[219] | 1 | #include "inetcdf4.hpp" |
---|
[599] | 2 | #include "netCdfInterface.hpp" |
---|
[782] | 3 | #include "netCdf_cf_constant.hpp" |
---|
[219] | 4 | |
---|
| 5 | #include <boost/algorithm/string.hpp> |
---|
| 6 | |
---|
[335] | 7 | namespace xios |
---|
[219] | 8 | { |
---|
[1485] | 9 | CINetCDF4::CINetCDF4(const StdString& filename, const MPI_Comm* comm /*= NULL*/, bool multifile /*= true*/, |
---|
| 10 | bool readMetaDataPar /*= false*/, const StdString& timeCounterName /*= "time_counter"*/) |
---|
[599] | 11 | { |
---|
[736] | 12 | // Don't use parallel mode if there is only one process |
---|
| 13 | if (comm) |
---|
[599] | 14 | { |
---|
[736] | 15 | int commSize = 0; |
---|
| 16 | MPI_Comm_size(*comm, &commSize); |
---|
| 17 | if (commSize <= 1) |
---|
| 18 | comm = NULL; |
---|
[599] | 19 | } |
---|
[1485] | 20 | mpi = comm && !multifile && readMetaDataPar; |
---|
[736] | 21 | |
---|
| 22 | // The file format will be detected automatically by NetCDF, it is safe to always set NC_MPIIO |
---|
| 23 | // even if Parallel NetCDF ends up being used. |
---|
| 24 | if (mpi) |
---|
| 25 | CNetCdfInterface::openPar(filename, NC_NOWRITE | NC_MPIIO, *comm, MPI_INFO_NULL, this->ncidp); |
---|
| 26 | else |
---|
| 27 | CNetCdfInterface::open(filename, NC_NOWRITE, this->ncidp); |
---|
[802] | 28 | |
---|
| 29 | this->timeCounterName = timeCounterName; |
---|
[811] | 30 | if (!CNetCdfInterface::isDimExisted(this->ncidp, this->timeCounterName)) this->timeCounterName=this->getUnlimitedDimensionName() ; |
---|
[825] | 31 | |
---|
[599] | 32 | } |
---|
[219] | 33 | |
---|
[599] | 34 | CINetCDF4::~CINetCDF4(void) |
---|
| 35 | { /* Nothing to do */ } |
---|
[219] | 36 | |
---|
[599] | 37 | //--------------------------------------------------------------- |
---|
[219] | 38 | |
---|
[599] | 39 | void CINetCDF4::close(void) |
---|
| 40 | { |
---|
[686] | 41 | CNetCdfInterface::close(this->ncidp); |
---|
[599] | 42 | } |
---|
[219] | 43 | |
---|
[599] | 44 | //--------------------------------------------------------------- |
---|
[219] | 45 | |
---|
[599] | 46 | int CINetCDF4::getGroup(const CVarPath* const path) |
---|
| 47 | { |
---|
| 48 | int retvalue = this->ncidp; |
---|
| 49 | if (path == NULL) return retvalue; |
---|
| 50 | CVarPath::const_iterator it = path->begin(), end = path->end(); |
---|
[219] | 51 | |
---|
[599] | 52 | for (; it != end; it++) |
---|
| 53 | { |
---|
| 54 | const StdString& groupid = *it; |
---|
[686] | 55 | CNetCdfInterface::inqNcId(retvalue, groupid, retvalue); |
---|
[599] | 56 | } |
---|
[219] | 57 | |
---|
[599] | 58 | return retvalue; |
---|
| 59 | } |
---|
[219] | 60 | |
---|
[599] | 61 | int CINetCDF4::getVariable(const StdString& varname, |
---|
| 62 | const CVarPath* const path) |
---|
| 63 | { |
---|
| 64 | int varid = 0; |
---|
| 65 | int grpid = this->getGroup(path); |
---|
[825] | 66 | if (this->hasVariable(varname, path)) |
---|
| 67 | CNetCdfInterface::inqVarId(grpid, varname, varid); |
---|
[599] | 68 | return varid; |
---|
| 69 | } |
---|
[219] | 70 | |
---|
[599] | 71 | int CINetCDF4::getDimension(const StdString& dimname, |
---|
| 72 | const CVarPath* const path) |
---|
| 73 | { |
---|
| 74 | int dimid = 0; |
---|
| 75 | int grpid = this->getGroup(path); |
---|
[686] | 76 | CNetCdfInterface::inqDimId(grpid, dimname, dimid); |
---|
[599] | 77 | return dimid; |
---|
| 78 | } |
---|
[219] | 79 | |
---|
[599] | 80 | std::pair<nc_type, StdSize> CINetCDF4::getAttribute(const StdString& attname, |
---|
| 81 | const StdString* const var, |
---|
| 82 | const CVarPath* const path) |
---|
| 83 | { |
---|
| 84 | std::pair<nc_type, StdSize> retvalue; |
---|
| 85 | int grpid = this->getGroup(path); |
---|
[1447] | 86 | int varid = (var != NULL && this->hasVariable(*var, path)) ? this->getVariable(*var, path) : NC_GLOBAL; |
---|
[686] | 87 | CNetCdfInterface::inqAtt(grpid, varid, attname, retvalue.first, retvalue.second); |
---|
[599] | 88 | return retvalue; |
---|
| 89 | } |
---|
[219] | 90 | |
---|
[599] | 91 | int CINetCDF4::getUnlimitedDimension(const CVarPath* const path) |
---|
| 92 | { |
---|
| 93 | int dimid = 0; |
---|
| 94 | int grpid = this->getGroup(path); |
---|
[686] | 95 | CNetCdfInterface::inqUnLimDim(grpid, dimid); |
---|
[599] | 96 | return dimid; |
---|
| 97 | } |
---|
[219] | 98 | |
---|
[599] | 99 | StdString CINetCDF4::getUnlimitedDimensionName(const CVarPath* const path) |
---|
| 100 | { |
---|
| 101 | int grpid = this->getGroup(path); |
---|
| 102 | int dimid = this->getUnlimitedDimension(path); |
---|
[219] | 103 | |
---|
[686] | 104 | StdString dimname; |
---|
| 105 | if (dimid != -1) |
---|
| 106 | CNetCdfInterface::inqDimName(grpid, dimid, dimname); |
---|
[599] | 107 | return dimname; |
---|
| 108 | } |
---|
[219] | 109 | |
---|
[599] | 110 | //--------------------------------------------------------------- |
---|
[686] | 111 | |
---|
[599] | 112 | StdSize CINetCDF4::getNbVertex(const StdString& name, |
---|
| 113 | const CVarPath* const path) |
---|
| 114 | { |
---|
[219] | 115 | |
---|
[599] | 116 | if (this->isRectilinear(name, path) || |
---|
| 117 | this->isCurvilinear(name, path)) |
---|
| 118 | { |
---|
| 119 | if (this->is3Dim(name, path)) return 8; |
---|
| 120 | else return 4; |
---|
| 121 | } |
---|
| 122 | if (this->isUnstructured(name, path)) |
---|
| 123 | { |
---|
| 124 | StdString bound = this->getBoundsId |
---|
| 125 | (this->getCoordinatesIdList(name, path).back(), path); |
---|
| 126 | StdString dim = this->getDimensionsList(&bound, path).back(); |
---|
[686] | 127 | return this->getDimensions(&bound, path)[dim]; |
---|
[599] | 128 | } |
---|
| 129 | return size_t(-1); |
---|
| 130 | } |
---|
[219] | 131 | |
---|
[599] | 132 | //--------------------------------------------------------------- |
---|
[219] | 133 | |
---|
[599] | 134 | std::list<StdString> CINetCDF4::getGroups(const CVarPath* const path) |
---|
| 135 | { |
---|
| 136 | int nbgroup = 0, *groupid = NULL; |
---|
| 137 | int grpid = this->getGroup(path); |
---|
| 138 | std::list<StdString> retvalue; |
---|
[219] | 139 | |
---|
[686] | 140 | CNetCdfInterface::inqGrpIds(grpid, nbgroup, NULL); |
---|
[599] | 141 | groupid = new int[nbgroup](); |
---|
[686] | 142 | CNetCdfInterface::inqGrpIds(grpid, nbgroup, groupid); |
---|
[219] | 143 | |
---|
[599] | 144 | for (int i = 0; i < nbgroup; i++) |
---|
| 145 | { |
---|
[686] | 146 | StdString fullGrpName; |
---|
| 147 | CNetCdfInterface::inqGrpFullName(groupid[i], fullGrpName); |
---|
| 148 | retvalue.push_back(fullGrpName); |
---|
[599] | 149 | } |
---|
[219] | 150 | |
---|
[599] | 151 | delete [] groupid; |
---|
| 152 | return retvalue; |
---|
| 153 | } |
---|
[219] | 154 | |
---|
[599] | 155 | std::list<StdString> CINetCDF4::getVariables(const CVarPath* const path) |
---|
| 156 | { |
---|
| 157 | int nbvar = 0, *varid = NULL; |
---|
| 158 | int grpid = this->getGroup(path); |
---|
| 159 | std::list<StdString> retvalue; |
---|
[219] | 160 | |
---|
[686] | 161 | CNetCdfInterface::inqVarIds(grpid, nbvar, NULL); |
---|
[599] | 162 | varid = new int[nbvar](); |
---|
[686] | 163 | CNetCdfInterface::inqVarIds(grpid, nbvar, varid); |
---|
[219] | 164 | |
---|
[599] | 165 | for (int i = 0; i < nbvar; i++) |
---|
| 166 | { |
---|
[686] | 167 | StdString varName; |
---|
| 168 | CNetCdfInterface::inqVarName(grpid, varid[i], varName); |
---|
| 169 | retvalue.push_back(varName); |
---|
[599] | 170 | } |
---|
| 171 | |
---|
| 172 | delete [] varid; |
---|
| 173 | return retvalue; |
---|
| 174 | } |
---|
| 175 | |
---|
| 176 | StdSize CINetCDF4::getNbOfTimestep(const CVarPath* const path) |
---|
| 177 | { |
---|
[686] | 178 | return this->getDimensions(NULL, path)[this->getUnlimitedDimensionName(path)]; |
---|
[599] | 179 | } |
---|
| 180 | |
---|
| 181 | std::set<StdString> CINetCDF4::getBoundVariables(const CVarPath* const path) |
---|
| 182 | { |
---|
| 183 | std::set<StdString> retvalue; |
---|
| 184 | std::list<StdString> variables = this->getVariables(path); |
---|
| 185 | std::list<StdString>::const_iterator it = variables.begin(), end = variables.end(); |
---|
| 186 | for (; it != end; it++) |
---|
| 187 | { |
---|
| 188 | const StdString& var = *it; |
---|
| 189 | if (this->hasBounds(var, path)) |
---|
| 190 | retvalue.insert(retvalue.end(), this->getBoundsId(var, path)); |
---|
| 191 | } |
---|
| 192 | return retvalue; |
---|
| 193 | } |
---|
| 194 | |
---|
| 195 | std::set<StdString> CINetCDF4::getCoordVariables(const CVarPath* const path) |
---|
| 196 | { |
---|
| 197 | std::set<StdString> retvalue; |
---|
| 198 | std::list<StdString> variables = this->getVariables(path); |
---|
| 199 | std::list<StdString>::const_iterator it = variables.begin(), end = variables.end(); |
---|
| 200 | for (; it != end; it++) |
---|
| 201 | { |
---|
| 202 | const StdString& var = *it; |
---|
| 203 | std::list<StdString> coords = this->getCoordinatesIdList(var, path); |
---|
| 204 | std::list<StdString>::const_iterator it = coords.begin(), end = coords.end(); |
---|
| 205 | for (; it != end; it++) |
---|
[219] | 206 | { |
---|
[599] | 207 | const StdString& coord = *it; |
---|
| 208 | if (this->hasVariable(coord, path)) |
---|
| 209 | retvalue.insert(retvalue.end(), coord); |
---|
[219] | 210 | } |
---|
[599] | 211 | } |
---|
| 212 | return retvalue; |
---|
| 213 | } |
---|
[219] | 214 | |
---|
[599] | 215 | std::list<StdString> CINetCDF4::getDimensionsList(const StdString* const var, const CVarPath* const path) |
---|
| 216 | { |
---|
| 217 | int nbdim = 0, *dimid = NULL; |
---|
| 218 | int grpid = this->getGroup(path); |
---|
[1447] | 219 | int varid = (var != NULL && this->hasVariable(*var, path)) ? this->getVariable(*var, path) : NC_GLOBAL; |
---|
[599] | 220 | std::list<StdString> retvalue; |
---|
[219] | 221 | |
---|
[1447] | 222 | if (var != NULL && this->hasVariable(*var, path)) |
---|
[599] | 223 | { |
---|
[686] | 224 | CNetCdfInterface::inqVarNDims(grpid, varid, nbdim); |
---|
[599] | 225 | dimid = new int[nbdim](); |
---|
[686] | 226 | CNetCdfInterface::inqVarDimId(grpid, varid, dimid); |
---|
[599] | 227 | } |
---|
| 228 | else |
---|
| 229 | { |
---|
[686] | 230 | CNetCdfInterface::inqDimIds(grpid, nbdim, NULL, 1); |
---|
[599] | 231 | dimid = new int[nbdim](); |
---|
[686] | 232 | CNetCdfInterface::inqDimIds(grpid, nbdim, dimid, 1); |
---|
[599] | 233 | } |
---|
[219] | 234 | |
---|
[599] | 235 | for (int i = 0; i < nbdim; i++) |
---|
| 236 | { |
---|
[686] | 237 | std::string dimname; |
---|
| 238 | CNetCdfInterface::inqDimName(grpid, dimid[i], dimname); |
---|
[599] | 239 | retvalue.push_back(dimname); |
---|
| 240 | } |
---|
| 241 | delete [] dimid; |
---|
[219] | 242 | |
---|
[599] | 243 | return retvalue; |
---|
| 244 | } |
---|
[219] | 245 | |
---|
[599] | 246 | std::map<StdString, StdSize> CINetCDF4::getDimensions(const StdString* const var, const CVarPath* const path) |
---|
| 247 | { |
---|
| 248 | int nbdim = 0, *dimid = NULL; |
---|
| 249 | int grpid = this->getGroup(path); |
---|
[1447] | 250 | int varid = (var != NULL && this->hasVariable(*var, path)) ? this->getVariable(*var, path) : NC_GLOBAL; |
---|
[599] | 251 | std::map<StdString, StdSize> retvalue; |
---|
[219] | 252 | |
---|
[1447] | 253 | if (var != NULL && this->hasVariable(*var, path)) |
---|
[599] | 254 | { |
---|
[686] | 255 | CNetCdfInterface::inqVarNDims(grpid, varid, nbdim); |
---|
[599] | 256 | dimid = new int[nbdim](); |
---|
[686] | 257 | CNetCdfInterface::inqVarDimId(grpid, varid, dimid); |
---|
[599] | 258 | } |
---|
| 259 | else |
---|
| 260 | { |
---|
[686] | 261 | CNetCdfInterface::inqDimIds(grpid, nbdim, NULL, 1); |
---|
[599] | 262 | dimid = new int[nbdim](); |
---|
[686] | 263 | CNetCdfInterface::inqDimIds(grpid, nbdim, dimid, 1); |
---|
[599] | 264 | } |
---|
[219] | 265 | |
---|
[599] | 266 | for (int i = 0; i < nbdim; i++) |
---|
| 267 | { |
---|
[686] | 268 | std::string dimname; |
---|
| 269 | CNetCdfInterface::inqDimName(grpid, dimid[i], dimname); |
---|
| 270 | StdSize size = 0; |
---|
| 271 | CNetCdfInterface::inqDimLen(grpid, dimid[i], size); |
---|
[219] | 272 | |
---|
[599] | 273 | retvalue.insert(retvalue.end(), std::make_pair(dimname, size)); |
---|
| 274 | } |
---|
| 275 | delete [] dimid; |
---|
[219] | 276 | |
---|
[599] | 277 | return retvalue; |
---|
| 278 | } |
---|
[219] | 279 | |
---|
[686] | 280 | std::list<StdString> CINetCDF4::getAttributes(const StdString* const var, const CVarPath* const path) |
---|
[599] | 281 | { |
---|
| 282 | int nbatt = 0; |
---|
| 283 | std::list<StdString> retvalue; |
---|
| 284 | int grpid = this->getGroup(path); |
---|
[1447] | 285 | int varid = (var != NULL && this->hasVariable(*var, path)) ? this->getVariable(*var, path) : NC_GLOBAL; |
---|
[219] | 286 | |
---|
[1447] | 287 | if (var != NULL && this->hasVariable(*var, path)) |
---|
[686] | 288 | CNetCdfInterface::inqVarNAtts(grpid, varid, nbatt); |
---|
[599] | 289 | else |
---|
[686] | 290 | CNetCdfInterface::inqNAtts(grpid, nbatt); |
---|
[219] | 291 | |
---|
[599] | 292 | for (int i = 0; i < nbatt; i++) |
---|
| 293 | { |
---|
[686] | 294 | StdString attname; |
---|
| 295 | CNetCdfInterface::inqAttName(grpid, varid, i, attname); |
---|
[599] | 296 | retvalue.push_back(attname); |
---|
| 297 | } |
---|
| 298 | return retvalue; |
---|
| 299 | } |
---|
[219] | 300 | |
---|
[599] | 301 | int CINetCDF4::getAttributeId(const StdString& name, |
---|
| 302 | const StdString* const var, |
---|
| 303 | const CVarPath* const path) |
---|
| 304 | { |
---|
| 305 | int retvalue = 0; |
---|
| 306 | std::list<StdString> atts = this->getAttributes(var, path); |
---|
| 307 | std::list<StdString>::const_iterator it = atts.begin(), end = atts.end(); |
---|
| 308 | for (; it != end; it++) |
---|
| 309 | { |
---|
| 310 | const StdString& attname = *it; |
---|
[782] | 311 | if (attname.compare(0, name.size(), name) == 0) |
---|
[599] | 312 | return retvalue; |
---|
| 313 | retvalue++; |
---|
| 314 | } |
---|
| 315 | return -1; |
---|
| 316 | } |
---|
[219] | 317 | |
---|
[599] | 318 | //--------------------------------------------------------------- |
---|
[219] | 319 | |
---|
[599] | 320 | bool CINetCDF4::hasMissingValue(const StdString& name, |
---|
| 321 | const CVarPath* const path) |
---|
| 322 | { |
---|
[686] | 323 | return (this->hasAttribute("missing_value", &name, path) || this->hasAttribute("_FillValue", &name, path)); |
---|
[599] | 324 | } |
---|
[219] | 325 | |
---|
[599] | 326 | bool CINetCDF4::hasAttribute(const StdString& name, |
---|
| 327 | const StdString* const var , |
---|
| 328 | const CVarPath* const path) |
---|
| 329 | { |
---|
| 330 | std::list<StdString> atts = this->getAttributes(var, path); |
---|
| 331 | std::list<StdString>::const_iterator it = atts.begin(), end = atts.end(); |
---|
| 332 | for (; it != end; it++) |
---|
| 333 | { |
---|
| 334 | const StdString& attname = *it; |
---|
[782] | 335 | if (attname.compare(0, name.size(), name) == 0) return true; |
---|
[599] | 336 | } |
---|
| 337 | return false; |
---|
| 338 | } |
---|
[219] | 339 | |
---|
[599] | 340 | bool CINetCDF4::hasVariable(const StdString& name, |
---|
| 341 | const CVarPath* const path) |
---|
| 342 | { |
---|
| 343 | std::list<StdString> variables = this->getVariables(path); |
---|
| 344 | std::list<StdString>::const_iterator it = variables.begin(), end = variables.end(); |
---|
| 345 | for (; it != end; it++) |
---|
| 346 | { |
---|
| 347 | const StdString& varname = *it; |
---|
[825] | 348 | if ((varname.compare(0, name.size(), name) == 0) && (0 != name.size())) return true; |
---|
[599] | 349 | } |
---|
| 350 | return false; |
---|
| 351 | } |
---|
[219] | 352 | |
---|
[599] | 353 | bool CINetCDF4::hasCoordinates(const StdString& name, |
---|
| 354 | const CVarPath* const path) |
---|
| 355 | { |
---|
[782] | 356 | return this->hasAttribute(CCFKeywords::XIOS_CF_coordinates, &name, path); |
---|
[599] | 357 | } |
---|
[219] | 358 | |
---|
[599] | 359 | bool CINetCDF4::hasBounds(const StdString& name, |
---|
| 360 | const CVarPath* const path) |
---|
| 361 | { |
---|
[782] | 362 | return this->hasAttribute(CCFKeywords::XIOS_CF_bounds, &name, path); |
---|
[599] | 363 | } |
---|
[219] | 364 | |
---|
[599] | 365 | bool CINetCDF4::hasTemporalDim(const CVarPath* const path) |
---|
| 366 | { |
---|
[802] | 367 | std::list<StdString> dims = this->getDimensionsList(NULL, path); |
---|
| 368 | return (std::find(dims.begin(), dims.end(), timeCounterName) != dims.end()); |
---|
[599] | 369 | } |
---|
[219] | 370 | |
---|
[599] | 371 | //--------------------------------------------------------------- |
---|
[219] | 372 | |
---|
[686] | 373 | template <class T> |
---|
| 374 | std::vector<T> CINetCDF4::getAttributeValue(const StdString& name, |
---|
| 375 | const StdString* const var, |
---|
| 376 | const CVarPath* const path) |
---|
| 377 | { |
---|
| 378 | int grpid = this->getGroup(path); |
---|
[1447] | 379 | int varid = (var != NULL && this->hasVariable(*var, path)) ? this->getVariable(*var, path) : NC_GLOBAL; |
---|
[686] | 380 | std::pair<nc_type , StdSize> attinfos = this->getAttribute(name, var, path); |
---|
| 381 | std::vector<T> retvalue(attinfos.second); |
---|
| 382 | nc_type type = CNetCdfInterface::getNcType<T>(); |
---|
| 383 | if (attinfos.first != type) |
---|
| 384 | ERROR("CINetCDF4::getAttributeValue<T>(name, var, path)", |
---|
| 385 | << "[ name : " << name |
---|
| 386 | << ", type requested :" << attinfos.first |
---|
| 387 | << ", type stored : " << type << "]" |
---|
| 388 | << " Invalid type !"); |
---|
| 389 | CNetCdfInterface::getAttType(grpid, varid, name.c_str(), &retvalue[0]); |
---|
| 390 | return retvalue; |
---|
[599] | 391 | } |
---|
[219] | 392 | |
---|
[686] | 393 | template std::vector<double> CINetCDF4::getAttributeValue(const StdString& name, |
---|
| 394 | const StdString* const var, |
---|
| 395 | const CVarPath* const path); |
---|
| 396 | template std::vector<float> CINetCDF4::getAttributeValue(const StdString& name, |
---|
| 397 | const StdString* const var, |
---|
| 398 | const CVarPath* const path); |
---|
| 399 | template std::vector<int> CINetCDF4::getAttributeValue(const StdString& name, |
---|
| 400 | const StdString* const var, |
---|
| 401 | const CVarPath* const path); |
---|
| 402 | template std::vector<char> CINetCDF4::getAttributeValue(const StdString& name, |
---|
| 403 | const StdString* const var, |
---|
| 404 | const CVarPath* const path); |
---|
[219] | 405 | |
---|
[599] | 406 | StdString CINetCDF4::getAttributeValue(const StdString& name, |
---|
| 407 | const StdString* const var, |
---|
| 408 | const CVarPath* const path) |
---|
| 409 | { |
---|
[686] | 410 | std::vector<char> data = this->getAttributeValue<char>(name, var, path); |
---|
[219] | 411 | |
---|
[686] | 412 | return StdString(data.begin(), data.end()); |
---|
[599] | 413 | } |
---|
[219] | 414 | |
---|
[686] | 415 | template <class T> |
---|
| 416 | T CINetCDF4::getMissingValue(const StdString& name, const CVarPath* const path) |
---|
[599] | 417 | { |
---|
| 418 | if (this->hasAttribute("missing_value", &name, path)) |
---|
[686] | 419 | return this->getAttributeValue<T>("missing_value", &name, path)[0]; |
---|
[599] | 420 | if (this->hasAttribute("_FillValue", &name, path)) |
---|
[686] | 421 | return this->getAttributeValue<T>("_FillValue", &name, path)[0]; |
---|
[599] | 422 | return 0; |
---|
| 423 | } |
---|
[219] | 424 | |
---|
[686] | 425 | template double CINetCDF4::getMissingValue(const StdString& name, const CVarPath* const path); |
---|
| 426 | template float CINetCDF4::getMissingValue(const StdString& name, const CVarPath* const path); |
---|
| 427 | template int CINetCDF4::getMissingValue(const StdString& name, const CVarPath* const path); |
---|
| 428 | template char CINetCDF4::getMissingValue(const StdString& name, const CVarPath* const path); |
---|
[219] | 429 | |
---|
[599] | 430 | //--------------------------------------------------------------- |
---|
[219] | 431 | |
---|
[599] | 432 | std::list<StdString> CINetCDF4::getCoordinatesIdList(const StdString& name, const CVarPath* const path) |
---|
| 433 | { |
---|
| 434 | std::list<StdString> retvalue; |
---|
| 435 | StdString value = this->getCoordinatesId(name, path); |
---|
[219] | 436 | |
---|
[599] | 437 | boost::split(retvalue, value, boost::is_any_of(" ")); |
---|
[219] | 438 | |
---|
[599] | 439 | std::list<StdString>::iterator it = retvalue.begin(), end = retvalue.end(); |
---|
| 440 | for (; it != end; it++) |
---|
| 441 | { |
---|
| 442 | StdString& coord = *it; |
---|
| 443 | coord.assign(coord.data()); |
---|
| 444 | } |
---|
| 445 | return retvalue; |
---|
| 446 | } |
---|
[219] | 447 | |
---|
[599] | 448 | StdString CINetCDF4::getCoordinatesId(const StdString& name, const CVarPath* const path) |
---|
| 449 | { |
---|
| 450 | StdString retvalue; |
---|
[782] | 451 | if (this->hasAttribute(CCFKeywords::XIOS_CF_coordinates, &name, path)) |
---|
[599] | 452 | { |
---|
[782] | 453 | return this->getAttributeValue(CCFKeywords::XIOS_CF_coordinates, &name, path); |
---|
[599] | 454 | } |
---|
| 455 | else |
---|
| 456 | { |
---|
| 457 | std::list<StdString> dims = this->getDimensionsList(&name, path); |
---|
| 458 | std::list<StdString>::const_iterator it = dims.begin(), end = dims.end(); |
---|
| 459 | for (; it != end; it++) |
---|
[219] | 460 | { |
---|
[599] | 461 | const StdString& value = *it; |
---|
| 462 | retvalue.append(value).push_back(' '); |
---|
[219] | 463 | } |
---|
[599] | 464 | retvalue.erase(retvalue.end() - 1) ; |
---|
| 465 | } |
---|
[219] | 466 | |
---|
[599] | 467 | return retvalue; |
---|
| 468 | } |
---|
| 469 | |
---|
| 470 | StdString CINetCDF4::getBoundsId(const StdString& name, |
---|
| 471 | const CVarPath* const path) |
---|
| 472 | { |
---|
| 473 | StdString retvalue; |
---|
[782] | 474 | if (this->hasAttribute(CCFKeywords::XIOS_CF_bounds, &name, path)) |
---|
| 475 | retvalue = this->getAttributeValue(CCFKeywords::XIOS_CF_bounds, &name, path); |
---|
[599] | 476 | return retvalue; |
---|
| 477 | } |
---|
| 478 | |
---|
| 479 | //--------------------------------------------------------------- |
---|
| 480 | |
---|
| 481 | bool CINetCDF4::isBound(const StdString& name, |
---|
| 482 | const CVarPath* const path) |
---|
| 483 | { |
---|
| 484 | std::set<StdString> bounds = this->getBoundVariables(path); |
---|
| 485 | return (bounds.find(name) != bounds.end()); |
---|
| 486 | } |
---|
| 487 | |
---|
| 488 | bool CINetCDF4::isCoordinate(const StdString& name, |
---|
| 489 | const CVarPath* const path) |
---|
| 490 | { |
---|
| 491 | std::set<StdString> coords = this->getCoordVariables(path); |
---|
| 492 | return (coords.find(name) != coords.end()); |
---|
| 493 | } |
---|
| 494 | |
---|
| 495 | bool CINetCDF4::isRectilinear(const StdString& name, const CVarPath* const path) |
---|
| 496 | { |
---|
[1447] | 497 | std::list<StdString> varCoords = this->getCoordinatesIdList(name, path); |
---|
| 498 | std::list<StdString> varDims = this->getDimensionsList(&name, path); |
---|
| 499 | std::list<StdString>::const_iterator it = varCoords.begin(), end = varCoords.end(); |
---|
| 500 | std::set<StdString> varDims1D; |
---|
[1432] | 501 | |
---|
[1447] | 502 | // Firstly, loop over coordinate list |
---|
[599] | 503 | for (; it != end; it++) |
---|
| 504 | { |
---|
| 505 | const StdString& coord = *it; |
---|
[1447] | 506 | if (this->hasVariable(coord, path) && !this->isTemporal(coord, path) ) |
---|
[219] | 507 | { |
---|
[1447] | 508 | std::map<StdString, StdSize> coordDims = this->getDimensions(&coord, path); |
---|
| 509 | for (std::map<StdString, StdSize>::const_iterator itTmp = coordDims.begin(); itTmp != coordDims.end(); itTmp++) |
---|
[1432] | 510 | { |
---|
[1447] | 511 | varDims.remove(itTmp->first); |
---|
| 512 | } |
---|
| 513 | if (this->isLonOrLat(coord, path) && coordDims.size() == 1) |
---|
| 514 | { |
---|
| 515 | varDims1D.insert(coordDims.begin()->first); |
---|
[1445] | 516 | continue; |
---|
[1432] | 517 | } |
---|
[219] | 518 | } |
---|
[599] | 519 | } |
---|
[1447] | 520 | // Secondly, loop over remaining dimensions |
---|
| 521 | for (it= varDims.begin(); it != varDims.end(); it++) |
---|
| 522 | { |
---|
| 523 | const StdString& coord = *it; |
---|
| 524 | std::map<StdString, StdSize> coordDims = this->getDimensions(&coord, path); |
---|
| 525 | if (this->hasVariable(coord, path) && !this->isTemporal(coord, path) ) |
---|
| 526 | { |
---|
| 527 | if (this->isLonOrLat(coord, path) && coordDims.size() == 1) |
---|
| 528 | { |
---|
| 529 | varDims1D.insert(coordDims.begin()->first); |
---|
| 530 | continue; |
---|
| 531 | } |
---|
| 532 | } |
---|
| 533 | } |
---|
| 534 | |
---|
| 535 | return (varDims1D.size() == 2); |
---|
[599] | 536 | } |
---|
[219] | 537 | |
---|
[599] | 538 | bool CINetCDF4::isCurvilinear(const StdString& name, const CVarPath* const path) |
---|
| 539 | { |
---|
| 540 | if (this->isRectilinear(name, path) || !this->hasCoordinates(name, path)) |
---|
| 541 | return false; |
---|
| 542 | |
---|
[782] | 543 | bool isCurVi = true; |
---|
| 544 | unsigned int nbLonLat = 0; |
---|
[599] | 545 | std::list<StdString> coords = this->getCoordinatesIdList(name, path); |
---|
| 546 | std::list<StdString>::const_iterator it = coords.begin(), end = coords.end(); |
---|
| 547 | for (; it != end; it++) |
---|
| 548 | { |
---|
| 549 | const StdString& coord = *it; |
---|
[1445] | 550 | if (this->hasVariable(coord, path) && !this->isTemporal(coord, path) && this->isLonOrLat(coord, path)) |
---|
[219] | 551 | { |
---|
[599] | 552 | std::map<StdString, StdSize> dimvar = this->getDimensions(&coord, path); |
---|
[782] | 553 | if (2 == dimvar.size()) ++nbLonLat; |
---|
[219] | 554 | } |
---|
[599] | 555 | } |
---|
[782] | 556 | if (2 != nbLonLat) isCurVi = false; |
---|
| 557 | |
---|
| 558 | return isCurVi; |
---|
[599] | 559 | } |
---|
[219] | 560 | |
---|
[599] | 561 | bool CINetCDF4::isUnstructured(const StdString& name, const CVarPath* const path) |
---|
| 562 | { |
---|
| 563 | if (this->isRectilinear(name, path) || |
---|
| 564 | this->isCurvilinear(name, path) || |
---|
| 565 | !this->hasCoordinates(name, path)) |
---|
| 566 | return false; |
---|
[948] | 567 | else return true ; |
---|
| 568 | |
---|
| 569 | // check this part above |
---|
[599] | 570 | StdString dimname = this->getDimensionsList(&name, path).back(); |
---|
[219] | 571 | |
---|
[599] | 572 | std::list<StdString> coords = this->getCoordinatesIdList(name, path); |
---|
| 573 | std::list<StdString>::const_iterator it = coords.begin(), end = coords.end(); |
---|
| 574 | for (; it != end; it++) |
---|
| 575 | { |
---|
| 576 | const StdString& coord = *it; |
---|
[1445] | 577 | if (this->hasVariable(coord, path) && !this->isTemporal(coord, path) && this->isLonOrLat(coord, path)) |
---|
[219] | 578 | { |
---|
[599] | 579 | std::map<StdString, StdSize> dimvar = this->getDimensions(&coord, path); |
---|
| 580 | if ((dimvar.size() == 1) && |
---|
| 581 | (dimvar.find(dimname) != dimvar.end())) |
---|
| 582 | continue; |
---|
| 583 | else |
---|
| 584 | return false; |
---|
| 585 | } |
---|
| 586 | } |
---|
[219] | 587 | |
---|
[599] | 588 | return true; |
---|
| 589 | } |
---|
[219] | 590 | |
---|
[599] | 591 | bool CINetCDF4::isUnknown(const StdString& name, const CVarPath* const path) |
---|
| 592 | { |
---|
| 593 | return !(this->isRectilinear(name, path) || this->isCurvilinear(name, path) || this->isUnstructured(name, path)); |
---|
| 594 | } |
---|
[219] | 595 | |
---|
[599] | 596 | bool CINetCDF4::isTemporal(const StdString& name, const CVarPath* const path) |
---|
| 597 | { |
---|
[802] | 598 | std::list<StdString> dims = this->getDimensionsList(&name, path); |
---|
| 599 | return (std::find(dims.begin(), dims.end(), timeCounterName) != dims.end()); |
---|
[599] | 600 | } |
---|
[219] | 601 | |
---|
[599] | 602 | bool CINetCDF4::is3Dim(const StdString& name, const CVarPath* const path) |
---|
| 603 | { |
---|
| 604 | int i = 0; |
---|
| 605 | std::list<StdString> coords = this->getCoordinatesIdList(name, path); |
---|
| 606 | std::list<StdString>::const_iterator it = coords.begin(), end = coords.end(); |
---|
| 607 | for (; it != end; it++) |
---|
| 608 | { |
---|
| 609 | const StdString& coord = *it; |
---|
| 610 | if (this->hasVariable(coord, path)) |
---|
[219] | 611 | { |
---|
[599] | 612 | if (this->isTemporal(coord, path)) |
---|
| 613 | continue; |
---|
| 614 | i++; |
---|
[219] | 615 | } |
---|
[599] | 616 | else |
---|
[219] | 617 | { |
---|
[782] | 618 | StdString unlimitedDimName = this->getUnlimitedDimensionName(); |
---|
| 619 | if (coord.compare(0, unlimitedDimName.size(), unlimitedDimName) == 0) |
---|
[599] | 620 | continue; |
---|
| 621 | i++; |
---|
[219] | 622 | } |
---|
[599] | 623 | } |
---|
| 624 | return (i == 3); |
---|
| 625 | } |
---|
[219] | 626 | |
---|
[599] | 627 | bool CINetCDF4::isCellGrid(const StdString& name, const CVarPath* const path) |
---|
| 628 | { |
---|
| 629 | if (this->isCoordinate(name, path)) |
---|
| 630 | { |
---|
[686] | 631 | return this->hasBounds(name, path); |
---|
[599] | 632 | } |
---|
| 633 | else |
---|
| 634 | { |
---|
| 635 | std::list<StdString> coords = this->getCoordinatesIdList(name, path); |
---|
| 636 | std::list<StdString>::const_iterator it = coords.begin(), end = coords.end(); |
---|
| 637 | for (; it != end; it++) |
---|
[219] | 638 | { |
---|
[599] | 639 | const StdString& coord = *it; |
---|
| 640 | if (this->hasVariable(coord, path)) |
---|
| 641 | { |
---|
| 642 | if (this->isTemporal(coord, path)) |
---|
| 643 | continue; |
---|
| 644 | if (this->isCellGrid(coord, path)) |
---|
| 645 | continue; |
---|
| 646 | return false; |
---|
| 647 | } |
---|
| 648 | else |
---|
| 649 | { |
---|
[782] | 650 | StdString unlimitedDimName = this->getUnlimitedDimensionName(); |
---|
| 651 | if (coord.compare(0, unlimitedDimName.size(), unlimitedDimName) == 0) |
---|
[599] | 652 | continue; |
---|
| 653 | return false; |
---|
| 654 | } |
---|
[219] | 655 | } |
---|
[599] | 656 | } |
---|
[219] | 657 | |
---|
[599] | 658 | return true; |
---|
| 659 | } |
---|
[219] | 660 | |
---|
[599] | 661 | //--------------------------------------------------------------- |
---|
[219] | 662 | |
---|
[599] | 663 | std::list<StdString> CINetCDF4::getDataVariables(bool _is3D, bool _isRecti, |
---|
| 664 | bool _isCurvi, bool _isUnstr, |
---|
| 665 | bool _isCellData, bool _isTemporal, |
---|
| 666 | const CVarPath* const path) |
---|
| 667 | { |
---|
| 668 | std::list<StdString> retvalue; |
---|
| 669 | std::list<StdString> allvars = this->getVariables(path); |
---|
| 670 | std::set<StdString> allcoords = this->getCoordVariables(path); |
---|
[219] | 671 | |
---|
[599] | 672 | std::list<StdString>::const_iterator it = allvars.begin(), end = allvars.end(); |
---|
| 673 | for (; it != end; it++) |
---|
| 674 | { |
---|
| 675 | const StdString& var = *it; |
---|
| 676 | if (this->isCoordinate(var, path)) continue; |
---|
[219] | 677 | |
---|
[599] | 678 | if (!_isRecti && this->isRectilinear(var, path)) continue; |
---|
| 679 | if (!_isCurvi && this->isCurvilinear(var, path)) continue; |
---|
| 680 | if (!_isUnstr && this->isUnstructured(var, path)) continue; |
---|
[219] | 681 | |
---|
[599] | 682 | if (!_isTemporal && this->isTemporal(var, path)) continue; |
---|
| 683 | if (!_is3D && this->is3Dim(var, path)) continue; |
---|
| 684 | if (!_isCellData && this->isCellGrid(var, path)) continue; |
---|
[219] | 685 | |
---|
[599] | 686 | if (this->isUnknown(var, path)) continue; |
---|
[219] | 687 | |
---|
[599] | 688 | retvalue.push_back(var); |
---|
| 689 | } |
---|
| 690 | return retvalue; |
---|
| 691 | } |
---|
[219] | 692 | |
---|
[599] | 693 | //--------------------------------------------------------------- |
---|
[219] | 694 | |
---|
[599] | 695 | void CINetCDF4::getDataInfo(const StdString& var, const CVarPath* const path, StdSize record, |
---|
| 696 | std::vector<StdSize>& sstart, std::vector<StdSize>& scount, StdSize& array_size, |
---|
| 697 | const std::vector<StdSize>* start /*= NULL*/, const std::vector<StdSize>* count /*= NULL*/) |
---|
| 698 | { |
---|
| 699 | std::list<StdString> dimlist = this->getDimensionsList(&var, path); |
---|
| 700 | std::map<StdString, StdSize> dimmap = this->getDimensions(&var, path); |
---|
| 701 | std::list<StdString>::iterator it = dimlist.begin(); |
---|
| 702 | if (this->isTemporal(var, path)) |
---|
| 703 | { |
---|
| 704 | if (record != UNLIMITED_DIM) |
---|
| 705 | sstart.push_back(record); |
---|
| 706 | else |
---|
| 707 | sstart.push_back(0); |
---|
| 708 | scount.push_back(1); |
---|
| 709 | it++; |
---|
| 710 | } |
---|
| 711 | for (int i = 0; it != dimlist.end(); it++, i++) |
---|
| 712 | { |
---|
| 713 | if (start && count) |
---|
[219] | 714 | { |
---|
[599] | 715 | sstart.push_back((*start)[i]); |
---|
| 716 | scount.push_back((*count)[i]); |
---|
| 717 | array_size *= (*count)[i]; |
---|
[219] | 718 | } |
---|
[599] | 719 | else |
---|
[219] | 720 | { |
---|
[599] | 721 | sstart.push_back(0); |
---|
| 722 | scount.push_back(dimmap[*it]); |
---|
| 723 | array_size *= dimmap[*it]; |
---|
[219] | 724 | } |
---|
[599] | 725 | } |
---|
| 726 | } |
---|
[219] | 727 | |
---|
[686] | 728 | template <class T> |
---|
| 729 | void CINetCDF4::getData(CArray<T, 1>& data, const StdString& var, |
---|
[599] | 730 | const CVarPath* const path, StdSize record) |
---|
| 731 | { |
---|
| 732 | std::vector<StdSize> start, count; |
---|
| 733 | int grpid = this->getGroup(path); |
---|
| 734 | int varid = this->getVariable(var, path); |
---|
| 735 | StdSize array_size = 1; |
---|
| 736 | this->getDataInfo(var, path, record, start, count, array_size); |
---|
| 737 | data.resize(array_size); |
---|
[686] | 738 | CNetCdfInterface::getVaraType(grpid, varid, &start[0], &count[0], data.dataFirst()); |
---|
[599] | 739 | } |
---|
[219] | 740 | |
---|
[599] | 741 | template <> |
---|
[686] | 742 | void CINetCDF4::getData(CArray<int, 1>& data, const StdString& var, |
---|
| 743 | const CVarPath* const path, StdSize record); |
---|
| 744 | template <> |
---|
[599] | 745 | void CINetCDF4::getData(CArray<double, 1>& data, const StdString& var, |
---|
[686] | 746 | const CVarPath* const path, StdSize record); |
---|
[599] | 747 | template <> |
---|
| 748 | void CINetCDF4::getData(CArray<float, 1>& data, const StdString& var, |
---|
[686] | 749 | const CVarPath* const path, StdSize record); |
---|
[219] | 750 | |
---|
[599] | 751 | //--------------------------------------------------------------- |
---|
| 752 | |
---|
| 753 | StdString CINetCDF4::getLonCoordName(const StdString& varname, |
---|
| 754 | const CVarPath* const path) |
---|
| 755 | { |
---|
[825] | 756 | StdString lonName; |
---|
[782] | 757 | std::list<StdString>::const_iterator itbList, itList, iteList; |
---|
[599] | 758 | std::list<StdString> clist = this->getCoordinatesIdList(varname, path); |
---|
[782] | 759 | itbList = clist.begin(); iteList = clist.end(); |
---|
| 760 | for (itList = itbList; itList != iteList; ++itList) |
---|
| 761 | { |
---|
| 762 | if (this->hasAttribute(CCFKeywords::XIOS_CF_units, &(*itList), path)) |
---|
| 763 | { |
---|
| 764 | StdString unit = this->getAttributeValue(CCFKeywords::XIOS_CF_units, &(*itList), path); |
---|
| 765 | if (CCFConvention::XIOS_CF_Longitude_units.end() != CCFConvention::XIOS_CF_Longitude_units.find(unit)) |
---|
[825] | 766 | { |
---|
| 767 | lonName = *itList; |
---|
| 768 | return lonName; |
---|
| 769 | } |
---|
[782] | 770 | } |
---|
| 771 | } |
---|
[825] | 772 | return lonName; |
---|
[599] | 773 | } |
---|
| 774 | |
---|
| 775 | StdString CINetCDF4::getLatCoordName(const StdString& varname, |
---|
| 776 | const CVarPath* const path) |
---|
| 777 | { |
---|
[825] | 778 | StdString latName; |
---|
[782] | 779 | std::list<StdString>::const_iterator itbList, itList, iteList; |
---|
[599] | 780 | std::list<StdString> clist = this->getCoordinatesIdList(varname, path); |
---|
[782] | 781 | itbList = clist.begin(); iteList = clist.end(); |
---|
| 782 | for (itList = itbList; itList != iteList; ++itList) |
---|
| 783 | { |
---|
| 784 | if (this->hasAttribute(CCFKeywords::XIOS_CF_units, &(*itList), path)) |
---|
| 785 | { |
---|
| 786 | StdString unit = this->getAttributeValue(CCFKeywords::XIOS_CF_units, &(*itList), path); |
---|
| 787 | if (CCFConvention::XIOS_CF_Latitude_units.end() != CCFConvention::XIOS_CF_Latitude_units.find(unit)) |
---|
[825] | 788 | { |
---|
| 789 | latName = *itList; |
---|
| 790 | return latName; |
---|
| 791 | } |
---|
[782] | 792 | } |
---|
| 793 | } |
---|
[825] | 794 | return latName; |
---|
[599] | 795 | } |
---|
| 796 | |
---|
| 797 | StdString CINetCDF4::getVertCoordName(const StdString& varname, |
---|
| 798 | const CVarPath* const path) |
---|
| 799 | { |
---|
| 800 | if (!this->is3Dim(varname, path)) return ""; |
---|
| 801 | std::list<StdString> clist = this->getCoordinatesIdList(varname, path); |
---|
| 802 | if (this->hasCoordinates(varname, path)) |
---|
[686] | 803 | return *(++(++clist.begin())); |
---|
[599] | 804 | else |
---|
[686] | 805 | return *(++(++clist.rbegin())); |
---|
[599] | 806 | } |
---|
[1445] | 807 | |
---|
| 808 | bool CINetCDF4::isLonOrLat(const StdString& varname, const CVarPath* const path) |
---|
| 809 | { |
---|
[1534] | 810 | if (this->hasAttribute(CCFKeywords::XIOS_CF_units, &varname, path)) |
---|
| 811 | { |
---|
| 812 | StdString unit = this->getAttributeValue(CCFKeywords::XIOS_CF_units, &varname, path); |
---|
| 813 | return (CCFConvention::XIOS_CF_Latitude_units.end() != CCFConvention::XIOS_CF_Latitude_units.find(unit) |
---|
| 814 | || CCFConvention::XIOS_CF_Longitude_units.end() != CCFConvention::XIOS_CF_Longitude_units.find(unit)); |
---|
[1445] | 815 | } |
---|
[1534] | 816 | else return false ; |
---|
[1445] | 817 | } |
---|
| 818 | |
---|
[335] | 819 | } // namespace xios |
---|