Mercurial > hg > octave-lyh
annotate src/ls-hdf5.cc @ 9881:b3089dba88bf
Remove HDF5 cruft for older versions of HDF5
| author | Kacper Kowalik |
|---|---|
| date | Sat, 28 Nov 2009 14:00:56 +0100 |
| parents | eb63fbe60fab |
| children | ac69e6f4b33d |
| rev | line source |
|---|---|
| 4634 | 1 /* |
| 2 | |
| 8920 | 3 Copyright (C) 1996, 1997, 2003, 2004, 2005, 2006, 2007, 2008, |
| 4 2009 John W. Eaton | |
| 4634 | 5 |
| 6 This file is part of Octave. | |
| 7 | |
| 8 Octave is free software; you can redistribute it and/or modify it | |
| 9 under the terms of the GNU General Public License as published by the | |
| 7016 | 10 Free Software Foundation; either version 3 of the License, or (at your |
| 11 option) any later version. | |
| 4634 | 12 |
| 13 Octave is distributed in the hope that it will be useful, but WITHOUT | |
| 14 ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or | |
| 15 FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License | |
| 16 for more details. | |
| 17 | |
| 18 You should have received a copy of the GNU General Public License | |
| 7016 | 19 along with Octave; see the file COPYING. If not, see |
| 20 <http://www.gnu.org/licenses/>. | |
| 4634 | 21 |
| 22 */ | |
| 23 | |
| 24 // Author: Steven G. Johnson <stevenj@alum.mit.edu> | |
| 25 | |
| 26 #ifdef HAVE_CONFIG_H | |
| 27 #include <config.h> | |
| 28 #endif | |
| 29 | |
| 30 #if defined (HAVE_HDF5) | |
| 31 | |
| 32 #include <cfloat> | |
| 33 #include <cstring> | |
| 34 #include <cctype> | |
| 35 | |
| 36 #include <fstream> | |
| 37 #include <iomanip> | |
| 38 #include <iostream> | |
| 39 #include <string> | |
| 4726 | 40 #include <vector> |
| 4634 | 41 |
| 42 #include "byte-swap.h" | |
| 43 #include "data-conv.h" | |
| 44 #include "file-ops.h" | |
| 45 #include "glob-match.h" | |
| 46 #include "lo-mappers.h" | |
| 47 #include "mach-info.h" | |
| 48 #include "oct-env.h" | |
| 49 #include "oct-time.h" | |
| 50 #include "quit.h" | |
| 51 #include "str-vec.h" | |
|
8377
25bc2d31e1bf
improve OCTAVE_LOCAL_BUFFER
Jaroslav Hajek <highegg@gmail.com>
parents:
7336
diff
changeset
|
52 #include "oct-locbuf.h" |
| 4634 | 53 |
| 54 #include "Cell.h" | |
| 55 #include "defun.h" | |
| 56 #include "error.h" | |
| 57 #include "gripes.h" | |
| 58 #include "load-save.h" | |
| 59 #include "oct-obj.h" | |
| 60 #include "oct-map.h" | |
| 61 #include "ov-cell.h" | |
| 62 #include "pager.h" | |
| 63 #include "pt-exp.h" | |
| 64 #include "sysdep.h" | |
| 65 #include "unwind-prot.h" | |
| 66 #include "utils.h" | |
| 67 #include "variables.h" | |
| 68 #include "version.h" | |
| 69 #include "dMatrix.h" | |
| 70 | |
| 71 #include "ls-utils.h" | |
| 72 #include "ls-hdf5.h" | |
| 73 | |
| 74 static std::string | |
| 75 make_valid_identifier (const std::string& nm) | |
| 76 { | |
| 77 std::string retval; | |
| 78 | |
| 79 size_t nm_len = nm.length (); | |
| 80 | |
| 81 if (nm_len > 0) | |
| 82 { | |
| 83 if (! isalpha (nm[0])) | |
| 84 retval += '_'; | |
| 85 | |
| 86 for (size_t i = 0; i < nm_len; i++) | |
| 87 { | |
| 88 char c = nm[i]; | |
| 89 retval += (isalnum (c) || c == '_') ? c : '_'; | |
| 90 } | |
| 91 } | |
| 92 | |
| 93 return retval; | |
| 94 } | |
| 95 | |
| 96 // Define this to 1 if/when HDF5 supports automatic conversion between | |
| 97 // integer and floating-point binary data: | |
| 98 #define HAVE_HDF5_INT2FLOAT_CONVERSIONS 0 | |
| 99 | |
| 100 // Given two compound types t1 and t2, determine whether they | |
| 101 // are compatible for reading/writing. This function only | |
| 102 // works for non-nested types composed of simple elements (ints, floats...), | |
| 103 // which is all we need it for | |
| 104 | |
| 105 bool | |
| 106 hdf5_types_compatible (hid_t t1, hid_t t2) | |
| 107 { | |
| 108 int n; | |
| 109 if ((n = H5Tget_nmembers (t1)) != H5Tget_nmembers (t2)) | |
| 110 return false; | |
| 111 | |
| 112 for (int i = 0; i < n; ++i) | |
| 113 { | |
| 114 hid_t mt1 = H5Tget_member_type (t1, i); | |
| 115 hid_t mt2 = H5Tget_member_type (t2, i); | |
| 116 | |
| 117 if (H5Tget_class (mt1) != H5Tget_class (mt2)) | |
| 118 return false; | |
| 119 | |
| 120 H5Tclose (mt2); | |
| 121 H5Tclose (mt1); | |
| 122 } | |
| 123 | |
| 124 return true; | |
| 125 } | |
| 126 | |
| 127 // Return true if loc_id has the attribute named attr_name, and false | |
| 128 // otherwise. | |
| 129 | |
| 130 bool | |
| 131 hdf5_check_attr (hid_t loc_id, const char *attr_name) | |
| 132 { | |
| 133 bool retval = false; | |
| 134 | |
| 135 // we have to pull some shenanigans here to make sure | |
| 136 // HDF5 doesn't print out all sorts of error messages if we | |
| 137 // call H5Aopen for a non-existing attribute | |
| 138 | |
| 139 H5E_auto_t err_func; | |
| 140 void *err_func_data; | |
| 141 | |
| 142 // turn off error reporting temporarily, but save the error | |
| 143 // reporting function: | |
| 144 | |
| 145 H5Eget_auto (&err_func, &err_func_data); | |
| 146 H5Eset_auto (0, 0); | |
| 147 | |
| 148 hid_t attr_id = H5Aopen_name (loc_id, attr_name); | |
| 149 | |
| 150 if (attr_id >= 0) | |
| 151 { | |
| 152 // successful | |
| 153 retval = 1; | |
| 154 H5Aclose (attr_id); | |
| 155 } | |
| 156 | |
| 157 // restore error reporting: | |
| 158 H5Eset_auto (err_func, err_func_data); | |
| 159 | |
| 160 return retval; | |
| 161 } | |
| 162 | |
| 4687 | 163 // The following subroutines creates an HDF5 representations of the way |
| 164 // we will store Octave complex types (pairs of floating-point numbers). | |
| 165 // NUM_TYPE is the HDF5 numeric type to use for storage (e.g. | |
| 166 // H5T_NATIVE_DOUBLE to save as 'double'). Note that any necessary | |
| 167 // conversions are handled automatically by HDF5. | |
| 4634 | 168 |
| 4687 | 169 hid_t |
| 4634 | 170 hdf5_make_complex_type (hid_t num_type) |
| 171 { | |
| 172 hid_t type_id = H5Tcreate (H5T_COMPOUND, sizeof (double) * 2); | |
| 173 | |
| 174 H5Tinsert (type_id, "real", 0 * sizeof (double), num_type); | |
| 175 H5Tinsert (type_id, "imag", 1 * sizeof (double), num_type); | |
| 176 | |
| 177 return type_id; | |
| 178 } | |
| 179 | |
| 180 // This function is designed to be passed to H5Giterate, which calls it | |
| 181 // on each data item in an HDF5 file. For the item whose name is NAME in | |
| 182 // the group GROUP_ID, this function sets dv->tc to an Octave representation | |
| 183 // of that item. (dv must be a pointer to hdf5_callback_data.) (It also | |
| 184 // sets the other fields of dv). | |
| 185 // | |
| 186 // It returns 1 on success (in which case H5Giterate stops and returns), | |
| 187 // -1 on error, and 0 to tell H5Giterate to continue on to the next item | |
| 188 // (e.g. if NAME was a data type we don't recognize). | |
| 189 | |
| 4687 | 190 herr_t |
| 4634 | 191 hdf5_read_next_data (hid_t group_id, const char *name, void *dv) |
| 192 { | |
| 193 hdf5_callback_data *d = static_cast <hdf5_callback_data *> (dv); | |
| 4687 | 194 hid_t type_id = -1, type_class_id = -1, data_id = -1, subgroup_id = -1, |
| 195 space_id = -1; | |
| 4634 | 196 |
| 197 H5G_stat_t info; | |
| 198 herr_t retval = 0; | |
| 199 bool ident_valid = valid_identifier (name); | |
| 200 | |
| 201 std::string vname = name; | |
| 202 | |
| 203 // Allow identifiers as all digits so we can load lists saved by | |
| 204 // earlier versions of Octave. | |
| 205 | |
| 4687 | 206 if (! ident_valid ) |
| 4634 | 207 { |
| 208 // fix the identifier, replacing invalid chars with underscores | |
| 209 vname = make_valid_identifier (vname); | |
| 210 | |
| 211 // check again (in case vname was null, empty, or some such thing): | |
| 212 ident_valid = valid_identifier (vname); | |
| 213 } | |
| 214 | |
| 215 H5Gget_objinfo (group_id, name, 1, &info); | |
| 216 | |
| 4687 | 217 if (info.type == H5G_GROUP && ident_valid) |
| 4634 | 218 { |
| 4687 | 219 subgroup_id = H5Gopen (group_id, name); |
| 4634 | 220 |
| 221 if (subgroup_id < 0) | |
| 222 { | |
| 223 retval = subgroup_id; | |
| 224 goto done; | |
| 225 } | |
| 226 | |
| 4687 | 227 if (hdf5_check_attr (subgroup_id, "OCTAVE_NEW_FORMAT")) |
| 228 { | |
| 229 data_id = H5Dopen (subgroup_id, "type"); | |
| 4634 | 230 |
| 4687 | 231 if (data_id < 0) |
| 4634 | 232 { |
| 4687 | 233 retval = data_id; |
| 234 goto done; | |
| 4634 | 235 } |
| 236 | |
| 4687 | 237 type_id = H5Dget_type (data_id); |
| 238 | |
| 239 type_class_id = H5Tget_class (type_id); | |
| 240 | |
| 241 if (type_class_id != H5T_STRING) | |
| 242 goto done; | |
| 243 | |
| 244 space_id = H5Dget_space (data_id); | |
| 245 hsize_t rank = H5Sget_simple_extent_ndims (space_id); | |
| 246 | |
| 247 if (rank != 0) | |
| 248 goto done; | |
| 249 | |
| 250 int slen = H5Tget_size (type_id); | |
| 251 if (slen < 0) | |
| 252 goto done; | |
| 253 | |
| 254 OCTAVE_LOCAL_BUFFER (char, typ, slen); | |
| 255 | |
| 256 // create datatype for (null-terminated) string to read into: | |
| 257 hid_t st_id = H5Tcopy (H5T_C_S1); | |
| 258 H5Tset_size (st_id, slen); | |
| 259 | |
| 260 if (H5Dread (data_id, st_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, | |
| 5760 | 261 typ) < 0) |
| 4687 | 262 goto done; |
| 263 | |
| 264 H5Tclose (st_id); | |
| 265 H5Dclose (data_id); | |
| 266 | |
| 267 d->tc = octave_value_typeinfo::lookup_type (typ); | |
| 268 | |
|
9881
b3089dba88bf
Remove HDF5 cruft for older versions of HDF5
Kacper Kowalik
parents:
8920
diff
changeset
|
269 retval = (d->tc.load_hdf5 (subgroup_id, "value") ? 1 : -1); |
| 4687 | 270 |
| 271 // check for OCTAVE_GLOBAL attribute: | |
| 272 d->global = hdf5_check_attr (subgroup_id, "OCTAVE_GLOBAL"); | |
| 273 | |
| 274 H5Gclose (subgroup_id); | |
| 4634 | 275 } |
| 276 else | |
| 277 { | |
| 4687 | 278 // an HDF5 group is treated as an octave structure by |
| 279 // default (since that preserves name information), and an | |
| 280 // octave list otherwise. | |
| 281 | |
| 282 if (hdf5_check_attr (subgroup_id, "OCTAVE_LIST")) | |
| 283 d->tc = octave_value_typeinfo::lookup_type ("list"); | |
| 284 else | |
| 4948 | 285 d->tc = octave_value_typeinfo::lookup_type ("struct"); |
| 4687 | 286 |
| 287 // check for OCTAVE_GLOBAL attribute: | |
| 288 d->global = hdf5_check_attr (subgroup_id, "OCTAVE_GLOBAL"); | |
| 289 | |
| 290 H5Gclose (subgroup_id); | |
| 4634 | 291 |
|
9881
b3089dba88bf
Remove HDF5 cruft for older versions of HDF5
Kacper Kowalik
parents:
8920
diff
changeset
|
292 retval = (d->tc.load_hdf5 (group_id, name) ? 1 : -1); |
| 4687 | 293 } |
| 294 | |
| 295 } | |
| 296 else if (info.type == H5G_DATASET && ident_valid) | |
| 297 { | |
| 298 // For backwards compatiability. | |
| 299 data_id = H5Dopen (group_id, name); | |
| 300 | |
| 301 if (data_id < 0) | |
| 302 { | |
| 303 retval = data_id; | |
| 304 goto done; | |
| 4634 | 305 } |
| 306 | |
| 4687 | 307 type_id = H5Dget_type (data_id); |
| 308 | |
| 309 type_class_id = H5Tget_class (type_id); | |
| 310 | |
| 311 if (type_class_id == H5T_FLOAT) | |
| 312 { | |
| 313 space_id = H5Dget_space (data_id); | |
| 314 | |
| 315 hsize_t rank = H5Sget_simple_extent_ndims (space_id); | |
| 316 | |
| 317 if (rank == 0) | |
| 318 d->tc = octave_value_typeinfo::lookup_type ("scalar"); | |
| 319 else | |
| 320 d->tc = octave_value_typeinfo::lookup_type ("matrix"); | |
| 321 | |
| 322 H5Sclose (space_id); | |
| 323 } | |
| 4948 | 324 else if (type_class_id == H5T_INTEGER) |
| 325 { | |
| 326 // What integer type do we really have.. | |
| 327 std::string int_typ; | |
| 328 #ifdef HAVE_H5T_GET_NATIVE_TYPE | |
| 5775 | 329 // FIXME test this code and activated with an autoconf |
| 5351 | 330 // test!! It is also incorrect for 64-bit indexing!! |
| 331 | |
| 4948 | 332 switch (H5Tget_native_type (type_id, H5T_DIR_ASCEND)) |
| 333 { | |
| 334 case H5T_NATIVE_CHAR: | |
| 335 int_typ = "int8 "; | |
| 336 break; | |
| 337 | |
| 338 case H5T_NATIVE_SHORT: | |
| 339 int_typ = "int16 "; | |
| 340 break; | |
| 341 | |
| 342 case H5T_NATIVE_INT: | |
| 343 case H5T_NATIVE_LONG: | |
| 344 int_typ = "int32 "; | |
| 345 break; | |
| 346 | |
| 347 case H5T_NATIVE_LLONG: | |
| 348 int_typ = "int64 "; | |
| 349 break; | |
| 350 | |
| 351 case H5T_NATIVE_UCHAR: | |
| 352 int_typ = "uint8 "; | |
| 353 break; | |
| 354 | |
| 355 case H5T_NATIVE_USHORT: | |
| 356 int_typ = "uint16 "; | |
| 357 break; | |
| 358 | |
| 359 case H5T_NATIVE_UINT: | |
| 360 case H5T_NATIVE_ULONG: | |
| 361 int_typ = "uint32 "; | |
| 362 break; | |
| 363 | |
| 364 case H5T_NATIVE_ULLONG: | |
| 365 int_typ = "uint64 "; | |
| 366 break; | |
| 367 } | |
| 368 #else | |
| 369 hid_t int_sign = H5Tget_sign (type_id); | |
| 370 | |
| 371 if (int_sign == H5T_SGN_ERROR) | |
| 372 warning ("load: can't read `%s' (unknown datatype)", name); | |
| 373 else | |
| 374 { | |
| 375 if (int_sign == H5T_SGN_NONE) | |
| 376 int_typ.append ("u"); | |
| 377 int_typ.append ("int"); | |
| 378 | |
| 379 int slen = H5Tget_size (type_id); | |
| 380 if (slen < 0) | |
| 381 warning ("load: can't read `%s' (unknown datatype)", name); | |
| 382 else | |
| 383 { | |
| 384 switch (slen) | |
| 385 { | |
| 386 case 1: | |
| 387 int_typ.append ("8 "); | |
| 388 break; | |
| 389 | |
| 390 case 2: | |
| 391 int_typ.append ("16 "); | |
| 392 break; | |
| 393 | |
| 394 case 4: | |
| 395 int_typ.append ("32 "); | |
| 396 break; | |
| 397 | |
| 398 case 8: | |
| 399 int_typ.append ("64 "); | |
| 400 break; | |
| 401 | |
| 402 default: | |
| 403 warning ("load: can't read `%s' (unknown datatype)", | |
| 404 name); | |
| 405 int_typ = ""; | |
| 406 break; | |
| 407 } | |
| 408 } | |
| 409 } | |
| 410 #endif | |
| 411 if (int_typ == "") | |
| 412 warning ("load: can't read `%s' (unknown datatype)", name); | |
| 413 else | |
| 414 { | |
| 415 // Matrix or scalar? | |
| 416 space_id = H5Dget_space (data_id); | |
| 417 | |
| 418 hsize_t rank = H5Sget_simple_extent_ndims (space_id); | |
| 419 | |
| 420 if (rank == 0) | |
| 421 int_typ.append ("scalar"); | |
| 422 else | |
| 423 int_typ.append ("matrix"); | |
| 424 | |
| 425 d->tc = octave_value_typeinfo::lookup_type (int_typ); | |
| 426 H5Sclose (space_id); | |
| 427 } | |
| 428 } | |
| 4687 | 429 else if (type_class_id == H5T_STRING) |
| 430 d->tc = octave_value_typeinfo::lookup_type ("string"); | |
| 431 else if (type_class_id == H5T_COMPOUND) | |
| 432 { | |
| 433 hid_t complex_type = hdf5_make_complex_type (H5T_NATIVE_DOUBLE); | |
| 434 | |
| 435 if (hdf5_types_compatible (type_id, complex_type)) | |
| 436 { | |
| 437 // read complex matrix or scalar variable | |
| 438 space_id = H5Dget_space (data_id); | |
| 439 hsize_t rank = H5Sget_simple_extent_ndims (space_id); | |
| 440 | |
| 441 if (rank == 0) | |
| 442 d->tc = octave_value_typeinfo::lookup_type ("complex scalar"); | |
| 443 else | |
| 444 d->tc = octave_value_typeinfo::lookup_type ("complex matrix"); | |
| 445 | |
| 446 H5Sclose (space_id); | |
| 447 } | |
| 448 else | |
| 449 // Assume that if its not complex its a range. If its not | |
| 450 // it'll be rejected later in the range code | |
| 451 d->tc = octave_value_typeinfo::lookup_type ("range"); | |
| 452 | |
| 453 H5Tclose (complex_type); | |
| 454 } | |
| 455 else | |
| 456 { | |
| 457 warning ("load: can't read `%s' (unknown datatype)", name); | |
| 458 retval = 0; // unknown datatype; skip | |
| 459 } | |
| 460 | |
| 461 // check for OCTAVE_GLOBAL attribute: | |
| 462 d->global = hdf5_check_attr (data_id, "OCTAVE_GLOBAL"); | |
| 463 | |
| 464 H5Tclose (type_id); | |
| 465 H5Dclose (data_id); | |
| 466 | |
|
9881
b3089dba88bf
Remove HDF5 cruft for older versions of HDF5
Kacper Kowalik
parents:
8920
diff
changeset
|
467 retval = (d->tc.load_hdf5 (group_id, name) ? 1 : -1); |
| 4634 | 468 } |
| 4687 | 469 |
| 470 if (!ident_valid) | |
| 4634 | 471 { |
| 472 // should we attempt to handle invalid identifiers by converting | |
| 473 // bad characters to '_', say? | |
| 474 warning ("load: skipping invalid identifier `%s' in hdf5 file", | |
| 475 name); | |
| 476 } | |
| 477 | |
| 478 done: | |
| 479 if (retval < 0) | |
| 480 error ("load: error while reading hdf5 item %s", name); | |
| 4687 | 481 |
| 4634 | 482 if (retval > 0) |
| 483 { | |
| 484 // get documentation string, if any: | |
| 485 int comment_length = H5Gget_comment (group_id, name, 0, 0); | |
| 486 | |
| 487 if (comment_length > 1) | |
| 488 { | |
| 489 OCTAVE_LOCAL_BUFFER (char, tdoc, comment_length); | |
| 490 H5Gget_comment (group_id, name, comment_length, tdoc); | |
| 491 d->doc = tdoc; | |
| 492 } | |
| 493 else if (vname != name) | |
| 494 { | |
| 4687 | 495 // the name was changed; store the original name |
| 4634 | 496 // as the documentation string: |
| 497 d->doc = name; | |
| 498 } | |
| 499 | |
| 500 // copy name (actually, vname): | |
| 501 d->name = vname; | |
| 502 } | |
| 503 | |
| 504 return retval; | |
| 505 } | |
| 506 | |
| 507 // Read the next Octave variable from the stream IS, which must really be | |
| 508 // an hdf5_ifstream. Return the variable value in tc, its doc string | |
| 509 // in doc, and whether it is global in global. The return value is | |
| 510 // the name of the variable, or NULL if none were found or there was | |
| 4687 | 511 // and error. |
| 4634 | 512 std::string |
| 4687 | 513 read_hdf5_data (std::istream& is, const std::string& /* filename */, |
| 514 bool& global, octave_value& tc, std::string& doc) | |
| 4634 | 515 { |
| 516 std::string retval; | |
| 517 | |
| 518 doc.resize (0); | |
| 519 | |
| 5760 | 520 hdf5_ifstream& hs = dynamic_cast<hdf5_ifstream&> (is); |
| 4634 | 521 hdf5_callback_data d; |
| 522 | |
| 4696 | 523 herr_t H5Giterate_retval = -1; |
| 524 | |
| 525 hsize_t num_obj = 0; | |
| 5060 | 526 hid_t group_id = H5Gopen (hs.file_id, "/"); |
| 527 H5Gget_num_objs (group_id, &num_obj); | |
| 528 H5Gclose (group_id); | |
| 4696 | 529 if (hs.current_item < static_cast<int> (num_obj)) |
| 530 H5Giterate_retval = H5Giterate (hs.file_id, "/", &hs.current_item, | |
| 531 hdf5_read_next_data, &d); | |
| 4634 | 532 |
| 533 | |
| 534 if (H5Giterate_retval > 0) | |
| 535 { | |
| 536 global = d.global; | |
| 537 tc = d.tc; | |
| 538 doc = d.doc; | |
| 539 } | |
| 540 else | |
| 541 { | |
| 542 // an error occurred (H5Giterate_retval < 0) or there are no | |
| 543 // more datasets print an error message if retval < 0? | |
| 544 // hdf5_read_next_data already printed one, probably. | |
| 545 } | |
| 546 | |
| 547 if (! d.name.empty ()) | |
| 548 retval = d.name; | |
| 549 | |
| 550 return retval; | |
| 551 } | |
| 552 | |
| 553 // Add an attribute named attr_name to loc_id (a simple scalar | |
| 554 // attribute with value 1). Return value is >= 0 on success. | |
| 555 static herr_t | |
| 556 hdf5_add_attr (hid_t loc_id, const char *attr_name) | |
| 557 { | |
| 558 herr_t retval = 0; | |
| 559 | |
| 560 hid_t as_id = H5Screate (H5S_SCALAR); | |
| 561 | |
| 562 if (as_id >= 0) | |
| 563 { | |
| 564 hid_t a_id = H5Acreate (loc_id, attr_name, | |
| 565 H5T_NATIVE_UCHAR, as_id, H5P_DEFAULT); | |
| 566 | |
| 567 if (a_id >= 0) | |
| 568 { | |
| 569 unsigned char attr_val = 1; | |
| 570 | |
| 5760 | 571 retval = H5Awrite (a_id, H5T_NATIVE_UCHAR, &attr_val); |
| 4634 | 572 |
| 573 H5Aclose (a_id); | |
| 574 } | |
| 575 else | |
| 576 retval = a_id; | |
| 577 | |
| 578 H5Sclose (as_id); | |
| 579 } | |
| 580 else | |
| 581 retval = as_id; | |
| 582 | |
| 583 return retval; | |
| 584 } | |
| 585 | |
| 4805 | 586 // Save an empty matrix, if needed. Returns |
| 587 // > 0 Saved empty matrix | |
| 588 // = 0 Not an empty matrix; did nothing | |
| 589 // < 0 Error condition | |
| 590 int | |
| 591 save_hdf5_empty (hid_t loc_id, const char *name, const dim_vector d) | |
| 592 { | |
| 593 hsize_t sz = d.length (); | |
| 6276 | 594 OCTAVE_LOCAL_BUFFER (octave_idx_type, dims, sz); |
| 4805 | 595 bool empty = false; |
| 596 hid_t space_hid = -1, data_hid = -1; | |
| 597 int retval; | |
| 598 for (hsize_t i = 0; i < sz; i++) | |
| 599 { | |
| 600 dims[i] = d(i); | |
| 601 if (dims[i] < 1) | |
| 602 empty = true; | |
| 603 } | |
| 604 | |
| 605 if (!empty) | |
| 606 return 0; | |
| 607 | |
| 5760 | 608 space_hid = H5Screate_simple (1, &sz, 0); |
| 4805 | 609 if (space_hid < 0) return space_hid; |
| 610 | |
| 5351 | 611 data_hid = H5Dcreate (loc_id, name, H5T_NATIVE_IDX, space_hid, |
| 4805 | 612 H5P_DEFAULT); |
| 613 if (data_hid < 0) | |
| 614 { | |
| 615 H5Sclose (space_hid); | |
| 616 return data_hid; | |
| 617 } | |
| 618 | |
| 5351 | 619 retval = H5Dwrite (data_hid, H5T_NATIVE_IDX, H5S_ALL, H5S_ALL, |
| 5760 | 620 H5P_DEFAULT, dims) >= 0; |
| 4805 | 621 |
| 622 H5Dclose (data_hid); | |
| 623 H5Sclose (space_hid); | |
| 624 | |
| 625 if (retval >= 0) | |
| 626 retval = hdf5_add_attr (loc_id, "OCTAVE_EMPTY_MATRIX"); | |
| 627 | |
| 628 return (retval == 0 ? 1 : retval); | |
| 629 } | |
| 630 | |
| 631 // Load an empty matrix, if needed. Returns | |
| 632 // > 0 loaded empty matrix, dimensions returned | |
| 633 // = 0 Not an empty matrix; did nothing | |
| 634 // < 0 Error condition | |
| 635 int | |
| 636 load_hdf5_empty (hid_t loc_id, const char *name, dim_vector &d) | |
| 637 { | |
| 638 if (!hdf5_check_attr(loc_id, "OCTAVE_EMPTY_MATRIX")) | |
| 639 return 0; | |
| 640 | |
| 641 hsize_t hdims, maxdims; | |
| 642 hid_t data_hid = H5Dopen (loc_id, name); | |
| 643 hid_t space_id = H5Dget_space (data_hid); | |
| 644 H5Sget_simple_extent_dims (space_id, &hdims, &maxdims); | |
| 645 int retval; | |
| 646 | |
| 5351 | 647 OCTAVE_LOCAL_BUFFER (octave_idx_type, dims, hdims); |
| 648 | |
| 649 retval = H5Dread (data_hid, H5T_NATIVE_IDX, H5S_ALL, H5S_ALL, | |
| 5760 | 650 H5P_DEFAULT, dims); |
| 4805 | 651 if (retval >= 0) |
| 652 { | |
| 653 d.resize (hdims); | |
| 654 for (hsize_t i = 0; i < hdims; i++) | |
| 655 d(i) = dims[i]; | |
| 656 } | |
| 657 | |
| 658 H5Sclose (space_id); | |
| 659 H5Dclose (data_hid); | |
| 660 | |
| 661 return (retval == 0 ? hdims : retval); | |
| 662 } | |
| 663 | |
| 4634 | 664 // save_type_to_hdf5 is not currently used, since hdf5 doesn't yet support |
| 665 // automatic float<->integer conversions: | |
| 666 | |
| 667 #if HAVE_HDF5_INT2FLOAT_CONVERSIONS | |
| 668 | |
| 669 // return the HDF5 type id corresponding to the Octave save_type | |
| 670 | |
| 4687 | 671 hid_t |
| 4634 | 672 save_type_to_hdf5 (save_type st) |
| 673 { | |
| 674 switch (st) | |
| 675 { | |
| 676 case LS_U_CHAR: | |
| 677 return H5T_NATIVE_UCHAR; | |
| 678 | |
| 679 case LS_U_SHORT: | |
| 680 return H5T_NATIVE_USHORT; | |
| 681 | |
| 682 case LS_U_INT: | |
| 683 return H5T_NATIVE_UINT; | |
| 684 | |
| 685 case LS_CHAR: | |
| 686 return H5T_NATIVE_CHAR; | |
| 687 | |
| 688 case LS_SHORT: | |
| 689 return H5T_NATIVE_SHORT; | |
| 690 | |
| 691 case LS_INT: | |
| 692 return H5T_NATIVE_INT; | |
| 693 | |
| 694 case LS_FLOAT: | |
| 695 return H5T_NATIVE_FLOAT; | |
| 696 | |
| 697 case LS_DOUBLE: | |
| 698 default: | |
| 699 return H5T_NATIVE_DOUBLE; | |
| 700 } | |
| 701 } | |
| 702 #endif /* HAVE_HDF5_INT2FLOAT_CONVERSIONS */ | |
| 703 | |
| 704 // Add the data from TC to the HDF5 location loc_id, which could | |
| 705 // be either a file or a group within a file. Return true if | |
| 706 // successful. This function calls itself recursively for lists | |
| 707 // (stored as HDF5 groups). | |
| 708 | |
| 4687 | 709 bool |
| 4634 | 710 add_hdf5_data (hid_t loc_id, const octave_value& tc, |
| 711 const std::string& name, const std::string& doc, | |
| 712 bool mark_as_global, bool save_as_floats) | |
| 713 { | |
| 714 hsize_t dims[3]; | |
| 4687 | 715 hid_t type_id = -1, space_id = -1, data_id = -1, data_type_id = -1; |
| 716 bool retval = false; | |
| 717 octave_value val = tc; | |
|
8401
712cfdc2e417
allow saving diagonal & permutation matrices to hdf5 as full
Jaroslav Hajek <highegg@gmail.com>
parents:
8377
diff
changeset
|
718 // 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
|
719 // 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
|
720 // This is a temporary hack. |
|
712cfdc2e417
allow saving diagonal & permutation matrices to hdf5 as full
Jaroslav Hajek <highegg@gmail.com>
parents:
8377
diff
changeset
|
721 if (val.is_diag_matrix () || val.is_perm_matrix ()) |
|
8914
354179c24c79
fix hdf5 saving of diag & perm matrices
Jaroslav Hajek <highegg@gmail.com>
parents:
8676
diff
changeset
|
722 val = val.full_value (); |
|
8401
712cfdc2e417
allow saving diagonal & permutation matrices to hdf5 as full
Jaroslav Hajek <highegg@gmail.com>
parents:
8377
diff
changeset
|
723 |
|
712cfdc2e417
allow saving diagonal & permutation matrices to hdf5 as full
Jaroslav Hajek <highegg@gmail.com>
parents:
8377
diff
changeset
|
724 std::string t = val.type_name(); |
| 4634 | 725 |
| 4687 | 726 data_id = H5Gcreate (loc_id, name.c_str (), 0); |
| 727 if (data_id < 0) | |
| 728 goto error_cleanup; | |
| 4634 | 729 |
| 4687 | 730 // attach the type of the variable |
| 731 type_id = H5Tcopy (H5T_C_S1); H5Tset_size (type_id, t.length () + 1); | |
| 732 if (type_id < 0) | |
| 733 goto error_cleanup; | |
| 4634 | 734 |
| 4687 | 735 dims[0] = 0; |
| 5760 | 736 space_id = H5Screate_simple (0 , dims, 0); |
| 4687 | 737 if (space_id < 0) |
| 738 goto error_cleanup; | |
| 4634 | 739 |
| 4687 | 740 data_type_id = H5Dcreate (data_id, "type", type_id, space_id, H5P_DEFAULT); |
| 741 if (data_type_id < 0 || H5Dwrite (data_type_id, type_id, H5S_ALL, H5S_ALL, | |
| 5760 | 742 H5P_DEFAULT, t.c_str ()) < 0) |
| 4687 | 743 goto error_cleanup; |
| 4634 | 744 |
| 4687 | 745 // Now call the real function to save the variable |
| 746 retval = val.save_hdf5 (data_id, "value", save_as_floats); | |
| 4634 | 747 |
| 748 // attach doc string as comment: | |
| 4687 | 749 if (retval && doc.length () > 0 |
| 4634 | 750 && H5Gset_comment (loc_id, name.c_str (), doc.c_str ()) < 0) |
| 4687 | 751 retval = false; |
| 4634 | 752 |
| 753 // if it's global, add an attribute "OCTAVE_GLOBAL" with value 1 | |
| 4687 | 754 if (retval && mark_as_global) |
| 4634 | 755 retval = hdf5_add_attr (data_id, "OCTAVE_GLOBAL") >= 0; |
| 756 | |
| 4687 | 757 // We are saving in the new variable format, so mark it |
| 758 if (retval) | |
| 759 retval = hdf5_add_attr (data_id, "OCTAVE_NEW_FORMAT") >= 0; | |
| 760 | |
| 4634 | 761 error_cleanup: |
| 762 | |
| 4687 | 763 if (data_type_id >= 0) |
| 764 H5Dclose (data_type_id); | |
| 4634 | 765 |
| 4687 | 766 if (type_id >= 0) |
| 767 H5Tclose (type_id); | |
| 4634 | 768 |
| 769 if (space_id >= 0) | |
| 770 H5Sclose (space_id); | |
| 771 | |
| 4687 | 772 if (data_id >= 0) |
| 773 H5Gclose (data_id); | |
| 774 | |
| 775 if (! retval) | |
| 776 error ("save: error while writing `%s' to hdf5 file", name.c_str ()); | |
| 4634 | 777 |
| 778 return retval; | |
| 779 } | |
| 780 | |
| 781 // Write data from TC in HDF5 (binary) format to the stream OS, | |
| 782 // which must be an hdf5_ofstream, returning true on success. | |
| 783 | |
| 784 bool | |
| 785 save_hdf5_data (std::ostream& os, const octave_value& tc, | |
| 786 const std::string& name, const std::string& doc, | |
| 787 bool mark_as_global, bool save_as_floats) | |
| 788 { | |
| 5760 | 789 hdf5_ofstream& hs = dynamic_cast<hdf5_ofstream&> (os); |
| 4634 | 790 |
| 791 return add_hdf5_data (hs.file_id, tc, name, doc, | |
| 792 mark_as_global, save_as_floats); | |
| 793 } | |
| 794 | |
| 795 #endif | |
| 796 | |
| 797 /* | |
| 798 ;;; Local Variables: *** | |
| 799 ;;; mode: C++ *** | |
| 800 ;;; End: *** | |
| 801 */ |