1 | /* ************************************************************************** * |
---|
2 | * Copyright © IPSL/LSCE, XMLIOServer, Avril 2010 - Octobre 2011 * |
---|
3 | * ************************************************************************** */ |
---|
4 | |
---|
5 | /** |
---|
6 | * \file inetcdf4.hpp |
---|
7 | * \brief Lecture des fichiers de données au format netCDF-4 (implémentation). |
---|
8 | * \author Hervé Ozdoba |
---|
9 | * \version 0.4 |
---|
10 | * \date 15 Juin 2011 |
---|
11 | */ |
---|
12 | |
---|
13 | // XMLIOServer headers |
---|
14 | #include "inetcdf4.hpp" |
---|
15 | #include "inetcdf4_impl.hpp" |
---|
16 | |
---|
17 | // /////////////////////////////// Définitions ////////////////////////////// // |
---|
18 | |
---|
19 | namespace xmlioserver { |
---|
20 | namespace io { |
---|
21 | |
---|
22 | CINetCDF4::CINetCDF4(const std::string & filename) |
---|
23 | { |
---|
24 | CheckError(nc_open(filename.c_str(), NC_NOWRITE, &this->ncidp)); |
---|
25 | } |
---|
26 | |
---|
27 | CINetCDF4::~CINetCDF4(void) |
---|
28 | { |
---|
29 | CheckError(nc_close(this->ncidp)); |
---|
30 | } |
---|
31 | |
---|
32 | void CINetCDF4::CheckError(int _status) throw (CException) |
---|
33 | { |
---|
34 | if (_status != NC_NOERR) |
---|
35 | { |
---|
36 | std::string errormsg (nc_strerror(_status)); // fuite mémoire ici ? |
---|
37 | XIOS_ERROR("CONetCDF4::CheckError(int status)", |
---|
38 | << "[ status = " << _status << " ] " << errormsg); |
---|
39 | } |
---|
40 | } |
---|
41 | |
---|
42 | int CINetCDF4::getCurrentGroup(void) |
---|
43 | { |
---|
44 | return (this->getGroup(this->getCurrentPath())); |
---|
45 | } |
---|
46 | |
---|
47 | int CINetCDF4::getGroup(const CNetCDF4Path & path) |
---|
48 | { |
---|
49 | int retvalue = this->ncidp; |
---|
50 | |
---|
51 | CNetCDF4Path::const_iterator |
---|
52 | it = path.begin(), end = path.end(); |
---|
53 | |
---|
54 | for (;it != end; it++) |
---|
55 | { |
---|
56 | const std::string & groupid = *it; |
---|
57 | CheckError(nc_inq_ncid(retvalue, const_cast<char*>(groupid.c_str()), &retvalue)); |
---|
58 | } |
---|
59 | return (retvalue); |
---|
60 | } |
---|
61 | |
---|
62 | int CINetCDF4::getVariable(const std::string & varname) |
---|
63 | { |
---|
64 | int varid = 0; |
---|
65 | int grpid = this->getCurrentGroup(); |
---|
66 | CheckError(nc_inq_varid (grpid, varname.c_str(), &varid)); |
---|
67 | return (varid); |
---|
68 | } |
---|
69 | |
---|
70 | int CINetCDF4::getDimension(const std::string & dimname) |
---|
71 | { |
---|
72 | int dimid = 0; |
---|
73 | int grpid = this->getCurrentGroup(); |
---|
74 | CheckError(nc_inq_dimid (grpid, dimname.c_str(), &dimid)); |
---|
75 | return (dimid); |
---|
76 | } |
---|
77 | |
---|
78 | int CINetCDF4::getUnlimitedDimension(void) |
---|
79 | { |
---|
80 | int dimid = 0; |
---|
81 | int grpid = this->getCurrentGroup(); |
---|
82 | CheckError(nc_inq_unlimdim (grpid, &dimid)); |
---|
83 | return (dimid); |
---|
84 | } |
---|
85 | |
---|
86 | std::vector<std::size_t> CINetCDF4::getDimensions(const std::string & varname) |
---|
87 | { |
---|
88 | std::size_t size = 0; |
---|
89 | std::vector<std::size_t> retvalue; |
---|
90 | int grpid = this->getCurrentGroup(); |
---|
91 | int varid = this->getVariable(varname); |
---|
92 | int nbdim = 0, *dimid = NULL; |
---|
93 | |
---|
94 | CheckError(nc_inq_varndims(grpid, varid, &nbdim)); |
---|
95 | dimid = new int[nbdim](); |
---|
96 | CheckError(nc_inq_vardimid(grpid, varid, dimid)); |
---|
97 | |
---|
98 | for (int i = 0; i < nbdim; i++) |
---|
99 | { |
---|
100 | CheckError(nc_inq_dimlen (grpid, dimid[i], &size)); |
---|
101 | if (size == NC_UNLIMITED) |
---|
102 | size = UNLIMITED_DIM; |
---|
103 | retvalue.push_back(size); |
---|
104 | } |
---|
105 | |
---|
106 | return (retvalue); |
---|
107 | } |
---|
108 | |
---|
109 | const CINetCDF4::CNetCDF4Path & CINetCDF4::getCurrentPath(void) const |
---|
110 | { |
---|
111 | return (this->path); |
---|
112 | } |
---|
113 | |
---|
114 | void CINetCDF4::setCurrentPath(const CNetCDF4Path & path) |
---|
115 | { |
---|
116 | this->path = path; |
---|
117 | } |
---|
118 | |
---|
119 | void CINetCDF4::getReadDataInfos(const std::string & _varname, |
---|
120 | std::size_t _record, |
---|
121 | std::size_t & _array_size, |
---|
122 | std::vector<std::size_t> & _sstart, |
---|
123 | std::vector<std::size_t> & _scount, |
---|
124 | const std::vector<std::size_t> * _start, |
---|
125 | const std::vector<std::size_t> * _count) |
---|
126 | { |
---|
127 | std::vector<std::size_t> sizes = this->getDimensions(_varname); |
---|
128 | std::vector<std::string> iddims = this->getDimensionsIdList (&_varname); |
---|
129 | std::vector<std::size_t>::const_iterator |
---|
130 | it = sizes.begin(), end = sizes.end(); |
---|
131 | int i = 0; |
---|
132 | |
---|
133 | if (iddims.begin()->compare(this->getUnlimitedDimensionName()) == 0) |
---|
134 | { |
---|
135 | _sstart.push_back(_record); |
---|
136 | _scount.push_back(1); |
---|
137 | if ((_start == NULL) && |
---|
138 | (_count == NULL)) i++; |
---|
139 | it++; |
---|
140 | } |
---|
141 | |
---|
142 | for (;it != end; it++) |
---|
143 | { |
---|
144 | if ((_start != NULL) && (_count != NULL)) |
---|
145 | { |
---|
146 | _sstart.push_back((*_start)[i]); |
---|
147 | _scount.push_back((*_count)[i]); |
---|
148 | _array_size *= (*_count)[i]; |
---|
149 | i++; |
---|
150 | } |
---|
151 | else |
---|
152 | { |
---|
153 | _sstart.push_back(0); |
---|
154 | _scount.push_back(sizes[i]); |
---|
155 | _array_size *= sizes[i]; |
---|
156 | i++; |
---|
157 | } |
---|
158 | } |
---|
159 | } |
---|
160 | |
---|
161 | void CINetCDF4::readAttribute |
---|
162 | (const std::string & _attname, std::string & _value, const std::string * _varname) |
---|
163 | { |
---|
164 | std::vector<char> chart; |
---|
165 | this->readAttribute(_attname,chart , _varname); |
---|
166 | _value.assign(&(chart[0]), chart.size()); |
---|
167 | } |
---|
168 | |
---|
169 | std::vector<std::string> CINetCDF4::getAttributes(const std::string * const _varname) |
---|
170 | { |
---|
171 | int nbatt = 0; |
---|
172 | char full_name_in[NC_MAX_NAME +1]; |
---|
173 | std::vector<std::string> retvalue; |
---|
174 | int grpid = this->getCurrentGroup(); |
---|
175 | int varid = (_varname != NULL) ? this->getVariable(*_varname) : NC_GLOBAL; |
---|
176 | |
---|
177 | if (_varname != NULL) |
---|
178 | CheckError(nc_inq_varnatts (grpid, varid, &nbatt)); |
---|
179 | else |
---|
180 | CheckError(nc_inq_natts(grpid, &nbatt)); |
---|
181 | |
---|
182 | for (int i = 0; i < nbatt; i++) |
---|
183 | { |
---|
184 | CheckError(nc_inq_attname(grpid, varid, i, full_name_in)); |
---|
185 | std::string attname(full_name_in); |
---|
186 | retvalue.push_back(attname); |
---|
187 | } |
---|
188 | return (retvalue); |
---|
189 | } |
---|
190 | |
---|
191 | |
---|
192 | std::map<std::string, std::size_t> CINetCDF4::getDimensions(const std::string * const _varname) |
---|
193 | { |
---|
194 | std::size_t size = 0; |
---|
195 | char full_name_in[NC_MAX_NAME +1]; |
---|
196 | int nbdim = 0, *dimid = NULL; |
---|
197 | int grpid = this->getCurrentGroup(); |
---|
198 | int varid = (_varname != NULL) ? this->getVariable(*_varname) : NC_GLOBAL; |
---|
199 | std::map<std::string, std::size_t> retvalue; |
---|
200 | |
---|
201 | if (_varname != NULL) |
---|
202 | { |
---|
203 | CheckError(nc_inq_varndims(grpid, varid, &nbdim)); |
---|
204 | dimid = new int[nbdim](); |
---|
205 | CheckError(nc_inq_vardimid(grpid, varid, dimid)); |
---|
206 | } |
---|
207 | else |
---|
208 | { |
---|
209 | CheckError(nc_inq_dimids(grpid, &nbdim, NULL, 1)); |
---|
210 | dimid = new int[nbdim](); |
---|
211 | CheckError(nc_inq_dimids(grpid, NULL, dimid, 1)); |
---|
212 | } |
---|
213 | |
---|
214 | for (int i = 0; i < nbdim; i++) |
---|
215 | { |
---|
216 | CheckError(nc_inq_dimname(grpid, dimid[i], full_name_in)); |
---|
217 | CheckError(nc_inq_dimlen (grpid, dimid[i], &size)); |
---|
218 | |
---|
219 | std::string dimname(full_name_in); |
---|
220 | retvalue.insert(retvalue.end(), std::make_pair(dimname, size)); |
---|
221 | } |
---|
222 | delete [] dimid; |
---|
223 | |
---|
224 | return (retvalue); |
---|
225 | } |
---|
226 | |
---|
227 | std::vector<std::string> CINetCDF4::getGroups(void) |
---|
228 | { |
---|
229 | std::size_t strlen = 0; |
---|
230 | char full_name_in[NC_MAX_NAME +1]; |
---|
231 | int nbgroup = 0, *groupid = NULL; |
---|
232 | int grpid = this->getCurrentGroup(); |
---|
233 | std::vector<std::string> retvalue; |
---|
234 | |
---|
235 | CheckError(nc_inq_grps(grpid, &nbgroup, NULL)); |
---|
236 | groupid = new int[nbgroup](); |
---|
237 | CheckError(nc_inq_grps(grpid, NULL, groupid)); |
---|
238 | |
---|
239 | for (int i = 0; i < nbgroup; i++) |
---|
240 | { |
---|
241 | CheckError(nc_inq_grpname_full(groupid[i], &strlen, full_name_in)); |
---|
242 | std::string groupname(full_name_in, strlen); |
---|
243 | retvalue.push_back(groupname); |
---|
244 | } |
---|
245 | |
---|
246 | delete [] groupid; |
---|
247 | return (retvalue); |
---|
248 | } |
---|
249 | |
---|
250 | std::vector<std::string> CINetCDF4::getVariables(void) |
---|
251 | { |
---|
252 | char full_name_in[NC_MAX_NAME +1]; |
---|
253 | int nbvar = 0, *varid = NULL; |
---|
254 | int grpid = this->getCurrentGroup(); |
---|
255 | std::vector<std::string> retvalue; |
---|
256 | |
---|
257 | CheckError(nc_inq_varids(grpid, &nbvar, NULL)); |
---|
258 | varid = new int[nbvar](); |
---|
259 | CheckError(nc_inq_varids(grpid, NULL, varid)); |
---|
260 | |
---|
261 | for (int i = 0; i < nbvar; i++) |
---|
262 | { |
---|
263 | CheckError(nc_inq_varname(grpid, varid[i], full_name_in)); |
---|
264 | std::string varname(full_name_in); |
---|
265 | retvalue.push_back(varname); |
---|
266 | } |
---|
267 | |
---|
268 | delete [] varid; |
---|
269 | return (retvalue); |
---|
270 | } |
---|
271 | |
---|
272 | std::size_t CINetCDF4::getNbOfTimestep(void) |
---|
273 | { |
---|
274 | int dimid = this->getUnlimitedDimension(); |
---|
275 | if (dimid == -1) return (1); |
---|
276 | return (this->getDimensions(NULL)[this->getUnlimitedDimensionName()]); |
---|
277 | } |
---|
278 | |
---|
279 | std::string CINetCDF4::getUnlimitedDimensionName(void) |
---|
280 | { |
---|
281 | char full_name_in[NC_MAX_NAME +1]; |
---|
282 | int grpid = this->getGroup(path); |
---|
283 | int dimid = this->getUnlimitedDimension(); |
---|
284 | |
---|
285 | if (dimid == -1) return (std::string()); |
---|
286 | CheckError(nc_inq_dimname(grpid, dimid, full_name_in)); |
---|
287 | |
---|
288 | std::string dimname(full_name_in); |
---|
289 | return (dimname); |
---|
290 | } |
---|
291 | |
---|
292 | std::vector<std::string> CINetCDF4::getDimensionsIdList (const std::string * _varname) |
---|
293 | { |
---|
294 | char full_name_in[NC_MAX_NAME +1]; |
---|
295 | int nbdim = 0, *dimid = NULL; |
---|
296 | int grpid = this->getCurrentGroup(); |
---|
297 | int varid = (_varname != NULL) ? this->getVariable(*_varname) : NC_GLOBAL; |
---|
298 | std::vector<std::string> retvalue; |
---|
299 | |
---|
300 | if (_varname != NULL) |
---|
301 | { |
---|
302 | CheckError(nc_inq_varndims(grpid, varid, &nbdim)); |
---|
303 | dimid = new int[nbdim](); |
---|
304 | CheckError(nc_inq_vardimid(grpid, varid, dimid)); |
---|
305 | } |
---|
306 | else |
---|
307 | { |
---|
308 | CheckError(nc_inq_dimids(grpid, &nbdim, NULL, 1)); |
---|
309 | dimid = new int[nbdim](); |
---|
310 | CheckError(nc_inq_dimids(grpid, NULL, dimid, 1)); |
---|
311 | } |
---|
312 | |
---|
313 | for (int i = 0; i < nbdim; i++) |
---|
314 | { |
---|
315 | CheckError(nc_inq_dimname(grpid, dimid[i], full_name_in)); |
---|
316 | std::string dimname(full_name_in); |
---|
317 | retvalue.push_back(dimname); |
---|
318 | } |
---|
319 | delete [] dimid; |
---|
320 | |
---|
321 | return (retvalue); |
---|
322 | } |
---|
323 | |
---|
324 | template <> |
---|
325 | void CINetCDF4::readData_(int _grpid, int _varid, |
---|
326 | const std::vector<std::size_t> & _sstart, |
---|
327 | const std::vector<std::size_t> & _scount, |
---|
328 | float * _data) |
---|
329 | { |
---|
330 | CheckError(nc_get_vara_float(_grpid, _varid, &(_sstart[0]), &(_scount[0]), _data)); |
---|
331 | } |
---|
332 | |
---|
333 | template <> |
---|
334 | void CINetCDF4::readData_(int _grpid, int _varid, |
---|
335 | const std::vector<std::size_t> & _sstart, |
---|
336 | const std::vector<std::size_t> & _scount, |
---|
337 | int * _data) |
---|
338 | { |
---|
339 | CheckError(nc_get_vara_int(_grpid, _varid, &(_sstart[0]), &(_scount[0]), _data)); |
---|
340 | } |
---|
341 | |
---|
342 | template <> |
---|
343 | void CINetCDF4::readData_(int _grpid, int _varid, |
---|
344 | const std::vector<std::size_t> & _sstart, |
---|
345 | const std::vector<std::size_t> & _scount, |
---|
346 | double * _data) |
---|
347 | { |
---|
348 | CheckError(nc_get_vara_double(_grpid, _varid, &(_sstart[0]), &(_scount[0]), _data)); |
---|
349 | } |
---|
350 | |
---|
351 | template <> |
---|
352 | void CINetCDF4::readAttribute_ |
---|
353 | (const std::string & _attname, double * _value, int _grpid, int _varid) |
---|
354 | { |
---|
355 | CheckError(nc_get_att_double(_grpid, _varid, _attname.c_str(), _value)); |
---|
356 | } |
---|
357 | |
---|
358 | template <> |
---|
359 | void CINetCDF4::readAttribute_ |
---|
360 | (const std::string & _attname, float * _value, int _grpid, int _varid) |
---|
361 | { |
---|
362 | CheckError(nc_get_att_float(_grpid, _varid, _attname.c_str(), _value)); |
---|
363 | } |
---|
364 | |
---|
365 | template <> |
---|
366 | void CINetCDF4::readAttribute_ |
---|
367 | (const std::string & _attname, int * _value, int _grpid, int _varid) |
---|
368 | { |
---|
369 | CheckError(nc_get_att_int(_grpid, _varid, _attname.c_str(), _value)); |
---|
370 | } |
---|
371 | |
---|
372 | template <> |
---|
373 | void CINetCDF4::readAttribute_ |
---|
374 | (const std::string & _attname, char * _value, int _grpid, int _varid) |
---|
375 | { |
---|
376 | CheckError(nc_get_att_text(_grpid, _varid, _attname.c_str(), _value)); |
---|
377 | } |
---|
378 | |
---|
379 | bool CINetCDF4::varExist(const std::string & _varname) |
---|
380 | { |
---|
381 | int varid = 0; |
---|
382 | int grpid = this->getCurrentGroup(); |
---|
383 | return (nc_inq_varid (grpid, _varname.c_str(), &varid) == NC_NOERR); |
---|
384 | } |
---|
385 | |
---|
386 | } // namespace io |
---|
387 | } // namespace xmlioserver |
---|