 | |
| 536 H5get_libversion (&vers_major, &vers_minor, &vers_release); | |
| 537 | |
| 5775 | 538 // FIXME -- this test looks wrong. |
| 4634 | 539 have_h5giterate_bug |
| 540 = (vers_major < 1 | |
| 541 || (vers_major == 1 && (vers_minor < 2 | |
| 542 || (vers_minor == 2 && vers_release < 2)))); | |
| 543 | |
| 4696 | 544 herr_t H5Giterate_retval = -1; |
| 545 | |
| 546 #ifdef HAVE_H5GGET_NUM_OBJS | |
| 547 hsize_t num_obj = 0; | |
| 5060 | 548 hid_t group_id = H5Gopen (hs.file_id, "/"); |
| 549 H5Gget_num_objs (group_id, &num_obj); | |
| 550 H5Gclose (group_id); | |
| 4696 | 551 if (hs.current_item < static_cast<int> (num_obj)) |
| 552 #endif | |
| 553 H5Giterate_retval = H5Giterate (hs.file_id, "/", &hs.current_item, | |
| 554 hdf5_read_next_data, &d); | |
| 4634 | 555 |
| 556 if (have_h5giterate_bug) | |
| 557 { | |
| 558 // H5Giterate sets current_item to the last item processed; we want | |
| 559 // the index of the next item (for the next call to read_hdf5_data) | |
| 560 | |
| 561 hs.current_item++; | |
| 562 } | |
| 563 | |
| 564 if (H5Giterate_retval > 0) | |
| 565 { | |
| 566 global = d.global; | |
| 567 tc = d.tc; | |
| 568 doc = d.doc; | |
| 569 } | |
| 570 else | |
| 571 { | |
| 572 // an error occurred (H5Giterate_retval < 0) or there are no | |
| 573 // more datasets print an error message if retval < 0? | |
| 574 // hdf5_read_next_data already printed one, probably. | |
| 575 } | |
| 576 | |
| 577 if (! d.name.empty ()) | |
| 578 retval = d.name; | |
| 579 | |
| 580 return retval; | |
| 581 } | |
| 582 | |
| 583 // Add an attribute named attr_name to loc_id (a simple scalar | |
| 584 // attribute with value 1). Return value is >= 0 on success. | |
| 585 static herr_t | |
| 586 hdf5_add_attr (hid_t loc_id, const char *attr_name) | |
| 587 { | |
| 588 herr_t retval = 0; | |
| 589 | |
| 590 hid_t as_id = H5Screate (H5S_SCALAR); | |
| 591 | |
| 592 if (as_id >= 0) | |
| 593 { | |
| 594 hid_t a_id = H5Acreate (loc_id, attr_name, | |
| 595 H5T_NATIVE_UCHAR, as_id, H5P_DEFAULT); | |
| 596 | |
| 597 if (a_id >= 0) | |
| 598 { | |
| 599 unsigned char attr_val = 1; | |
| 600 | |
| 5760 | 601 retval = H5Awrite (a_id, H5T_NATIVE_UCHAR, &attr_val); |
| 4634 | 602 |
| 603 H5Aclose (a_id); | |
| 604 } | |
| 605 else | |
| 606 retval = a_id; | |
| 607 | |
| 608 H5Sclose (as_id); | |
| 609 } | |
| 610 else | |
| 611 retval = as_id; | |
| 612 | |
| 613 return retval; | |
| 614 } | |
| 615 | |
| 4805 | 616 // Save an empty matrix, if needed. Returns |
| 617 // > 0 Saved empty matrix | |
| 618 // = 0 Not an empty matrix; did nothing | |
| 619 // < 0 Error condition | |
| 620 int | |
| 621 save_hdf5_empty (hid_t loc_id, const char *name, const dim_vector d) | |
| 622 { | |
| 623 hsize_t sz = d.length (); | |
| 6276 | 624 OCTAVE_LOCAL_BUFFER (octave_idx_type, dims, sz); |
| 4805 | 625 bool empty = false; |
| 626 hid_t space_hid = -1, data_hid = -1; | |
| 627 int retval; | |
| 628 for (hsize_t i = 0; i < sz; i++) | |
| 629 { | |
| 630 dims[i] = d(i); | |
| 631 if (dims[i] < 1) | |
| 632 empty = true; | |
| 633 } | |
| 634 | |
| 635 if (!empty) | |
| 636 return 0; | |
| 637 | |
| 5760 | 638 space_hid = H5Screate_simple (1, &sz, 0); |
| 4805 | 639 if (space_hid < 0) return space_hid; |
| 640 | |
| 5351 | 641 data_hid = H5Dcreate (loc_id, name, H5T_NATIVE_IDX, space_hid, |
| 4805 | 642 H5P_DEFAULT); |
| 643 if (data_hid < 0) | |
| 644 { | |
| 645 H5Sclose (space_hid); | |
| 646 return data_hid; | |
| 647 } | |
| 648 | |
| 5351 | 649 retval = H5Dwrite (data_hid, H5T_NATIVE_IDX, H5S_ALL, H5S_ALL, |
| 5760 | 650 H5P_DEFAULT, dims) >= 0; |
| 4805 | 651 |
| 652 H5Dclose (data_hid); | |
| 653 H5Sclose (space_hid); | |
| 654 | |
| 655 if (retval >= 0) | |
| 656 retval = hdf5_add_attr (loc_id, "OCTAVE_EMPTY_MATRIX"); | |
| 657 | |
| 658 return (retval == 0 ? 1 : retval); | |
| 659 } | |
| 660 | |
| 661 // Load an empty matrix, if needed. Returns | |
| 662 // > 0 loaded empty matrix, dimensions returned | |
| 663 // = 0 Not an empty matrix; did nothing | |
| 664 // < 0 Error condition | |
| 665 int | |
| 666 load_hdf5_empty (hid_t loc_id, const char *name, dim_vector &d) | |
| 667 { | |
| 668 if (!hdf5_check_attr(loc_id, "OCTAVE_EMPTY_MATRIX")) | |
| 669 return 0; | |
| 670 | |
| 671 hsize_t hdims, maxdims; | |
| 672 hid_t data_hid = H5Dopen (loc_id, name); | |
| 673 hid_t space_id = H5Dget_space (data_hid); | |
| 674 H5Sget_simple_extent_dims (space_id, &hdims, &maxdims); | |
| 675 int retval; | |
| 676 | |
| 5351 | 677 OCTAVE_LOCAL_BUFFER (octave_idx_type, dims, hdims); |
| 678 | |
| 679 retval = H5Dread (data_hid, H5T_NATIVE_IDX, H5S_ALL, H5S_ALL, | |
| 5760 | 680 H5P_DEFAULT, dims); |
| 4805 | 681 if (retval >= 0) |
| 682 { | |
| 683 d.resize (hdims); | |
| 684 for (hsize_t i = 0; i < hdims; i++) | |
| 685 d(i) = dims[i]; | |
| 686 } | |
| 687 | |
| 688 H5Sclose (space_id); | |
| 689 H5Dclose (data_hid); | |
| 690 | |
| 691 return (retval == 0 ? hdims : retval); | |
| 692 } | |
| 693 | |
| 4634 | 694 // save_type_to_hdf5 is not currently used, since hdf5 doesn't yet support |
| 695 // automatic float<->integer conversions: | |
| 696 | |
| 697 #if HAVE_HDF5_INT2FLOAT_CONVERSIONS | |
| 698 | |
| 699 // return the HDF5 type id corresponding to the Octave save_type | |
| 700 | |
| 4687 | 701 hid_t |
| 4634 | 702 save_type_to_hdf5 (save_type st) |
| 703 { | |
| 704 switch (st) | |
| 705 { | |
| 706 case LS_U_CHAR: | |
| 707 return H5T_NATIVE_UCHAR; | |
| 708 | |
| 709 case LS_U_SHORT: | |
| 710 return H5T_NATIVE_USHORT; | |
| 711 | |
| 712 case LS_U_INT: | |
| 713 return H5T_NATIVE_UINT; | |
| 714 | |
| 715 case LS_CHAR: | |
| 716 return H5T_NATIVE_CHAR; | |
| 717 | |
| 718 case LS_SHORT: | |
| 719 return H5T_NATIVE_SHORT; | |
| 720 | |
| 721 case LS_INT: | |
| 722 return H5T_NATIVE_INT; | |
| 723 | |
| 724 case LS_FLOAT: | |
| 725 return H5T_NATIVE_FLOAT; | |
| 726 | |
| 727 case LS_DOUBLE: | |
| 728 default: | |
| 729 return H5T_NATIVE_DOUBLE; | |
| 730 } | |
| 731 } | |
| 732 #endif /* HAVE_HDF5_INT2FLOAT_CONVERSIONS */ | |
| 733 | |
| 734 // Add the data from TC to the HDF5 location loc_id, which could | |
| 735 // be either a file or a group within a file. Return true if | |
| 736 // successful. This function calls itself recursively for lists | |
| 737 // (stored as HDF5 groups). | |
| 738 | |
| 4687 | 739 bool |
| 4634 | 740 add_hdf5_data (hid_t loc_id, const octave_value& tc, |
| 741 const std::string& name, const std::string& doc, | |
| 742 bool mark_as_global, bool save_as_floats) | |
| 743 { | |
| 744 hsize_t dims[3]; | |
| 4687 | 745 hid_t type_id = -1, space_id = -1, data_id = -1, data_type_id = -1; |
| 746 bool retval = false; | |
| 747 octave_value val = tc; | |
|
8401
712cfdc2e417
allow saving diagonal & permutation matrices to hdf5 as full
Jaroslav Hajek <highegg@gmail.com>
parents:
8377
diff
changeset
|
748 // FIXME: diagonal & permutation matrices currently don't know how to save |
|
712cfdc2e417
allow saving diagonal & permutation matrices to hdf5 as full
Jaroslav Hajek <highegg@gmail.com>
parents:
8377
diff
changeset
|
749 // themselves, so we convert them first to normal matrices using A = A(:,:). |
|
712cfdc2e417
allow saving diagonal & permutation matrices to hdf5 as full
Jaroslav Hajek <highegg@gmail.com>
parents:
8377
diff
changeset
|
750 // This is a temporary hack. |
|
712cfdc2e417
allow saving diagonal & permutation matrices to hdf5 as full
Jaroslav Hajek <highegg@gmail.com>
parents:
8377
diff
changeset
|
751 if (val.is_diag_matrix () || val.is_perm_matrix ()) |
|
712cfdc2e417
allow saving diagonal & permutation matrices to hdf5 as full
Jaroslav Hajek <highegg@gmail.com>
parents:
8377
diff
changeset
|
752 val = val.do_index_op (octave_value_list (2, octave_value::magic_colon_t)); |
|
712cfdc2e417
allow saving diagonal & permutation matrices to hdf5 as full
Jaroslav Hajek <highegg@gmail.com>
parents:
8377
diff
changeset
|
753 |
|
712cfdc2e417
allow saving diagonal & permutation matrices to hdf5 as full
Jaroslav Hajek <highegg@gmail.com>
parents:
8377
diff
changeset
|
754 std::string t = val.type_name(); |
| 4634 | 755 |
| 4687 | 756 data_id = H5Gcreate (loc_id, name.c_str (), 0); |
| 757 if (data_id < 0) | |
| 758 goto error_cleanup; | |
| 4634 | 759 |
| 4687 | 760 // attach the type of the variable |
| 761 type_id = H5Tcopy (H5T_C_S1); H5Tset_size (type_id, t.length () + 1); | |
| 762 if (type_id < 0) | |
| 763 goto error_cleanup; | |
| 4634 | 764 |
| 4687 | 765 dims[0] = 0; |
| 5760 | 766 space_id = H5Screate_simple (0 , dims, 0); |
| 4687 | 767 if (space_id < 0) |
| 768 goto error_cleanup; | |
| 4634 | 769 |
| 4687 | 770 data_type_id = H5Dcreate (data_id, "type", type_id, space_id, H5P_DEFAULT); |
| 771 if (data_type_id < 0 || H5Dwrite (data_type_id, type_id, H5S_ALL, H5S_ALL, | |
| 5760 | 772 H5P_DEFAULT, t.c_str ()) < 0) |
| 4687 | 773 goto error_cleanup; |
| 4634 | 774 |
| 4687 | 775 // Now call the real function to save the variable |
| 776 retval = val.save_hdf5 (data_id, "value", save_as_floats); | |
| 4634 | 777 |
| 778 // attach doc string as comment: | |
| 4687 | 779 if (retval && doc.length () > 0 |
| 4634 | 780 && H5Gset_comment (loc_id, name.c_str (), doc.c_str ()) < 0) |
| 4687 | 781 retval = false; |
| 4634 | 782 |
| 783 // if it's global, add an attribute "OCTAVE_GLOBAL" with value 1 | |
| 4687 | 784 if (retval && mark_as_global) |
| 4634 | 785 retval = hdf5_add_attr (data_id, "OCTAVE_GLOBAL") >= 0; |
| 786 | |
| 4687 | 787 // We are saving in the new variable format, so mark it |
| 788 if (retval) | |
| 789 retval = hdf5_add_attr (data_id, "OCTAVE_NEW_FORMAT") >= 0; | |
| 790 | |
| 4634 | 791 error_cleanup: |
| 792 | |
| 4687 | 793 if (data_type_id >= 0) |
| 794 H5Dclose (data_type_id); | |
| 4634 | 795 |
| 4687 | 796 if (type_id >= 0) |
| 797 H5Tclose (type_id); | |
| 4634 | 798 |
| 799 if (space_id >= 0) | |
| 800 H5Sclose (space_id); | |
| 801 | |
| 4687 | 802 if (data_id >= 0) |
| 803 H5Gclose (data_id); | |
| 804 | |
| 805 if (! retval) | |
| 806 error ("save: error while writing `%s' to hdf5 file", name.c_str ()); | |
| 4634 | 807 |
| 808 return retval; | |
| 809 } | |
| 810 | |
| 811 // Write data from TC in HDF5 (binary) format to the stream OS, | |
| 812 // which must be an hdf5_ofstream, returning true on success. | |
| 813 | |
| 814 bool | |
| 815 save_hdf5_data (std::ostream& os, const octave_value& tc, | |
| 816 const std::string& name, const std::string& doc, | |
| 817 bool mark_as_global, bool save_as_floats) | |
| 818 { | |
| 5760 | 819 hdf5_ofstream& hs = dynamic_cast<hdf5_ofstream&> (os); |
| 4634 | 820 |
| 821 return add_hdf5_data (hs.file_id, tc, name, doc, | |
| 822 mark_as_global, save_as_floats); | |
| 823 } | |
| 824 | |
| 825 #endif | |
| 826 | |
| 827 /* | |
| 828 ;;; Local Variables: *** | |
| 829 ;;; mode: C++ *** | |
| 830 ;;; End: *** | |
| 831 */ |