Mercurial > octave
annotate src/ls-hdf5.cc @ 8401:712cfdc2e417
allow saving diagonal & permutation matrices to hdf5 as full
| author | Jaroslav Hajek <highegg@gmail.com> |
|---|---|
| date | Fri, 12 Dec 2008 13:35:10 +0100 |
| parents | 25bc2d31e1bf |
| children | 22462fd58e66 |
| 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 <hdf5.h> | |
| 42 | |
| 43 #include "byte-swap.h" | |
| 44 #include "data-conv.h" | |
| 45 #include "file-ops.h" | |
| 46 #include "glob-match.h" | |
| 47 #include "lo-mappers.h" | |
| 48 #include "mach-info.h" | |
| 49 #include "oct-env.h" | |
| 50 #include "oct-time.h" | |
| 51 #include "quit.h" | |
| 52 #include "str-vec.h" | |
|
8377
25bc2d31e1bf
improve OCTAVE_LOCAL_BUFFER
Jaroslav Hajek <highegg@gmail.com>
parents:
7336
diff
changeset
|
53 #include "oct-locbuf.h" |
| 4634 | 54 |
| 55 #include "Cell.h" | |
| 56 #include "defun.h" | |
| 57 #include "error.h" | |
| 58 #include "gripes.h" | |
| 59 #include "load-save.h" | |
| 60 #include "oct-obj.h" | |
| 61 #include "oct-map.h" | |
| 62 #include "ov-cell.h" | |
| 63 #include "pager.h" | |
| 64 #include "pt-exp.h" | |
| 65 #include "sysdep.h" | |
| 66 #include "unwind-prot.h" | |
| 67 #include "utils.h" | |
| 68 #include "variables.h" | |
| 69 #include "version.h" | |
| 70 #include "dMatrix.h" | |
| 71 | |
| 72 #include "ls-utils.h" | |
| 73 #include "ls-hdf5.h" | |
| 74 | |
| 75 static std::string | |
| 76 make_valid_identifier (const std::string& nm) | |
| 77 { | |
| 78 std::string retval; | |
| 79 | |
| 80 size_t nm_len = nm.length (); | |
| 81 | |
| 82 if (nm_len > 0) | |
| 83 { | |
| 84 if (! isalpha (nm[0])) | |
| 85 retval += '_'; | |
| 86 | |
| 87 for (size_t i = 0; i < nm_len; i++) | |
| 88 { | |
| 89 char c = nm[i]; | |
| 90 retval += (isalnum (c) || c == '_') ? c : '_'; | |
| 91 } | |
| 92 } | |
| 93 | |
| 94 return retval; | |
| 95 } | |
| 96 | |
| 97 // Define this to 1 if/when HDF5 supports automatic conversion between | |
| 98 // integer and floating-point binary data: | |
| 99 #define HAVE_HDF5_INT2FLOAT_CONVERSIONS 0 | |
| 100 | |
| 101 // Given two compound types t1 and t2, determine whether they | |
| 102 // are compatible for reading/writing. This function only | |
| 103 // works for non-nested types composed of simple elements (ints, floats...), | |
| 104 // which is all we need it for | |
| 105 | |
| 106 bool | |
| 107 hdf5_types_compatible (hid_t t1, hid_t t2) | |
| 108 { | |
| 109 int n; | |
| 110 if ((n = H5Tget_nmembers (t1)) != H5Tget_nmembers (t2)) | |
| 111 return false; | |
| 112 | |
| 113 for (int i = 0; i < n; ++i) | |
| 114 { | |
| 115 hid_t mt1 = H5Tget_member_type (t1, i); | |
| 116 hid_t mt2 = H5Tget_member_type (t2, i); | |
| 117 | |
| 118 if (H5Tget_class (mt1) != H5Tget_class (mt2)) | |
| 119 return false; | |
| 120 | |
| 121 H5Tclose (mt2); | |
| 122 H5Tclose (mt1); | |
| 123 } | |
| 124 | |
| 125 return true; | |
| 126 } | |
| 127 | |
| 128 // Return true if loc_id has the attribute named attr_name, and false | |
| 129 // otherwise. | |
| 130 | |
| 131 bool | |
| 132 hdf5_check_attr (hid_t loc_id, const char *attr_name) | |
| 133 { | |
| 134 bool retval = false; | |
| 135 | |
| 136 // we have to pull some shenanigans here to make sure | |
| 137 // HDF5 doesn't print out all sorts of error messages if we | |
| 138 // call H5Aopen for a non-existing attribute | |
| 139 | |
| 140 H5E_auto_t err_func; | |
| 141 void *err_func_data; | |
| 142 | |
| 143 // turn off error reporting temporarily, but save the error | |
| 144 // reporting function: | |
| 145 | |
| 146 H5Eget_auto (&err_func, &err_func_data); | |
| 147 H5Eset_auto (0, 0); | |
| 148 | |
| 149 hid_t attr_id = H5Aopen_name (loc_id, attr_name); | |
| 150 | |
| 151 if (attr_id >= 0) | |
| 152 { | |
| 153 // successful | |
| 154 retval = 1; | |
| 155 H5Aclose (attr_id); | |
| 156 } | |
| 157 | |
| 158 // restore error reporting: | |
| 159 H5Eset_auto (err_func, err_func_data); | |
| 160 | |
| 161 return retval; | |
| 162 } | |
| 163 | |
| 4687 | 164 // The following subroutines creates an HDF5 representations of the way |
| 165 // we will store Octave complex types (pairs of floating-point numbers). | |
| 166 // NUM_TYPE is the HDF5 numeric type to use for storage (e.g. | |
| 167 // H5T_NATIVE_DOUBLE to save as 'double'). Note that any necessary | |
| 168 // conversions are handled automatically by HDF5. | |
| 4634 | 169 |
| 4687 | 170 hid_t |
| 4634 | 171 hdf5_make_complex_type (hid_t num_type) |
| 172 { | |
| 173 hid_t type_id = H5Tcreate (H5T_COMPOUND, sizeof (double) * 2); | |
| 174 | |
| 175 H5Tinsert (type_id, "real", 0 * sizeof (double), num_type); | |
| 176 H5Tinsert (type_id, "imag", 1 * sizeof (double), num_type); | |
| 177 | |
| 178 return type_id; | |
| 179 } | |
| 180 | |
| 181 // This variable, set in read_hdf5_data(), tells whether we are using | |
| 182 // a version of HDF5 with a buggy H5Giterate (i.e. which neglects to | |
| 183 // increment the index parameter to the next unread item). | |
| 184 static bool have_h5giterate_bug = false; | |
| 185 | |
| 186 // This function is designed to be passed to H5Giterate, which calls it | |
| 187 // on each data item in an HDF5 file. For the item whose name is NAME in | |
| 188 // the group GROUP_ID, this function sets dv->tc to an Octave representation | |
| 189 // of that item. (dv must be a pointer to hdf5_callback_data.) (It also | |
| 190 // sets the other fields of dv). | |
| 191 // | |
| 192 // It returns 1 on success (in which case H5Giterate stops and returns), | |
| 193 // -1 on error, and 0 to tell H5Giterate to continue on to the next item | |
| 194 // (e.g. if NAME was a data type we don't recognize). | |
| 195 | |
| 4687 | 196 herr_t |
| 4634 | 197 hdf5_read_next_data (hid_t group_id, const char *name, void *dv) |
| 198 { | |
| 199 hdf5_callback_data *d = static_cast <hdf5_callback_data *> (dv); | |
| 4687 | 200 hid_t type_id = -1, type_class_id = -1, data_id = -1, subgroup_id = -1, |
| 201 space_id = -1; | |
| 4634 | 202 |
| 203 H5G_stat_t info; | |
| 204 herr_t retval = 0; | |
| 205 bool ident_valid = valid_identifier (name); | |
| 206 | |
| 207 std::string vname = name; | |
| 208 | |
| 209 // Allow identifiers as all digits so we can load lists saved by | |
| 210 // earlier versions of Octave. | |
| 211 | |
| 4687 | 212 if (! ident_valid ) |
| 4634 | 213 { |
| 214 // fix the identifier, replacing invalid chars with underscores | |
| 215 vname = make_valid_identifier (vname); | |
| 216 | |
| 217 // check again (in case vname was null, empty, or some such thing): | |
| 218 ident_valid = valid_identifier (vname); | |
| 219 } | |
| 220 | |
| 221 H5Gget_objinfo (group_id, name, 1, &info); | |
| 222 | |
| 4687 | 223 if (info.type == H5G_GROUP && ident_valid) |
| 4634 | 224 { |
| 4687 | 225 subgroup_id = H5Gopen (group_id, name); |
| 4634 | 226 |
| 227 if (subgroup_id < 0) | |
| 228 { | |
| 229 retval = subgroup_id; | |
| 230 goto done; | |
| 231 } | |
| 232 | |
| 4687 | 233 if (hdf5_check_attr (subgroup_id, "OCTAVE_NEW_FORMAT")) |
| 234 { | |
| 235 data_id = H5Dopen (subgroup_id, "type"); | |
| 4634 | 236 |
| 4687 | 237 if (data_id < 0) |
| 4634 | 238 { |
| 4687 | 239 retval = data_id; |
| 240 goto done; | |
| 4634 | 241 } |
| 242 | |
| 4687 | 243 type_id = H5Dget_type (data_id); |
| 244 | |
| 245 type_class_id = H5Tget_class (type_id); | |
| 246 | |
| 247 if (type_class_id != H5T_STRING) | |
| 248 goto done; | |
| 249 | |
| 250 space_id = H5Dget_space (data_id); | |
| 251 hsize_t rank = H5Sget_simple_extent_ndims (space_id); | |
| 252 | |
| 253 if (rank != 0) | |
| 254 goto done; | |
| 255 | |
| 256 int slen = H5Tget_size (type_id); | |
| 257 if (slen < 0) | |
| 258 goto done; | |
| 259 | |
| 260 OCTAVE_LOCAL_BUFFER (char, typ, slen); | |
| 261 | |
| 262 // create datatype for (null-terminated) string to read into: | |
| 263 hid_t st_id = H5Tcopy (H5T_C_S1); | |
| 264 H5Tset_size (st_id, slen); | |
| 265 | |
| 266 if (H5Dread (data_id, st_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, | |
| 5760 | 267 typ) < 0) |
| 4687 | 268 goto done; |
| 269 | |
| 270 H5Tclose (st_id); | |
| 271 H5Dclose (data_id); | |
| 272 | |
| 273 d->tc = octave_value_typeinfo::lookup_type (typ); | |
| 274 | |
| 275 retval = (d->tc.load_hdf5 (subgroup_id, "value", | |
| 276 have_h5giterate_bug) ? 1 : -1); | |
| 277 | |
| 278 // check for OCTAVE_GLOBAL attribute: | |
| 279 d->global = hdf5_check_attr (subgroup_id, "OCTAVE_GLOBAL"); | |
| 280 | |
| 281 H5Gclose (subgroup_id); | |
| 4634 | 282 } |
| 283 else | |
| 284 { | |
| 4687 | 285 // an HDF5 group is treated as an octave structure by |
| 286 // default (since that preserves name information), and an | |
| 287 // octave list otherwise. | |
| 288 | |
| 289 if (hdf5_check_attr (subgroup_id, "OCTAVE_LIST")) | |
| 290 d->tc = octave_value_typeinfo::lookup_type ("list"); | |
| 291 else | |
| 4948 | 292 d->tc = octave_value_typeinfo::lookup_type ("struct"); |
| 4687 | 293 |
| 294 // check for OCTAVE_GLOBAL attribute: | |
| 295 d->global = hdf5_check_attr (subgroup_id, "OCTAVE_GLOBAL"); | |
| 296 | |
| 297 H5Gclose (subgroup_id); | |
| 4634 | 298 |
| 4687 | 299 retval = (d->tc.load_hdf5 (group_id, name, have_h5giterate_bug) |
| 300 ? 1 : -1); | |
| 301 } | |
| 302 | |
| 303 } | |
| 304 else if (info.type == H5G_DATASET && ident_valid) | |
| 305 { | |
| 306 // For backwards compatiability. | |
| 307 data_id = H5Dopen (group_id, name); | |
| 308 | |
| 309 if (data_id < 0) | |
| 310 { | |
| 311 retval = data_id; | |
| 312 goto done; | |
| 4634 | 313 } |
| 314 | |
| 4687 | 315 type_id = H5Dget_type (data_id); |
| 316 | |
| 317 type_class_id = H5Tget_class (type_id); | |
| 318 | |
| 319 if (type_class_id == H5T_FLOAT) | |
| 320 { | |
| 321 space_id = H5Dget_space (data_id); | |
| 322 | |
| 323 hsize_t rank = H5Sget_simple_extent_ndims (space_id); | |
| 324 | |
| 325 if (rank == 0) | |
| 326 d->tc = octave_value_typeinfo::lookup_type ("scalar"); | |
| 327 else | |
| 328 d->tc = octave_value_typeinfo::lookup_type ("matrix"); | |
| 329 | |
| 330 H5Sclose (space_id); | |
| 331 } | |
| 4948 | 332 else if (type_class_id == H5T_INTEGER) |
| 333 { | |
| 334 // What integer type do we really have.. | |
| 335 std::string int_typ; | |
| 336 #ifdef HAVE_H5T_GET_NATIVE_TYPE | |
| 5775 | 337 // FIXME test this code and activated with an autoconf |
| 5351 | 338 // test!! It is also incorrect for 64-bit indexing!! |
| 339 | |
| 4948 | 340 switch (H5Tget_native_type (type_id, H5T_DIR_ASCEND)) |
| 341 { | |
| 342 case H5T_NATIVE_CHAR: | |
| 343 int_typ = "int8 "; | |
| 344 break; | |
| 345 | |
| 346 case H5T_NATIVE_SHORT: | |
| 347 int_typ = "int16 "; | |
| 348 break; | |
| 349 | |
| 350 case H5T_NATIVE_INT: | |
| 351 case H5T_NATIVE_LONG: | |
| 352 int_typ = "int32 "; | |
| 353 break; | |
| 354 | |
| 355 case H5T_NATIVE_LLONG: | |
| 356 int_typ = "int64 "; | |
| 357 break; | |
| 358 | |
| 359 case H5T_NATIVE_UCHAR: | |
| 360 int_typ = "uint8 "; | |
| 361 break; | |
| 362 | |
| 363 case H5T_NATIVE_USHORT: | |
| 364 int_typ = "uint16 "; | |
| 365 break; | |
| 366 | |
| 367 case H5T_NATIVE_UINT: | |
| 368 case H5T_NATIVE_ULONG: | |
| 369 int_typ = "uint32 "; | |
| 370 break; | |
| 371 | |
| 372 case H5T_NATIVE_ULLONG: | |
| 373 int_typ = "uint64 "; | |
| 374 break; | |
| 375 } | |
| 376 #else | |
| 377 hid_t int_sign = H5Tget_sign (type_id); | |
| 378 | |
| 379 if (int_sign == H5T_SGN_ERROR) | |
| 380 warning ("load: can't read `%s' (unknown datatype)", name); | |
| 381 else | |
| 382 { | |
| 383 if (int_sign == H5T_SGN_NONE) | |
| 384 int_typ.append ("u"); | |
| 385 int_typ.append ("int"); | |
| 386 | |
| 387 int slen = H5Tget_size (type_id); | |
| 388 if (slen < 0) | |
| 389 warning ("load: can't read `%s' (unknown datatype)", name); | |
| 390 else | |
| 391 { | |
| 392 switch (slen) | |
| 393 { | |
| 394 case 1: | |
| 395 int_typ.append ("8 "); | |
| 396 break; | |
| 397 | |
| 398 case 2: | |
| 399 int_typ.append ("16 "); | |
| 400 break; | |
| 401 | |
| 402 case 4: | |
| 403 int_typ.append ("32 "); | |
| 404 break; | |
| 405 | |
| 406 case 8: | |
| 407 int_typ.append ("64 "); | |
| 408 break; | |
| 409 | |
| 410 default: | |
| 411 warning ("load: can't read `%s' (unknown datatype)", | |
| 412 name); | |
| 413 int_typ = ""; | |
| 414 break; | |
| 415 } | |
| 416 } | |
| 417 } | |
| 418 #endif | |
| 419 if (int_typ == "") | |
| 420 warning ("load: can't read `%s' (unknown datatype)", name); | |
| 421 else | |
| 422 { | |
| 423 // Matrix or scalar? | |
| 424 space_id = H5Dget_space (data_id); | |
| 425 | |
| 426 hsize_t rank = H5Sget_simple_extent_ndims (space_id); | |
| 427 | |
| 428 if (rank == 0) | |
| 429 int_typ.append ("scalar"); | |
| 430 else | |
| 431 int_typ.append ("matrix"); | |
| 432 | |
| 433 d->tc = octave_value_typeinfo::lookup_type (int_typ); | |
| 434 H5Sclose (space_id); | |
| 435 } | |
| 436 } | |
| 4687 | 437 else if (type_class_id == H5T_STRING) |
| 438 d->tc = octave_value_typeinfo::lookup_type ("string"); | |
| 439 else if (type_class_id == H5T_COMPOUND) | |
| 440 { | |
| 441 hid_t complex_type = hdf5_make_complex_type (H5T_NATIVE_DOUBLE); | |
| 442 | |
| 443 if (hdf5_types_compatible (type_id, complex_type)) | |
| 444 { | |
| 445 // read complex matrix or scalar variable | |
| 446 space_id = H5Dget_space (data_id); | |
| 447 hsize_t rank = H5Sget_simple_extent_ndims (space_id); | |
| 448 | |
| 449 if (rank == 0) | |
| 450 d->tc = octave_value_typeinfo::lookup_type ("complex scalar"); | |
| 451 else | |
| 452 d->tc = octave_value_typeinfo::lookup_type ("complex matrix"); | |
| 453 | |
| 454 H5Sclose (space_id); | |
| 455 } | |
| 456 else | |
| 457 // Assume that if its not complex its a range. If its not | |
| 458 // it'll be rejected later in the range code | |
| 459 d->tc = octave_value_typeinfo::lookup_type ("range"); | |
| 460 | |
| 461 H5Tclose (complex_type); | |
| 462 } | |
| 463 else | |
| 464 { | |
| 465 warning ("load: can't read `%s' (unknown datatype)", name); | |
| 466 retval = 0; // unknown datatype; skip | |
| 467 } | |
| 468 | |
| 469 // check for OCTAVE_GLOBAL attribute: | |
| 470 d->global = hdf5_check_attr (data_id, "OCTAVE_GLOBAL"); | |
| 471 | |
| 472 H5Tclose (type_id); | |
| 473 H5Dclose (data_id); | |
| 474 | |
| 475 retval = (d->tc.load_hdf5 (group_id, name, have_h5giterate_bug) | |
| 476 ? 1 : -1); | |
| 4634 | 477 } |
| 4687 | 478 |
| 479 if (!ident_valid) | |
| 4634 | 480 { |
| 481 // should we attempt to handle invalid identifiers by converting | |
| 482 // bad characters to '_', say? | |
| 483 warning ("load: skipping invalid identifier `%s' in hdf5 file", | |
| 484 name); | |
| 485 } | |
| 486 | |
| 487 done: | |
| 488 if (retval < 0) | |
| 489 error ("load: error while reading hdf5 item %s", name); | |
| 4687 | 490 |
| 4634 | 491 if (retval > 0) |
| 492 { | |
| 493 // get documentation string, if any: | |
| 494 int comment_length = H5Gget_comment (group_id, name, 0, 0); | |
| 495 | |
| 496 if (comment_length > 1) | |
| 497 { | |
| 498 OCTAVE_LOCAL_BUFFER (char, tdoc, comment_length); | |
| 499 H5Gget_comment (group_id, name, comment_length, tdoc); | |
| 500 d->doc = tdoc; | |
| 501 } | |
| 502 else if (vname != name) | |
| 503 { | |
| 4687 | 504 // the name was changed; store the original name |
| 4634 | 505 // as the documentation string: |
| 506 d->doc = name; | |
| 507 } | |
| 508 | |
| 509 // copy name (actually, vname): | |
| 510 d->name = vname; | |
| 511 } | |
| 512 | |
| 513 return retval; | |
| 514 } | |
| 515 | |
| 516 // Read the next Octave variable from the stream IS, which must really be | |
| 517 // an hdf5_ifstream. Return the variable value in tc, its doc string | |
| 518 // in doc, and whether it is global in global. The return value is | |
| 519 // the name of the variable, or NULL if none were found or there was | |
| 4687 | 520 // and error. |
| 4634 | 521 std::string |
| 4687 | 522 read_hdf5_data (std::istream& is, const std::string& /* filename */, |
| 523 bool& global, octave_value& tc, std::string& doc) | |
| 4634 | 524 { |
| 525 std::string retval; | |
| 526 | |
| 527 doc.resize (0); | |
| 528 | |
| 5760 | 529 hdf5_ifstream& hs = dynamic_cast<hdf5_ifstream&> (is); |
| 4634 | 530 hdf5_callback_data d; |
| 531 | |
| 532 // Versions of HDF5 prior to 1.2.2 had a bug in H5Giterate where it | |
| 533 // would return the index of the last item processed instead of the | |
| 534 // next item to be processed, forcing us to increment the index manually. | |
| 535 | |
| 536 unsigned int vers_major, vers_minor, vers_release; | |
| 537 | |
| 538 H5get_libversion (&vers_major, &vers_minor, &vers_release); | |
| 539 | |
| 5775 | 540 // FIXME -- this test looks wrong. |
| 4634 | 541 have_h5giterate_bug |
| 542 = (vers_major < 1 | |
| 543 || (vers_major == 1 && (vers_minor < 2 | |
| 544 || (vers_minor == 2 && vers_release < 2)))); | |
| 545 | |
| 4696 | 546 herr_t H5Giterate_retval = -1; |
| 547 | |
| 548 #ifdef HAVE_H5GGET_NUM_OBJS | |
| 549 hsize_t num_obj = 0; | |
| 5060 | 550 hid_t group_id = H5Gopen (hs.file_id, "/"); |
| 551 H5Gget_num_objs (group_id, &num_obj); | |
| 552 H5Gclose (group_id); | |
| 4696 | 553 if (hs.current_item < static_cast<int> (num_obj)) |
| 554 #endif | |
| 555 H5Giterate_retval = H5Giterate (hs.file_id, "/", &hs.current_item, | |
| 556 hdf5_read_next_data, &d); | |
| 4634 | 557 |
| 558 if (have_h5giterate_bug) | |
| 559 { | |
| 560 // H5Giterate sets current_item to the last item processed; we want | |
| 561 // the index of the next item (for the next call to read_hdf5_data) | |
| 562 | |
| 563 hs.current_item++; | |
| 564 } | |
| 565 | |
| 566 if (H5Giterate_retval > 0) | |
| 567 { | |
| 568 global = d.global; | |
| 569 tc = d.tc; | |
| 570 doc = d.doc; | |
| 571 } | |
| 572 else | |
| 573 { | |
| 574 // an error occurred (H5Giterate_retval < 0) or there are no | |
| 575 // more datasets print an error message if retval < 0? | |
| 576 // hdf5_read_next_data already printed one, probably. | |
| 577 } | |
| 578 | |
| 579 if (! d.name.empty ()) | |
| 580 retval = d.name; | |
| 581 | |
| 582 return retval; | |
| 583 } | |
| 584 | |
| 585 // Add an attribute named attr_name to loc_id (a simple scalar | |
| 586 // attribute with value 1). Return value is >= 0 on success. | |
| 587 static herr_t | |
| 588 hdf5_add_attr (hid_t loc_id, const char *attr_name) | |
| 589 { | |
| 590 herr_t retval = 0; | |
| 591 | |
| 592 hid_t as_id = H5Screate (H5S_SCALAR); | |
| 593 | |
| 594 if (as_id >= 0) | |
| 595 { | |
| 596 hid_t a_id = H5Acreate (loc_id, attr_name, | |
| 597 H5T_NATIVE_UCHAR, as_id, H5P_DEFAULT); | |
| 598 | |
| 599 if (a_id >= 0) | |
| 600 { | |
| 601 unsigned char attr_val = 1; | |
| 602 | |
| 5760 | 603 retval = H5Awrite (a_id, H5T_NATIVE_UCHAR, &attr_val); |
| 4634 | 604 |
| 605 H5Aclose (a_id); | |
| 606 } | |
| 607 else | |
| 608 retval = a_id; | |
| 609 | |
| 610 H5Sclose (as_id); | |
| 611 } | |
| 612 else | |
| 613 retval = as_id; | |
| 614 | |
| 615 return retval; | |
| 616 } | |
| 617 | |
| 4805 | 618 // Save an empty matrix, if needed. Returns |
| 619 // > 0 Saved empty matrix | |
| 620 // = 0 Not an empty matrix; did nothing | |
| 621 // < 0 Error condition | |
| 622 int | |
| 623 save_hdf5_empty (hid_t loc_id, const char *name, const dim_vector d) | |
| 624 { | |
| 625 hsize_t sz = d.length (); | |
| 6276 | 626 OCTAVE_LOCAL_BUFFER (octave_idx_type, dims, sz); |
| 4805 | 627 bool empty = false; |
| 628 hid_t space_hid = -1, data_hid = -1; | |
| 629 int retval; | |
| 630 for (hsize_t i = 0; i < sz; i++) | |
| 631 { | |
| 632 dims[i] = d(i); | |
| 633 if (dims[i] < 1) | |
| 634 empty = true; | |
| 635 } | |
| 636 | |
| 637 if (!empty) | |
| 638 return 0; | |
| 639 | |
| 5760 | 640 space_hid = H5Screate_simple (1, &sz, 0); |
| 4805 | 641 if (space_hid < 0) return space_hid; |
| 642 | |
| 5351 | 643 data_hid = H5Dcreate (loc_id, name, H5T_NATIVE_IDX, space_hid, |
| 4805 | 644 H5P_DEFAULT); |
| 645 if (data_hid < 0) | |
| 646 { | |
| 647 H5Sclose (space_hid); | |
| 648 return data_hid; | |
| 649 } | |
| 650 | |
| 5351 | 651 retval = H5Dwrite (data_hid, H5T_NATIVE_IDX, H5S_ALL, H5S_ALL, |
| 5760 | 652 H5P_DEFAULT, dims) >= 0; |
| 4805 | 653 |
| 654 H5Dclose (data_hid); | |
| 655 H5Sclose (space_hid); | |
| 656 | |
| 657 if (retval >= 0) | |
| 658 retval = hdf5_add_attr (loc_id, "OCTAVE_EMPTY_MATRIX"); | |
| 659 | |
| 660 return (retval == 0 ? 1 : retval); | |
| 661 } | |
| 662 | |
| 663 // Load an empty matrix, if needed. Returns | |
| 664 // > 0 loaded empty matrix, dimensions returned | |
| 665 // = 0 Not an empty matrix; did nothing | |
| 666 // < 0 Error condition | |
| 667 int | |
| 668 load_hdf5_empty (hid_t loc_id, const char *name, dim_vector &d) | |
| 669 { | |
| 670 if (!hdf5_check_attr(loc_id, "OCTAVE_EMPTY_MATRIX")) | |
| 671 return 0; | |
| 672 | |
| 673 hsize_t hdims, maxdims; | |
| 674 hid_t data_hid = H5Dopen (loc_id, name); | |
| 675 hid_t space_id = H5Dget_space (data_hid); | |
| 676 H5Sget_simple_extent_dims (space_id, &hdims, &maxdims); | |
| 677 int retval; | |
| 678 | |
| 5351 | 679 OCTAVE_LOCAL_BUFFER (octave_idx_type, dims, hdims); |
| 680 | |
| 681 retval = H5Dread (data_hid, H5T_NATIVE_IDX, H5S_ALL, H5S_ALL, | |
| 5760 | 682 H5P_DEFAULT, dims); |
| 4805 | 683 if (retval >= 0) |
| 684 { | |
| 685 d.resize (hdims); | |
| 686 for (hsize_t i = 0; i < hdims; i++) | |
| 687 d(i) = dims[i]; | |
| 688 } | |
| 689 | |
| 690 H5Sclose (space_id); | |
| 691 H5Dclose (data_hid); | |
| 692 | |
| 693 return (retval == 0 ? hdims : retval); | |
| 694 } | |
| 695 | |
| 4634 | 696 // save_type_to_hdf5 is not currently used, since hdf5 doesn't yet support |
| 697 // automatic float<->integer conversions: | |
| 698 | |
| 699 #if HAVE_HDF5_INT2FLOAT_CONVERSIONS | |
| 700 | |
| 701 // return the HDF5 type id corresponding to the Octave save_type | |
| 702 | |
| 4687 | 703 hid_t |
| 4634 | 704 save_type_to_hdf5 (save_type st) |
| 705 { | |
| 706 switch (st) | |
| 707 { | |
| 708 case LS_U_CHAR: | |
| 709 return H5T_NATIVE_UCHAR; | |
| 710 | |
| 711 case LS_U_SHORT: | |
| 712 return H5T_NATIVE_USHORT; | |
| 713 | |
| 714 case LS_U_INT: | |
| 715 return H5T_NATIVE_UINT; | |
| 716 | |
| 717 case LS_CHAR: | |
| 718 return H5T_NATIVE_CHAR; | |
| 719 | |
| 720 case LS_SHORT: | |
| 721 return H5T_NATIVE_SHORT; | |
| 722 | |
| 723 case LS_INT: | |
| 724 return H5T_NATIVE_INT; | |
| 725 | |
| 726 case LS_FLOAT: | |
| 727 return H5T_NATIVE_FLOAT; | |
| 728 | |
| 729 case LS_DOUBLE: | |
| 730 default: | |
| 731 return H5T_NATIVE_DOUBLE; | |
| 732 } | |
| 733 } | |
| 734 #endif /* HAVE_HDF5_INT2FLOAT_CONVERSIONS */ | |
| 735 | |
| 736 // Add the data from TC to the HDF5 location loc_id, which could | |
| 737 // be either a file or a group within a file. Return true if | |
| 738 // successful. This function calls itself recursively for lists | |
| 739 // (stored as HDF5 groups). | |
| 740 | |
| 4687 | 741 bool |
| 4634 | 742 add_hdf5_data (hid_t loc_id, const octave_value& tc, |
| 743 const std::string& name, const std::string& doc, | |
| 744 bool mark_as_global, bool save_as_floats) | |
| 745 { | |
| 746 hsize_t dims[3]; | |
| 4687 | 747 hid_t type_id = -1, space_id = -1, data_id = -1, data_type_id = -1; |
| 748 bool retval = false; | |
| 749 octave_value val = tc; | |
|
8401
712cfdc2e417
allow saving diagonal & permutation matrices to hdf5 as full
Jaroslav Hajek <highegg@gmail.com>
parents:
8377
diff
changeset
|
750 // 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
|
751 // 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
|
752 // This is a temporary hack. |
|
712cfdc2e417
allow saving diagonal & permutation matrices to hdf5 as full
Jaroslav Hajek <highegg@gmail.com>
parents:
8377
diff
changeset
|
753 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
|
754 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
|
755 |
|
712cfdc2e417
allow saving diagonal & permutation matrices to hdf5 as full
Jaroslav Hajek <highegg@gmail.com>
parents:
8377
diff
changeset
|
756 std::string t = val.type_name(); |
| 4634 | 757 |
| 4687 | 758 data_id = H5Gcreate (loc_id, name.c_str (), 0); |
| 759 if (data_id < 0) | |
| 760 goto error_cleanup; | |
| 4634 | 761 |
| 4687 | 762 // attach the type of the variable |
| 763 type_id = H5Tcopy (H5T_C_S1); H5Tset_size (type_id, t.length () + 1); | |
| 764 if (type_id < 0) | |
| 765 goto error_cleanup; | |
| 4634 | 766 |
| 4687 | 767 dims[0] = 0; |
| 5760 | 768 space_id = H5Screate_simple (0 , dims, 0); |
| 4687 | 769 if (space_id < 0) |
| 770 goto error_cleanup; | |
| 4634 | 771 |
| 4687 | 772 data_type_id = H5Dcreate (data_id, "type", type_id, space_id, H5P_DEFAULT); |
| 773 if (data_type_id < 0 || H5Dwrite (data_type_id, type_id, H5S_ALL, H5S_ALL, | |
| 5760 | 774 H5P_DEFAULT, t.c_str ()) < 0) |
| 4687 | 775 goto error_cleanup; |
| 4634 | 776 |
| 4687 | 777 // Now call the real function to save the variable |
| 778 retval = val.save_hdf5 (data_id, "value", save_as_floats); | |
| 4634 | 779 |
| 780 // attach doc string as comment: | |
| 4687 | 781 if (retval && doc.length () > 0 |
| 4634 | 782 && H5Gset_comment (loc_id, name.c_str (), doc.c_str ()) < 0) |
| 4687 | 783 retval = false; |
| 4634 | 784 |
| 785 // if it's global, add an attribute "OCTAVE_GLOBAL" with value 1 | |
| 4687 | 786 if (retval && mark_as_global) |
| 4634 | 787 retval = hdf5_add_attr (data_id, "OCTAVE_GLOBAL") >= 0; |
| 788 | |
| 4687 | 789 // We are saving in the new variable format, so mark it |
| 790 if (retval) | |
| 791 retval = hdf5_add_attr (data_id, "OCTAVE_NEW_FORMAT") >= 0; | |
| 792 | |
| 4634 | 793 error_cleanup: |
| 794 | |
| 4687 | 795 if (data_type_id >= 0) |
| 796 H5Dclose (data_type_id); | |
| 4634 | 797 |
| 4687 | 798 if (type_id >= 0) |
| 799 H5Tclose (type_id); | |
| 4634 | 800 |
| 801 if (space_id >= 0) | |
| 802 H5Sclose (space_id); | |
| 803 | |
| 4687 | 804 if (data_id >= 0) |
| 805 H5Gclose (data_id); | |
| 806 | |
| 807 if (! retval) | |
| 808 error ("save: error while writing `%s' to hdf5 file", name.c_str ()); | |
| 4634 | 809 |
| 810 return retval; | |
| 811 } | |
| 812 | |
| 813 // Write data from TC in HDF5 (binary) format to the stream OS, | |
| 814 // which must be an hdf5_ofstream, returning true on success. | |
| 815 | |
| 816 bool | |
| 817 save_hdf5_data (std::ostream& os, const octave_value& tc, | |
| 818 const std::string& name, const std::string& doc, | |
| 819 bool mark_as_global, bool save_as_floats) | |
| 820 { | |
| 5760 | 821 hdf5_ofstream& hs = dynamic_cast<hdf5_ofstream&> (os); |
| 4634 | 822 |
| 823 return add_hdf5_data (hs.file_id, tc, name, doc, | |
| 824 mark_as_global, save_as_floats); | |
| 825 } | |
| 826 | |
| 827 #endif | |
| 828 | |
| 829 /* | |
| 830 ;;; Local Variables: *** | |
| 831 ;;; mode: C++ *** | |
| 832 ;;; End: *** | |
| 833 */ |