Mercurial > hg > octave-jordi
annotate src/ls-hdf5.cc @ 9825:7483fe200fab
narrow complex values with negative zero imaginary parts
| author | Jaroslav Hajek <highegg@gmail.com> |
|---|---|
| date | Fri, 13 Nov 2009 12:34:46 +0100 |
| parents | eb63fbe60fab |
| children | b3089dba88bf |
| 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 variable, set in read_hdf5_data(), tells whether we are using | |
| 181 // a version of HDF5 with a buggy H5Giterate (i.e. which neglects to | |
| 182 // increment the index parameter to the next unread item). | |
| 183 static bool have_h5giterate_bug = false; | |
| 184 | |
| 185 // This function is designed to be passed to H5Giterate, which calls it | |
| 186 // on each data item in an HDF5 file. For the item whose name is NAME in | |
| 187 // the group GROUP_ID, this function sets dv->tc to an Octave representation | |
| 188 // of that item. (dv must be a pointer to hdf5_callback_data.) (It also | |
| 189 // sets the other fields of dv). | |
| 190 // | |
| 191 // It returns 1 on success (in which case H5Giterate stops and returns), | |
| 192 // -1 on error, and 0 to tell H5Giterate to continue on to the next item | |
| 193 // (e.g. if NAME was a data type we don't recognize). | |
| 194 | |
| 4687 | 195 herr_t |
| 4634 | 196 hdf5_read_next_data (hid_t group_id, const char *name, void *dv) |
| 197 { | |
| 198 hdf5_callback_data *d = static_cast <hdf5_callback_data *> (dv); | |
| 4687 | 199 hid_t type_id = -1, type_class_id = -1, data_id = -1, subgroup_id = -1, |
| 200 space_id = -1; | |
| 4634 | 201 |
| 202 H5G_stat_t info; | |
| 203 herr_t retval = 0; | |
| 204 bool ident_valid = valid_identifier (name); | |
| 205 | |
| 206 std::string vname = name; | |
| 207 | |
| 208 // Allow identifiers as all digits so we can load lists saved by | |
| 209 // earlier versions of Octave. | |
| 210 | |
| 4687 | 211 if (! ident_valid ) |
| 4634 | 212 { |
| 213 // fix the identifier, replacing invalid chars with underscores | |
| 214 vname = make_valid_identifier (vname); | |
| 215 | |
| 216 // check again (in case vname was null, empty, or some such thing): | |
| 217 ident_valid = valid_identifier (vname); | |
| 218 } | |
| 219 | |
| 220 H5Gget_objinfo (group_id, name, 1, &info); | |
| 221 | |
| 4687 | 222 if (info.type == H5G_GROUP && ident_valid) |
| 4634 | 223 { |
| 4687 | 224 subgroup_id = H5Gopen (group_id, name); |
| 4634 | 225 |
| 226 if (subgroup_id < 0) | |
| 227 { | |
| 228 retval = subgroup_id; | |
| 229 goto done; | |
| 230 } | |
| 231 | |
| 4687 | 232 if (hdf5_check_attr (subgroup_id, "OCTAVE_NEW_FORMAT")) |
| 233 { | |
| 234 data_id = H5Dopen (subgroup_id, "type"); | |
| 4634 | 235 |
| 4687 | 236 if (data_id < 0) |
| 4634 | 237 { |
| 4687 | 238 retval = data_id; |
| 239 goto done; | |
| 4634 | 240 } |
| 241 | |
| 4687 | 242 type_id = H5Dget_type (data_id); |
| 243 | |
| 244 type_class_id = H5Tget_class (type_id); | |
| 245 | |
| 246 if (type_class_id != H5T_STRING) | |
| 247 goto done; | |
| 248 | |
| 249 space_id = H5Dget_space (data_id); | |
| 250 hsize_t rank = H5Sget_simple_extent_ndims (space_id); | |
| 251 | |
| 252 if (rank != 0) | |
| 253 goto done; | |
| 254 | |
| 255 int slen = H5Tget_size (type_id); | |
| 256 if (slen < 0) | |
| 257 goto done; | |
| 258 | |
| 259 OCTAVE_LOCAL_BUFFER (char, typ, slen); | |
| 260 | |
| 261 // create datatype for (null-terminated) string to read into: | |
| 262 hid_t st_id = H5Tcopy (H5T_C_S1); | |
| 263 H5Tset_size (st_id, slen); | |
| 264 | |
| 265 if (H5Dread (data_id, st_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, | |
| 5760 | 266 typ) < 0) |
| 4687 | 267 goto done; |
| 268 | |
| 269 H5Tclose (st_id); | |
| 270 H5Dclose (data_id); | |
| 271 | |
| 272 d->tc = octave_value_typeinfo::lookup_type (typ); | |
| 273 | |
| 274 retval = (d->tc.load_hdf5 (subgroup_id, "value", | |
| 275 have_h5giterate_bug) ? 1 : -1); | |
| 276 | |
| 277 // check for OCTAVE_GLOBAL attribute: | |
| 278 d->global = hdf5_check_attr (subgroup_id, "OCTAVE_GLOBAL"); | |
| 279 | |
| 280 H5Gclose (subgroup_id); | |
| 4634 | 281 } |
| 282 else | |
| 283 { | |
| 4687 | 284 // an HDF5 group is treated as an octave structure by |
| 285 // default (since that preserves name information), and an | |
| 286 // octave list otherwise. | |
| 287 | |
| 288 if (hdf5_check_attr (subgroup_id, "OCTAVE_LIST")) | |
| 289 d->tc = octave_value_typeinfo::lookup_type ("list"); | |
| 290 else | |
| 4948 | 291 d->tc = octave_value_typeinfo::lookup_type ("struct"); |
| 4687 | 292 |
| 293 // check for OCTAVE_GLOBAL attribute: | |
| 294 d->global = hdf5_check_attr (subgroup_id, "OCTAVE_GLOBAL"); | |
| 295 | |
| 296 H5Gclose (subgroup_id); | |
| 4634 | 297 |
| 4687 | 298 retval = (d->tc.load_hdf5 (group_id, name, have_h5giterate_bug) |
| 299 ? 1 : -1); | |
| 300 } | |
| 301 | |
| 302 } | |
| 303 else if (info.type == H5G_DATASET && ident_valid) | |
| 304 { | |
| 305 // For backwards compatiability. | |
| 306 data_id = H5Dopen (group_id, name); | |
| 307 | |
| 308 if (data_id < 0) | |
| 309 { | |
| 310 retval = data_id; | |
| 311 goto done; | |
| 4634 | 312 } |
| 313 | |
| 4687 | 314 type_id = H5Dget_type (data_id); |
| 315 | |
| 316 type_class_id = H5Tget_class (type_id); | |
| 317 | |
| 318 if (type_class_id == H5T_FLOAT) | |
| 319 { | |
| 320 space_id = H5Dget_space (data_id); | |
| 321 | |
| 322 hsize_t rank = H5Sget_simple_extent_ndims (space_id); | |
| 323 | |
| 324 if (rank == 0) | |
| 325 d->tc = octave_value_typeinfo::lookup_type ("scalar"); | |
| 326 else | |
| 327 d->tc = octave_value_typeinfo::lookup_type ("matrix"); | |
| 328 | |
| 329 H5Sclose (space_id); | |
| 330 } | |
| 4948 | 331 else if (type_class_id == H5T_INTEGER) |
| 332 { | |
| 333 // What integer type do we really have.. | |
| 334 std::string int_typ; | |
| 335 #ifdef HAVE_H5T_GET_NATIVE_TYPE | |
| 5775 | 336 // FIXME test this code and activated with an autoconf |
| 5351 | 337 // test!! It is also incorrect for 64-bit indexing!! |
| 338 | |
| 4948 | 339 switch (H5Tget_native_type (type_id, H5T_DIR_ASCEND)) |
| 340 { | |
| 341 case H5T_NATIVE_CHAR: | |
| 342 int_typ = "int8 "; | |
| 343 break; | |
| 344 | |
| 345 case H5T_NATIVE_SHORT: | |
| 346 int_typ = "int16 "; | |
| 347 break; | |
| 348 | |
| 349 case H5T_NATIVE_INT: | |
| 350 case H5T_NATIVE_LONG: | |
| 351 int_typ = "int32 "; | |
| 352 break; | |
| 353 | |
| 354 case H5T_NATIVE_LLONG: | |
| 355 int_typ = "int64 "; | |
| 356 break; | |
| 357 | |
| 358 case H5T_NATIVE_UCHAR: | |
| 359 int_typ = "uint8 "; | |
| 360 break; | |
| 361 | |
| 362 case H5T_NATIVE_USHORT: | |
| 363 int_typ = "uint16 "; | |
| 364 break; | |
| 365 | |
| 366 case H5T_NATIVE_UINT: | |
| 367 case H5T_NATIVE_ULONG: | |
| 368 int_typ = "uint32 "; | |
| 369 break; | |
| 370 | |
| 371 case H5T_NATIVE_ULLONG: | |
| 372 int_typ = "uint64 "; | |
| 373 break; | |
| 374 } | |
| 375 #else | |
| 376 hid_t int_sign = H5Tget_sign (type_id); | |
| 377 | |
| 378 if (int_sign == H5T_SGN_ERROR) | |
| 379 warning ("load: can't read `%s' (unknown datatype)", name); | |
| 380 else | |
| 381 { | |
| 382 if (int_sign == H5T_SGN_NONE) | |
| 383 int_typ.append ("u"); | |
| 384 int_typ.append ("int"); | |
| 385 | |
| 386 int slen = H5Tget_size (type_id); | |
| 387 if (slen < 0) | |
| 388 warning ("load: can't read `%s' (unknown datatype)", name); | |
| 389 else | |
| 390 { | |
| 391 switch (slen) | |
| 392 { | |
| 393 case 1: | |
| 394 int_typ.append ("8 "); | |
| 395 break; | |
| 396 | |
| 397 case 2: | |
| 398 int_typ.append ("16 "); | |
| 399 break; | |
| 400 | |
| 401 case 4: | |
| 402 int_typ.append ("32 "); | |
| 403 break; | |
| 404 | |
| 405 case 8: | |
| 406 int_typ.append ("64 "); | |
| 407 break; | |
| 408 | |
| 409 default: | |
| 410 warning ("load: can't read `%s' (unknown datatype)", | |
| 411 name); | |
| 412 int_typ = ""; | |
| 413 break; | |
| 414 } | |
| 415 } | |
| 416 } | |
| 417 #endif | |
| 418 if (int_typ == "") | |
| 419 warning ("load: can't read `%s' (unknown datatype)", name); | |
| 420 else | |
| 421 { | |
| 422 // Matrix or scalar? | |
| 423 space_id = H5Dget_space (data_id); | |
| 424 | |
| 425 hsize_t rank = H5Sget_simple_extent_ndims (space_id); | |
| 426 | |
| 427 if (rank == 0) | |
| 428 int_typ.append ("scalar"); | |
| 429 else | |
| 430 int_typ.append ("matrix"); | |
| 431 | |
| 432 d->tc = octave_value_typeinfo::lookup_type (int_typ); | |
| 433 H5Sclose (space_id); | |
| 434 } | |
| 435 } | |
| 4687 | 436 else if (type_class_id == H5T_STRING) |
| 437 d->tc = octave_value_typeinfo::lookup_type ("string"); | |
| 438 else if (type_class_id == H5T_COMPOUND) | |
| 439 { | |
| 440 hid_t complex_type = hdf5_make_complex_type (H5T_NATIVE_DOUBLE); | |
| 441 | |
| 442 if (hdf5_types_compatible (type_id, complex_type)) | |
| 443 { | |
| 444 // read complex matrix or scalar variable | |
| 445 space_id = H5Dget_space (data_id); | |
| 446 hsize_t rank = H5Sget_simple_extent_ndims (space_id); | |
| 447 | |
| 448 if (rank == 0) | |
| 449 d->tc = octave_value_typeinfo::lookup_type ("complex scalar"); | |
| 450 else | |
| 451 d->tc = octave_value_typeinfo::lookup_type ("complex matrix"); | |
| 452 | |
| 453 H5Sclose (space_id); | |
| 454 } | |
| 455 else | |
| 456 // Assume that if its not complex its a range. If its not | |
| 457 // it'll be rejected later in the range code | |
| 458 d->tc = octave_value_typeinfo::lookup_type ("range"); | |
| 459 | |
| 460 H5Tclose (complex_type); | |
| 461 } | |
| 462 else | |
| 463 { | |
| 464 warning ("load: can't read `%s' (unknown datatype)", name); | |
| 465 retval = 0; // unknown datatype; skip | |
| 466 } | |
| 467 | |
| 468 // check for OCTAVE_GLOBAL attribute: | |
| 469 d->global = hdf5_check_attr (data_id, "OCTAVE_GLOBAL"); | |
| 470 | |
| 471 H5Tclose (type_id); | |
| 472 H5Dclose (data_id); | |
| 473 | |
| 474 retval = (d->tc.load_hdf5 (group_id, name, have_h5giterate_bug) | |
| 475 ? 1 : -1); | |
| 4634 | 476 } |
| 4687 | 477 |
| 478 if (!ident_valid) | |
| 4634 | 479 { |
| 480 // should we attempt to handle invalid identifiers by converting | |
| 481 // bad characters to '_', say? | |
| 482 warning ("load: skipping invalid identifier `%s' in hdf5 file", | |
| 483 name); | |
| 484 } | |
| 485 | |
| 486 done: | |
| 487 if (retval < 0) | |
| 488 error ("load: error while reading hdf5 item %s", name); | |
| 4687 | 489 |
| 4634 | 490 if (retval > 0) |
| 491 { | |
| 492 // get documentation string, if any: | |
| 493 int comment_length = H5Gget_comment (group_id, name, 0, 0); | |
| 494 | |
| 495 if (comment_length > 1) | |
| 496 { | |
| 497 OCTAVE_LOCAL_BUFFER (char, tdoc, comment_length); | |
| 498 H5Gget_comment (group_id, name, comment_length, tdoc); | |
| 499 d->doc = tdoc; | |
| 500 } | |
| 501 else if (vname != name) | |
| 502 { | |
| 4687 | 503 // the name was changed; store the original name |
| 4634 | 504 // as the documentation string: |
| 505 d->doc = name; | |
| 506 } | |
| 507 | |
| 508 // copy name (actually, vname): | |
| 509 d->name = vname; | |
| 510 } | |
| 511 | |
| 512 return retval; | |
| 513 } | |
| 514 | |
| 515 // Read the next Octave variable from the stream IS, which must really be | |
| 516 // an hdf5_ifstream. Return the variable value in tc, its doc string | |
| 517 // in doc, and whether it is global in global. The return value is | |
| 518 // the name of the variable, or NULL if none were found or there was | |
| 4687 | 519 // and error. |
| 4634 | 520 std::string |
| 4687 | 521 read_hdf5_data (std::istream& is, const std::string& /* filename */, |
| 522 bool& global, octave_value& tc, std::string& doc) | |
| 4634 | 523 { |
| 524 std::string retval; | |
| 525 | |
| 526 doc.resize (0); | |
| 527 | |
| 5760 | 528 hdf5_ifstream& hs = dynamic_cast<hdf5_ifstream&> (is); |
| 4634 | 529 hdf5_callback_data d; |
| 530 | |
| 531 // Versions of HDF5 prior to 1.2.2 had a bug in H5Giterate where it | |
| 532 // would return the index of the last item processed instead of the | |
| 533 // next item to be processed, forcing us to increment the index manually. | |
| 534 | |
| 535 unsigned int vers_major, vers_minor, vers_release; | |
| 536 | |
| 537 H5get_libversion (&vers_major, &vers_minor, &vers_release); | |
| 538 | |
| 5775 | 539 // FIXME -- this test looks wrong. |
| 4634 | 540 have_h5giterate_bug |
| 541 = (vers_major < 1 | |
| 542 || (vers_major == 1 && (vers_minor < 2 | |
| 543 || (vers_minor == 2 && vers_release < 2)))); | |
| 544 | |
| 4696 | 545 herr_t H5Giterate_retval = -1; |
| 546 | |
| 547 #ifdef HAVE_H5GGET_NUM_OBJS | |
| 548 hsize_t num_obj = 0; | |
| 5060 | 549 hid_t group_id = H5Gopen (hs.file_id, "/"); |
| 550 H5Gget_num_objs (group_id, &num_obj); | |
| 551 H5Gclose (group_id); | |
| 4696 | 552 if (hs.current_item < static_cast<int> (num_obj)) |
| 553 #endif | |
| 554 H5Giterate_retval = H5Giterate (hs.file_id, "/", &hs.current_item, | |
| 555 hdf5_read_next_data, &d); | |
| 4634 | 556 |
| 557 if (have_h5giterate_bug) | |
| 558 { | |
| 559 // H5Giterate sets current_item to the last item processed; we want | |
| 560 // the index of the next item (for the next call to read_hdf5_data) | |
| 561 | |
| 562 hs.current_item++; | |
| 563 } | |
| 564 | |
| 565 if (H5Giterate_retval > 0) | |
| 566 { | |
| 567 global = d.global; | |
| 568 tc = d.tc; | |
| 569 doc = d.doc; | |
| 570 } | |
| 571 else | |
| 572 { | |
| 573 // an error occurred (H5Giterate_retval < 0) or there are no | |
| 574 // more datasets print an error message if retval < 0? | |
| 575 // hdf5_read_next_data already printed one, probably. | |
| 576 } | |
| 577 | |
| 578 if (! d.name.empty ()) | |
| 579 retval = d.name; | |
| 580 | |
| 581 return retval; | |
| 582 } | |
| 583 | |
| 584 // Add an attribute named attr_name to loc_id (a simple scalar | |
| 585 // attribute with value 1). Return value is >= 0 on success. | |
| 586 static herr_t | |
| 587 hdf5_add_attr (hid_t loc_id, const char *attr_name) | |
| 588 { | |
| 589 herr_t retval = 0; | |
| 590 | |
| 591 hid_t as_id = H5Screate (H5S_SCALAR); | |
| 592 | |
| 593 if (as_id >= 0) | |
| 594 { | |
| 595 hid_t a_id = H5Acreate (loc_id, attr_name, | |
| 596 H5T_NATIVE_UCHAR, as_id, H5P_DEFAULT); | |
| 597 | |
| 598 if (a_id >= 0) | |
| 599 { | |
| 600 unsigned char attr_val = 1; | |
| 601 | |
| 5760 | 602 retval = H5Awrite (a_id, H5T_NATIVE_UCHAR, &attr_val); |
| 4634 | 603 |
| 604 H5Aclose (a_id); | |
| 605 } | |
| 606 else | |
| 607 retval = a_id; | |
| 608 | |
| 609 H5Sclose (as_id); | |
| 610 } | |
| 611 else | |
| 612 retval = as_id; | |
| 613 | |
| 614 return retval; | |
| 615 } | |
| 616 | |
| 4805 | 617 // Save an empty matrix, if needed. Returns |
| 618 // > 0 Saved empty matrix | |
| 619 // = 0 Not an empty matrix; did nothing | |
| 620 // < 0 Error condition | |
| 621 int | |
| 622 save_hdf5_empty (hid_t loc_id, const char *name, const dim_vector d) | |
| 623 { | |
| 624 hsize_t sz = d.length (); | |
| 6276 | 625 OCTAVE_LOCAL_BUFFER (octave_idx_type, dims, sz); |
| 4805 | 626 bool empty = false; |
| 627 hid_t space_hid = -1, data_hid = -1; | |
| 628 int retval; | |
| 629 for (hsize_t i = 0; i < sz; i++) | |
| 630 { | |
| 631 dims[i] = d(i); | |
| 632 if (dims[i] < 1) | |
| 633 empty = true; | |
| 634 } | |
| 635 | |
| 636 if (!empty) | |
| 637 return 0; | |
| 638 | |
| 5760 | 639 space_hid = H5Screate_simple (1, &sz, 0); |
| 4805 | 640 if (space_hid < 0) return space_hid; |
| 641 | |
| 5351 | 642 data_hid = H5Dcreate (loc_id, name, H5T_NATIVE_IDX, space_hid, |
| 4805 | 643 H5P_DEFAULT); |
| 644 if (data_hid < 0) | |
| 645 { | |
| 646 H5Sclose (space_hid); | |
| 647 return data_hid; | |
| 648 } | |
| 649 | |
| 5351 | 650 retval = H5Dwrite (data_hid, H5T_NATIVE_IDX, H5S_ALL, H5S_ALL, |
| 5760 | 651 H5P_DEFAULT, dims) >= 0; |
| 4805 | 652 |
| 653 H5Dclose (data_hid); | |
| 654 H5Sclose (space_hid); | |
| 655 | |
| 656 if (retval >= 0) | |
| 657 retval = hdf5_add_attr (loc_id, "OCTAVE_EMPTY_MATRIX"); | |
| 658 | |
| 659 return (retval == 0 ? 1 : retval); | |
| 660 } | |
| 661 | |
| 662 // Load an empty matrix, if needed. Returns | |
| 663 // > 0 loaded empty matrix, dimensions returned | |
| 664 // = 0 Not an empty matrix; did nothing | |
| 665 // < 0 Error condition | |
| 666 int | |
| 667 load_hdf5_empty (hid_t loc_id, const char *name, dim_vector &d) | |
| 668 { | |
| 669 if (!hdf5_check_attr(loc_id, "OCTAVE_EMPTY_MATRIX")) | |
| 670 return 0; | |
| 671 | |
| 672 hsize_t hdims, maxdims; | |
| 673 hid_t data_hid = H5Dopen (loc_id, name); | |
| 674 hid_t space_id = H5Dget_space (data_hid); | |
| 675 H5Sget_simple_extent_dims (space_id, &hdims, &maxdims); | |
| 676 int retval; | |
| 677 | |
| 5351 | 678 OCTAVE_LOCAL_BUFFER (octave_idx_type, dims, hdims); |
| 679 | |
| 680 retval = H5Dread (data_hid, H5T_NATIVE_IDX, H5S_ALL, H5S_ALL, | |
| 5760 | 681 H5P_DEFAULT, dims); |
| 4805 | 682 if (retval >= 0) |
| 683 { | |
| 684 d.resize (hdims); | |
| 685 for (hsize_t i = 0; i < hdims; i++) | |
| 686 d(i) = dims[i]; | |
| 687 } | |
| 688 | |
| 689 H5Sclose (space_id); | |
| 690 H5Dclose (data_hid); | |
| 691 | |
| 692 return (retval == 0 ? hdims : retval); | |
| 693 } | |
| 694 | |
| 4634 | 695 // save_type_to_hdf5 is not currently used, since hdf5 doesn't yet support |
| 696 // automatic float<->integer conversions: | |
| 697 | |
| 698 #if HAVE_HDF5_INT2FLOAT_CONVERSIONS | |
| 699 | |
| 700 // return the HDF5 type id corresponding to the Octave save_type | |
| 701 | |
| 4687 | 702 hid_t |
| 4634 | 703 save_type_to_hdf5 (save_type st) |
| 704 { | |
| 705 switch (st) | |
| 706 { | |
| 707 case LS_U_CHAR: | |
| 708 return H5T_NATIVE_UCHAR; | |
| 709 | |
| 710 case LS_U_SHORT: | |
| 711 return H5T_NATIVE_USHORT; | |
| 712 | |
| 713 case LS_U_INT: | |
| 714 return H5T_NATIVE_UINT; | |
| 715 | |
| 716 case LS_CHAR: | |
| 717 return H5T_NATIVE_CHAR; | |
| 718 | |
| 719 case LS_SHORT: | |
| 720 return H5T_NATIVE_SHORT; | |
| 721 | |
| 722 case LS_INT: | |
| 723 return H5T_NATIVE_INT; | |
| 724 | |
| 725 case LS_FLOAT: | |
| 726 return H5T_NATIVE_FLOAT; | |
| 727 | |
| 728 case LS_DOUBLE: | |
| 729 default: | |
| 730 return H5T_NATIVE_DOUBLE; | |
| 731 } | |
| 732 } | |
| 733 #endif /* HAVE_HDF5_INT2FLOAT_CONVERSIONS */ | |
| 734 | |
| 735 // Add the data from TC to the HDF5 location loc_id, which could | |
| 736 // be either a file or a group within a file. Return true if | |
| 737 // successful. This function calls itself recursively for lists | |
| 738 // (stored as HDF5 groups). | |
| 739 | |
| 4687 | 740 bool |
| 4634 | 741 add_hdf5_data (hid_t loc_id, const octave_value& tc, |
| 742 const std::string& name, const std::string& doc, | |
| 743 bool mark_as_global, bool save_as_floats) | |
| 744 { | |
| 745 hsize_t dims[3]; | |
| 4687 | 746 hid_t type_id = -1, space_id = -1, data_id = -1, data_type_id = -1; |
| 747 bool retval = false; | |
| 748 octave_value val = tc; | |
|
8401
712cfdc2e417
allow saving diagonal & permutation matrices to hdf5 as full
Jaroslav Hajek <highegg@gmail.com>
parents:
8377
diff
changeset
|
749 // 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
|
750 // 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
|
751 // This is a temporary hack. |
|
712cfdc2e417
allow saving diagonal & permutation matrices to hdf5 as full
Jaroslav Hajek <highegg@gmail.com>
parents:
8377
diff
changeset
|
752 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
|
753 val = val.full_value (); |
|
8401
712cfdc2e417
allow saving diagonal & permutation matrices to hdf5 as full
Jaroslav Hajek <highegg@gmail.com>
parents:
8377
diff
changeset
|
754 |
|
712cfdc2e417
allow saving diagonal & permutation matrices to hdf5 as full
Jaroslav Hajek <highegg@gmail.com>
parents:
8377
diff
changeset
|
755 std::string t = val.type_name(); |
| 4634 | 756 |
| 4687 | 757 data_id = H5Gcreate (loc_id, name.c_str (), 0); |
| 758 if (data_id < 0) | |
| 759 goto error_cleanup; | |
| 4634 | 760 |
| 4687 | 761 // attach the type of the variable |
| 762 type_id = H5Tcopy (H5T_C_S1); H5Tset_size (type_id, t.length () + 1); | |
| 763 if (type_id < 0) | |
| 764 goto error_cleanup; | |
| 4634 | 765 |
| 4687 | 766 dims[0] = 0; |
| 5760 | 767 space_id = H5Screate_simple (0 , dims, 0); |
| 4687 | 768 if (space_id < 0) |
| 769 goto error_cleanup; | |
| 4634 | 770 |
| 4687 | 771 data_type_id = H5Dcreate (data_id, "type", type_id, space_id, H5P_DEFAULT); |
| 772 if (data_type_id < 0 || H5Dwrite (data_type_id, type_id, H5S_ALL, H5S_ALL, | |
| 5760 | 773 H5P_DEFAULT, t.c_str ()) < 0) |
| 4687 | 774 goto error_cleanup; |
| 4634 | 775 |
| 4687 | 776 // Now call the real function to save the variable |
| 777 retval = val.save_hdf5 (data_id, "value", save_as_floats); | |
| 4634 | 778 |
| 779 // attach doc string as comment: | |
| 4687 | 780 if (retval && doc.length () > 0 |
| 4634 | 781 && H5Gset_comment (loc_id, name.c_str (), doc.c_str ()) < 0) |
| 4687 | 782 retval = false; |
| 4634 | 783 |
| 784 // if it's global, add an attribute "OCTAVE_GLOBAL" with value 1 | |
| 4687 | 785 if (retval && mark_as_global) |
| 4634 | 786 retval = hdf5_add_attr (data_id, "OCTAVE_GLOBAL") >= 0; |
| 787 | |
| 4687 | 788 // We are saving in the new variable format, so mark it |
| 789 if (retval) | |
| 790 retval = hdf5_add_attr (data_id, "OCTAVE_NEW_FORMAT") >= 0; | |
| 791 | |
| 4634 | 792 error_cleanup: |
| 793 | |
| 4687 | 794 if (data_type_id >= 0) |
| 795 H5Dclose (data_type_id); | |
| 4634 | 796 |
| 4687 | 797 if (type_id >= 0) |
| 798 H5Tclose (type_id); | |
| 4634 | 799 |
| 800 if (space_id >= 0) | |
| 801 H5Sclose (space_id); | |
| 802 | |
| 4687 | 803 if (data_id >= 0) |
| 804 H5Gclose (data_id); | |
| 805 | |
| 806 if (! retval) | |
| 807 error ("save: error while writing `%s' to hdf5 file", name.c_str ()); | |
| 4634 | 808 |
| 809 return retval; | |
| 810 } | |
| 811 | |
| 812 // Write data from TC in HDF5 (binary) format to the stream OS, | |
| 813 // which must be an hdf5_ofstream, returning true on success. | |
| 814 | |
| 815 bool | |
| 816 save_hdf5_data (std::ostream& os, const octave_value& tc, | |
| 817 const std::string& name, const std::string& doc, | |
| 818 bool mark_as_global, bool save_as_floats) | |
| 819 { | |
| 5760 | 820 hdf5_ofstream& hs = dynamic_cast<hdf5_ofstream&> (os); |
| 4634 | 821 |
| 822 return add_hdf5_data (hs.file_id, tc, name, doc, | |
| 823 mark_as_global, save_as_floats); | |
| 824 } | |
| 825 | |
| 826 #endif | |
| 827 | |
| 828 /* | |
| 829 ;;; Local Variables: *** | |
| 830 ;;; mode: C++ *** | |
| 831 ;;; End: *** | |
| 832 */ |