Mercurial > hg > octave-nkf
annotate src/ls-hdf5.cc @ 10325:8b3cfc1288e2
implement lazy index conversions
| author | Jaroslav Hajek <highegg@gmail.com> |
|---|---|
| date | Tue, 16 Feb 2010 15:28:53 +0100 |
| parents | 57a59eae83cc |
| children | 2271261f088a |
| 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" | |
|
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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" | |
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70 #include "ov-lazy-idx.h" |
| 4634 | 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])) | |
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85 retval += '_'; |
| 4634 | 86 |
| 87 for (size_t i = 0; i < nm_len; i++) | |
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88 { |
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89 char c = nm[i]; |
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90 retval += (isalnum (c) || c == '_') ? c : '_'; |
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91 } |
| 4634 | 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)) | |
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119 return false; |
| 4634 | 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 | |
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146 #if HAVE_HDF5_18 |
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147 H5Eget_auto (H5E_DEFAULT, &err_func, &err_func_data); |
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148 H5Eset_auto (H5E_DEFAULT, 0, 0); |
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149 #else |
| 4634 | 150 H5Eget_auto (&err_func, &err_func_data); |
| 151 H5Eset_auto (0, 0); | |
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152 #endif |
| 4634 | 153 |
| 154 hid_t attr_id = H5Aopen_name (loc_id, attr_name); | |
| 155 | |
| 156 if (attr_id >= 0) | |
| 157 { | |
| 158 // successful | |
| 159 retval = 1; | |
| 160 H5Aclose (attr_id); | |
| 161 } | |
| 162 | |
| 163 // restore error reporting: | |
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164 #if HAVE_HDF5_18 |
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165 H5Eset_auto (H5E_DEFAULT, err_func, err_func_data); |
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166 #else |
| 4634 | 167 H5Eset_auto (err_func, err_func_data); |
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168 #endif |
| 4634 | 169 return retval; |
| 170 } | |
| 171 | |
| 4687 | 172 // The following subroutines creates an HDF5 representations of the way |
| 173 // we will store Octave complex types (pairs of floating-point numbers). | |
| 174 // NUM_TYPE is the HDF5 numeric type to use for storage (e.g. | |
| 175 // H5T_NATIVE_DOUBLE to save as 'double'). Note that any necessary | |
| 176 // conversions are handled automatically by HDF5. | |
| 4634 | 177 |
| 4687 | 178 hid_t |
| 4634 | 179 hdf5_make_complex_type (hid_t num_type) |
| 180 { | |
| 181 hid_t type_id = H5Tcreate (H5T_COMPOUND, sizeof (double) * 2); | |
| 182 | |
| 183 H5Tinsert (type_id, "real", 0 * sizeof (double), num_type); | |
| 184 H5Tinsert (type_id, "imag", 1 * sizeof (double), num_type); | |
| 185 | |
| 186 return type_id; | |
| 187 } | |
| 188 | |
| 189 // This function is designed to be passed to H5Giterate, which calls it | |
| 190 // on each data item in an HDF5 file. For the item whose name is NAME in | |
| 191 // the group GROUP_ID, this function sets dv->tc to an Octave representation | |
| 192 // of that item. (dv must be a pointer to hdf5_callback_data.) (It also | |
| 193 // sets the other fields of dv). | |
| 194 // | |
| 195 // It returns 1 on success (in which case H5Giterate stops and returns), | |
| 196 // -1 on error, and 0 to tell H5Giterate to continue on to the next item | |
| 197 // (e.g. if NAME was a data type we don't recognize). | |
| 198 | |
| 4687 | 199 herr_t |
| 4634 | 200 hdf5_read_next_data (hid_t group_id, const char *name, void *dv) |
| 201 { | |
| 202 hdf5_callback_data *d = static_cast <hdf5_callback_data *> (dv); | |
| 4687 | 203 hid_t type_id = -1, type_class_id = -1, data_id = -1, subgroup_id = -1, |
| 204 space_id = -1; | |
| 4634 | 205 |
| 206 H5G_stat_t info; | |
| 207 herr_t retval = 0; | |
| 208 bool ident_valid = valid_identifier (name); | |
| 209 | |
| 210 std::string vname = name; | |
| 211 | |
| 212 // Allow identifiers as all digits so we can load lists saved by | |
| 213 // earlier versions of Octave. | |
| 214 | |
| 4687 | 215 if (! ident_valid ) |
| 4634 | 216 { |
| 217 // fix the identifier, replacing invalid chars with underscores | |
| 218 vname = make_valid_identifier (vname); | |
| 219 | |
| 220 // check again (in case vname was null, empty, or some such thing): | |
| 221 ident_valid = valid_identifier (vname); | |
| 222 } | |
| 223 | |
| 224 H5Gget_objinfo (group_id, name, 1, &info); | |
| 225 | |
| 4687 | 226 if (info.type == H5G_GROUP && ident_valid) |
| 4634 | 227 { |
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228 #if HAVE_HDF5_18 |
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229 subgroup_id = H5Gopen (group_id, name, H5P_DEFAULT); |
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230 #else |
| 4687 | 231 subgroup_id = H5Gopen (group_id, name); |
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232 #endif |
| 4634 | 233 |
| 234 if (subgroup_id < 0) | |
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235 { |
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236 retval = subgroup_id; |
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237 goto done; |
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238 } |
| 4634 | 239 |
| 4687 | 240 if (hdf5_check_attr (subgroup_id, "OCTAVE_NEW_FORMAT")) |
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241 { |
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242 #if HAVE_HDF5_18 |
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243 data_id = H5Dopen (subgroup_id, "type", H5P_DEFAULT); |
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244 #else |
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245 data_id = H5Dopen (subgroup_id, "type"); |
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246 #endif |
| 4634 | 247 |
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248 if (data_id < 0) |
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249 { |
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250 retval = data_id; |
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251 goto done; |
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252 } |
| 4634 | 253 |
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254 type_id = H5Dget_type (data_id); |
| 4687 | 255 |
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256 type_class_id = H5Tget_class (type_id); |
| 4687 | 257 |
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258 if (type_class_id != H5T_STRING) |
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259 goto done; |
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260 |
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261 space_id = H5Dget_space (data_id); |
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262 hsize_t rank = H5Sget_simple_extent_ndims (space_id); |
| 4687 | 263 |
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264 if (rank != 0) |
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265 goto done; |
| 4687 | 266 |
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267 int slen = H5Tget_size (type_id); |
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268 if (slen < 0) |
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269 goto done; |
| 4687 | 270 |
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271 OCTAVE_LOCAL_BUFFER (char, typ, slen); |
| 4687 | 272 |
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273 // create datatype for (null-terminated) string to read into: |
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274 hid_t st_id = H5Tcopy (H5T_C_S1); |
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275 H5Tset_size (st_id, slen); |
| 4687 | 276 |
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277 if (H5Dread (data_id, st_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, |
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278 typ) < 0) |
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279 goto done; |
| 4687 | 280 |
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281 H5Tclose (st_id); |
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282 H5Dclose (data_id); |
| 4687 | 283 |
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284 d->tc = octave_value_typeinfo::lookup_type (typ); |
| 4687 | 285 |
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286 retval = (d->tc.load_hdf5 (subgroup_id, "value") ? 1 : -1); |
| 4687 | 287 |
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288 // check for OCTAVE_GLOBAL attribute: |
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289 d->global = hdf5_check_attr (subgroup_id, "OCTAVE_GLOBAL"); |
| 4687 | 290 |
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291 H5Gclose (subgroup_id); |
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292 } |
| 4634 | 293 else |
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294 { |
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295 // an HDF5 group is treated as an octave structure by |
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296 // default (since that preserves name information), and an |
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297 // octave list otherwise. |
| 4687 | 298 |
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299 if (hdf5_check_attr (subgroup_id, "OCTAVE_LIST")) |
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300 d->tc = octave_value_typeinfo::lookup_type ("list"); |
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301 else |
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302 d->tc = octave_value_typeinfo::lookup_type ("struct"); |
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303 |
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304 // check for OCTAVE_GLOBAL attribute: |
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305 d->global = hdf5_check_attr (subgroup_id, "OCTAVE_GLOBAL"); |
| 4687 | 306 |
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307 H5Gclose (subgroup_id); |
| 4634 | 308 |
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309 retval = (d->tc.load_hdf5 (group_id, name) ? 1 : -1); |
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310 } |
| 4687 | 311 |
| 312 } | |
| 313 else if (info.type == H5G_DATASET && ident_valid) | |
| 314 { | |
| 315 // For backwards compatiability. | |
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316 #if HAVE_HDF5_18 |
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317 data_id = H5Dopen (group_id, name, H5P_DEFAULT); |
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318 #else |
| 4687 | 319 data_id = H5Dopen (group_id, name); |
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320 #endif |
| 4687 | 321 |
| 322 if (data_id < 0) | |
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323 { |
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324 retval = data_id; |
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325 goto done; |
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326 } |
| 4634 | 327 |
| 4687 | 328 type_id = H5Dget_type (data_id); |
| 329 | |
| 330 type_class_id = H5Tget_class (type_id); | |
| 331 | |
| 332 if (type_class_id == H5T_FLOAT) | |
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333 { |
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334 space_id = H5Dget_space (data_id); |
| 4687 | 335 |
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336 hsize_t rank = H5Sget_simple_extent_ndims (space_id); |
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337 |
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338 if (rank == 0) |
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339 d->tc = octave_value_typeinfo::lookup_type ("scalar"); |
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340 else |
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341 d->tc = octave_value_typeinfo::lookup_type ("matrix"); |
| 4687 | 342 |
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343 H5Sclose (space_id); |
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344 } |
| 4948 | 345 else if (type_class_id == H5T_INTEGER) |
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346 { |
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347 // What integer type do we really have.. |
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348 std::string int_typ; |
| 4948 | 349 #ifdef HAVE_H5T_GET_NATIVE_TYPE |
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350 // FIXME test this code and activated with an autoconf |
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351 // test!! It is also incorrect for 64-bit indexing!! |
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352 |
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353 switch (H5Tget_native_type (type_id, H5T_DIR_ASCEND)) |
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354 { |
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355 case H5T_NATIVE_CHAR: |
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356 int_typ = "int8 "; |
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357 break; |
| 4948 | 358 |
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359 case H5T_NATIVE_SHORT: |
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360 int_typ = "int16 "; |
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361 break; |
| 4948 | 362 |
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363 case H5T_NATIVE_INT: |
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364 case H5T_NATIVE_LONG: |
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365 int_typ = "int32 "; |
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366 break; |
| 4948 | 367 |
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368 case H5T_NATIVE_LLONG: |
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369 int_typ = "int64 "; |
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370 break; |
| 4948 | 371 |
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372 case H5T_NATIVE_UCHAR: |
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373 int_typ = "uint8 "; |
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374 break; |
| 4948 | 375 |
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376 case H5T_NATIVE_USHORT: |
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377 int_typ = "uint16 "; |
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378 break; |
| 4948 | 379 |
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380 case H5T_NATIVE_UINT: |
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381 case H5T_NATIVE_ULONG: |
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382 int_typ = "uint32 "; |
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383 break; |
| 4948 | 384 |
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385 case H5T_NATIVE_ULLONG: |
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386 int_typ = "uint64 "; |
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387 break; |
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388 } |
| 4948 | 389 #else |
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390 hid_t int_sign = H5Tget_sign (type_id); |
| 4948 | 391 |
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392 if (int_sign == H5T_SGN_ERROR) |
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393 warning ("load: can't read `%s' (unknown datatype)", name); |
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394 else |
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395 { |
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396 if (int_sign == H5T_SGN_NONE) |
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397 int_typ.append ("u"); |
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398 int_typ.append ("int"); |
| 4948 | 399 |
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400 int slen = H5Tget_size (type_id); |
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401 if (slen < 0) |
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402 warning ("load: can't read `%s' (unknown datatype)", name); |
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403 else |
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404 { |
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405 switch (slen) |
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406 { |
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407 case 1: |
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408 int_typ.append ("8 "); |
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409 break; |
| 4948 | 410 |
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411 case 2: |
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412 int_typ.append ("16 "); |
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413 break; |
| 4948 | 414 |
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415 case 4: |
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416 int_typ.append ("32 "); |
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417 break; |
| 4948 | 418 |
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419 case 8: |
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420 int_typ.append ("64 "); |
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421 break; |
| 4948 | 422 |
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423 default: |
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424 warning ("load: can't read `%s' (unknown datatype)", |
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425 name); |
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426 int_typ = ""; |
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427 break; |
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428 } |
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429 } |
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430 } |
| 4948 | 431 #endif |
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432 if (int_typ == "") |
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433 warning ("load: can't read `%s' (unknown datatype)", name); |
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434 else |
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435 { |
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436 // Matrix or scalar? |
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437 space_id = H5Dget_space (data_id); |
| 4948 | 438 |
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439 hsize_t rank = H5Sget_simple_extent_ndims (space_id); |
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440 |
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441 if (rank == 0) |
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442 int_typ.append ("scalar"); |
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443 else |
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444 int_typ.append ("matrix"); |
| 4948 | 445 |
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446 d->tc = octave_value_typeinfo::lookup_type (int_typ); |
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447 H5Sclose (space_id); |
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448 } |
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449 } |
| 4687 | 450 else if (type_class_id == H5T_STRING) |
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451 d->tc = octave_value_typeinfo::lookup_type ("string"); |
| 4687 | 452 else if (type_class_id == H5T_COMPOUND) |
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453 { |
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454 hid_t complex_type = hdf5_make_complex_type (H5T_NATIVE_DOUBLE); |
| 4687 | 455 |
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456 if (hdf5_types_compatible (type_id, complex_type)) |
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457 { |
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458 // read complex matrix or scalar variable |
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459 space_id = H5Dget_space (data_id); |
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460 hsize_t rank = H5Sget_simple_extent_ndims (space_id); |
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461 |
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462 if (rank == 0) |
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463 d->tc = octave_value_typeinfo::lookup_type ("complex scalar"); |
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464 else |
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465 d->tc = octave_value_typeinfo::lookup_type ("complex matrix"); |
| 4687 | 466 |
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467 H5Sclose (space_id); |
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468 } |
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469 else |
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470 // Assume that if its not complex its a range. If its not |
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471 // it'll be rejected later in the range code |
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472 d->tc = octave_value_typeinfo::lookup_type ("range"); |
| 4687 | 473 |
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474 H5Tclose (complex_type); |
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475 } |
| 4687 | 476 else |
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477 { |
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478 warning ("load: can't read `%s' (unknown datatype)", name); |
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479 retval = 0; // unknown datatype; skip |
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480 } |
| 4687 | 481 |
| 482 // check for OCTAVE_GLOBAL attribute: | |
| 483 d->global = hdf5_check_attr (data_id, "OCTAVE_GLOBAL"); | |
| 484 | |
| 485 H5Tclose (type_id); | |
| 486 H5Dclose (data_id); | |
| 487 | |
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488 retval = (d->tc.load_hdf5 (group_id, name) ? 1 : -1); |
| 4634 | 489 } |
| 4687 | 490 |
| 491 if (!ident_valid) | |
| 4634 | 492 { |
| 493 // should we attempt to handle invalid identifiers by converting | |
| 494 // bad characters to '_', say? | |
| 495 warning ("load: skipping invalid identifier `%s' in hdf5 file", | |
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496 name); |
| 4634 | 497 } |
| 498 | |
| 499 done: | |
| 500 if (retval < 0) | |
| 501 error ("load: error while reading hdf5 item %s", name); | |
| 4687 | 502 |
| 4634 | 503 if (retval > 0) |
| 504 { | |
| 505 // get documentation string, if any: | |
| 506 int comment_length = H5Gget_comment (group_id, name, 0, 0); | |
| 507 | |
| 508 if (comment_length > 1) | |
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509 { |
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510 OCTAVE_LOCAL_BUFFER (char, tdoc, comment_length); |
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511 H5Gget_comment (group_id, name, comment_length, tdoc); |
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512 d->doc = tdoc; |
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513 } |
| 4634 | 514 else if (vname != name) |
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515 { |
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516 // the name was changed; store the original name |
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517 // as the documentation string: |
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518 d->doc = name; |
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519 } |
| 4634 | 520 |
| 521 // copy name (actually, vname): | |
| 522 d->name = vname; | |
| 523 } | |
| 524 | |
| 525 return retval; | |
| 526 } | |
| 527 | |
| 528 // Read the next Octave variable from the stream IS, which must really be | |
| 529 // an hdf5_ifstream. Return the variable value in tc, its doc string | |
| 530 // in doc, and whether it is global in global. The return value is | |
| 531 // the name of the variable, or NULL if none were found or there was | |
| 4687 | 532 // and error. |
| 4634 | 533 std::string |
| 4687 | 534 read_hdf5_data (std::istream& is, const std::string& /* filename */, |
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535 bool& global, octave_value& tc, std::string& doc) |
| 4634 | 536 { |
| 537 std::string retval; | |
| 538 | |
| 539 doc.resize (0); | |
| 540 | |
| 5760 | 541 hdf5_ifstream& hs = dynamic_cast<hdf5_ifstream&> (is); |
| 4634 | 542 hdf5_callback_data d; |
| 543 | |
| 4696 | 544 herr_t H5Giterate_retval = -1; |
| 545 | |
| 546 hsize_t num_obj = 0; | |
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547 #if HAVE_HDF5_18 |
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548 hid_t group_id = H5Gopen (hs.file_id, "/", H5P_DEFAULT); |
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549 #else |
| 5060 | 550 hid_t group_id = H5Gopen (hs.file_id, "/"); |
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551 #endif |
| 5060 | 552 H5Gget_num_objs (group_id, &num_obj); |
| 553 H5Gclose (group_id); | |
| 4696 | 554 if (hs.current_item < static_cast<int> (num_obj)) |
| 555 H5Giterate_retval = H5Giterate (hs.file_id, "/", &hs.current_item, | |
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556 hdf5_read_next_data, &d); |
| 4634 | 557 |
| 558 if (H5Giterate_retval > 0) | |
| 559 { | |
| 560 global = d.global; | |
| 561 tc = d.tc; | |
| 562 doc = d.doc; | |
| 563 } | |
| 564 else | |
| 565 { | |
| 566 // an error occurred (H5Giterate_retval < 0) or there are no | |
| 567 // more datasets print an error message if retval < 0? | |
| 568 // hdf5_read_next_data already printed one, probably. | |
| 569 } | |
| 570 | |
| 571 if (! d.name.empty ()) | |
| 572 retval = d.name; | |
| 573 | |
| 574 return retval; | |
| 575 } | |
| 576 | |
| 577 // Add an attribute named attr_name to loc_id (a simple scalar | |
| 578 // attribute with value 1). Return value is >= 0 on success. | |
| 579 static herr_t | |
| 580 hdf5_add_attr (hid_t loc_id, const char *attr_name) | |
| 581 { | |
| 582 herr_t retval = 0; | |
| 583 | |
| 584 hid_t as_id = H5Screate (H5S_SCALAR); | |
| 585 | |
| 586 if (as_id >= 0) | |
| 587 { | |
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588 #if HAVE_HDF5_18 |
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589 hid_t a_id = H5Acreate (loc_id, attr_name, H5T_NATIVE_UCHAR, |
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590 as_id, H5P_DEFAULT, H5P_DEFAULT); |
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591 #else |
| 4634 | 592 hid_t a_id = H5Acreate (loc_id, attr_name, |
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593 H5T_NATIVE_UCHAR, as_id, H5P_DEFAULT); |
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594 #endif |
| 4634 | 595 if (a_id >= 0) |
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596 { |
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597 unsigned char attr_val = 1; |
| 4634 | 598 |
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599 retval = H5Awrite (a_id, H5T_NATIVE_UCHAR, &attr_val); |
| 4634 | 600 |
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601 H5Aclose (a_id); |
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602 } |
| 4634 | 603 else |
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604 retval = a_id; |
| 4634 | 605 |
| 606 H5Sclose (as_id); | |
| 607 } | |
| 608 else | |
| 609 retval = as_id; | |
| 610 | |
| 611 return retval; | |
| 612 } | |
| 613 | |
| 4805 | 614 // Save an empty matrix, if needed. Returns |
| 615 // > 0 Saved empty matrix | |
| 616 // = 0 Not an empty matrix; did nothing | |
| 617 // < 0 Error condition | |
| 618 int | |
| 619 save_hdf5_empty (hid_t loc_id, const char *name, const dim_vector d) | |
| 620 { | |
| 621 hsize_t sz = d.length (); | |
| 6276 | 622 OCTAVE_LOCAL_BUFFER (octave_idx_type, dims, sz); |
| 4805 | 623 bool empty = false; |
| 624 hid_t space_hid = -1, data_hid = -1; | |
| 625 int retval; | |
| 626 for (hsize_t i = 0; i < sz; i++) | |
| 627 { | |
| 628 dims[i] = d(i); | |
| 629 if (dims[i] < 1) | |
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630 empty = true; |
| 4805 | 631 } |
| 632 | |
| 633 if (!empty) | |
| 634 return 0; | |
| 635 | |
| 5760 | 636 space_hid = H5Screate_simple (1, &sz, 0); |
| 4805 | 637 if (space_hid < 0) return space_hid; |
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638 #if HAVE_HDF5_18 |
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639 data_hid = H5Dcreate (loc_id, name, H5T_NATIVE_IDX, space_hid, |
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640 H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); |
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641 #else |
| 5351 | 642 data_hid = H5Dcreate (loc_id, name, H5T_NATIVE_IDX, space_hid, |
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643 H5P_DEFAULT); |
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644 #endif |
| 4805 | 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, |
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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; | |
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674 #if HAVE_HDF5_18 |
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675 hid_t data_hid = H5Dopen (loc_id, name, H5P_DEFAULT); |
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676 #else |
| 4805 | 677 hid_t data_hid = H5Dopen (loc_id, name); |
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678 #endif |
| 4805 | 679 hid_t space_id = H5Dget_space (data_hid); |
| 680 H5Sget_simple_extent_dims (space_id, &hdims, &maxdims); | |
| 681 int retval; | |
| 682 | |
| 5351 | 683 OCTAVE_LOCAL_BUFFER (octave_idx_type, dims, hdims); |
| 684 | |
| 685 retval = H5Dread (data_hid, H5T_NATIVE_IDX, H5S_ALL, H5S_ALL, | |
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686 H5P_DEFAULT, dims); |
| 4805 | 687 if (retval >= 0) |
| 688 { | |
| 689 d.resize (hdims); | |
| 690 for (hsize_t i = 0; i < hdims; i++) | |
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691 d(i) = dims[i]; |
| 4805 | 692 } |
| 693 | |
| 694 H5Sclose (space_id); | |
| 695 H5Dclose (data_hid); | |
| 696 | |
| 697 return (retval == 0 ? hdims : retval); | |
| 698 } | |
| 699 | |
| 4634 | 700 // save_type_to_hdf5 is not currently used, since hdf5 doesn't yet support |
| 701 // automatic float<->integer conversions: | |
| 702 | |
| 703 #if HAVE_HDF5_INT2FLOAT_CONVERSIONS | |
| 704 | |
| 705 // return the HDF5 type id corresponding to the Octave save_type | |
| 706 | |
| 4687 | 707 hid_t |
| 4634 | 708 save_type_to_hdf5 (save_type st) |
| 709 { | |
| 710 switch (st) | |
| 711 { | |
| 712 case LS_U_CHAR: | |
| 713 return H5T_NATIVE_UCHAR; | |
| 714 | |
| 715 case LS_U_SHORT: | |
| 716 return H5T_NATIVE_USHORT; | |
| 717 | |
| 718 case LS_U_INT: | |
| 719 return H5T_NATIVE_UINT; | |
| 720 | |
| 721 case LS_CHAR: | |
| 722 return H5T_NATIVE_CHAR; | |
| 723 | |
| 724 case LS_SHORT: | |
| 725 return H5T_NATIVE_SHORT; | |
| 726 | |
| 727 case LS_INT: | |
| 728 return H5T_NATIVE_INT; | |
| 729 | |
| 730 case LS_FLOAT: | |
| 731 return H5T_NATIVE_FLOAT; | |
| 732 | |
| 733 case LS_DOUBLE: | |
| 734 default: | |
| 735 return H5T_NATIVE_DOUBLE; | |
| 736 } | |
| 737 } | |
| 738 #endif /* HAVE_HDF5_INT2FLOAT_CONVERSIONS */ | |
| 739 | |
| 740 // Add the data from TC to the HDF5 location loc_id, which could | |
| 741 // be either a file or a group within a file. Return true if | |
| 742 // successful. This function calls itself recursively for lists | |
| 743 // (stored as HDF5 groups). | |
| 744 | |
| 4687 | 745 bool |
| 4634 | 746 add_hdf5_data (hid_t loc_id, const octave_value& tc, |
|
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747 const std::string& name, const std::string& doc, |
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748 bool mark_as_global, bool save_as_floats) |
| 4634 | 749 { |
| 750 hsize_t dims[3]; | |
| 4687 | 751 hid_t type_id = -1, space_id = -1, data_id = -1, data_type_id = -1; |
| 752 bool retval = false; | |
| 753 octave_value val = tc; | |
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754 // FIXME: diagonal & permutation matrices currently don't know how to save |
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755 // themselves, so we convert them first to normal matrices using A = A(:,:). |
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756 // This is a temporary hack. |
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757 if (val.is_diag_matrix () || val.is_perm_matrix () |
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758 || val.type_id () == octave_lazy_index::static_type_id ()) |
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759 val = val.full_value (); |
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760 |
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761 std::string t = val.type_name(); |
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762 #if HAVE_HDF5_18 |
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763 data_id = H5Gcreate (loc_id, name.c_str (), H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); |
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764 #else |
| 4687 | 765 data_id = H5Gcreate (loc_id, name.c_str (), 0); |
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766 #endif |
| 4687 | 767 if (data_id < 0) |
| 768 goto error_cleanup; | |
| 4634 | 769 |
| 4687 | 770 // attach the type of the variable |
| 771 type_id = H5Tcopy (H5T_C_S1); H5Tset_size (type_id, t.length () + 1); | |
| 772 if (type_id < 0) | |
| 773 goto error_cleanup; | |
| 4634 | 774 |
| 4687 | 775 dims[0] = 0; |
| 5760 | 776 space_id = H5Screate_simple (0 , dims, 0); |
| 4687 | 777 if (space_id < 0) |
| 778 goto error_cleanup; | |
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779 #if HAVE_HDF5_18 |
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780 data_type_id = H5Dcreate (data_id, "type", type_id, space_id, |
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781 H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); |
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782 #else |
| 4687 | 783 data_type_id = H5Dcreate (data_id, "type", type_id, space_id, H5P_DEFAULT); |
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784 #endif |
| 4687 | 785 if (data_type_id < 0 || H5Dwrite (data_type_id, type_id, H5S_ALL, H5S_ALL, |
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786 H5P_DEFAULT, t.c_str ()) < 0) |
| 4687 | 787 goto error_cleanup; |
| 4634 | 788 |
| 4687 | 789 // Now call the real function to save the variable |
| 790 retval = val.save_hdf5 (data_id, "value", save_as_floats); | |
| 4634 | 791 |
| 792 // attach doc string as comment: | |
| 4687 | 793 if (retval && doc.length () > 0 |
| 4634 | 794 && H5Gset_comment (loc_id, name.c_str (), doc.c_str ()) < 0) |
| 4687 | 795 retval = false; |
| 4634 | 796 |
| 797 // if it's global, add an attribute "OCTAVE_GLOBAL" with value 1 | |
| 4687 | 798 if (retval && mark_as_global) |
| 4634 | 799 retval = hdf5_add_attr (data_id, "OCTAVE_GLOBAL") >= 0; |
| 800 | |
| 4687 | 801 // We are saving in the new variable format, so mark it |
| 802 if (retval) | |
| 803 retval = hdf5_add_attr (data_id, "OCTAVE_NEW_FORMAT") >= 0; | |
| 804 | |
| 4634 | 805 error_cleanup: |
| 806 | |
| 4687 | 807 if (data_type_id >= 0) |
| 808 H5Dclose (data_type_id); | |
| 4634 | 809 |
| 4687 | 810 if (type_id >= 0) |
| 811 H5Tclose (type_id); | |
| 4634 | 812 |
| 813 if (space_id >= 0) | |
| 814 H5Sclose (space_id); | |
| 815 | |
| 4687 | 816 if (data_id >= 0) |
| 817 H5Gclose (data_id); | |
| 818 | |
| 819 if (! retval) | |
| 820 error ("save: error while writing `%s' to hdf5 file", name.c_str ()); | |
| 4634 | 821 |
| 822 return retval; | |
| 823 } | |
| 824 | |
| 825 // Write data from TC in HDF5 (binary) format to the stream OS, | |
| 826 // which must be an hdf5_ofstream, returning true on success. | |
| 827 | |
| 828 bool | |
| 829 save_hdf5_data (std::ostream& os, const octave_value& tc, | |
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830 const std::string& name, const std::string& doc, |
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831 bool mark_as_global, bool save_as_floats) |
| 4634 | 832 { |
| 5760 | 833 hdf5_ofstream& hs = dynamic_cast<hdf5_ofstream&> (os); |
| 4634 | 834 |
| 835 return add_hdf5_data (hs.file_id, tc, name, doc, | |
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836 mark_as_global, save_as_floats); |
| 4634 | 837 } |
| 838 | |
| 839 #endif |