Context Navigation

source: XIOS2/trunk/src/io/nc4_data_output.cpp @ 2434

Last change on this file since 2434 was 2434, checked in by ymipsl, 19 months ago
Fix incorrect CF attribute : formula_term -> formula_terms in nectdf file. Note that the XIOS attribute formula_term remain unchanged for retro-compatibility YM
Property copyright set to Software name : XIOS (Xml I/O Server) http://forge.ipsl.jussieu.fr/ioserver Creation date : January 2009 Licence : CeCCIL version2 see license file in root directory : Licence_CeCILL_V2-en.txt or http://www.cecill.info/licences/Licence_CeCILL_V2-en.html Holder : CEA/LSCE (Laboratoire des Sciences du CLimat et de l'Environnement) CNRS/IPSL (Institut Pierre Simon Laplace) Project Manager : Yann Meurdesoif yann.meurdesoif@cea.fr Property svn:executable set to ``*
File size: 132.7 KB

Line
1	#include "nc4_data_output.hpp"
2
3	#include "attribute_template.hpp"
4	#include "group_template.hpp"
5
6	#include "file.hpp"
7	#include "calendar.hpp"
8	#include "context.hpp"
9	#include "context_server.hpp"
10	#include "netCdfException.hpp"
11	#include "exception.hpp"
12	#include "timer.hpp"
13	#include "uuid.hpp"
14	namespace xios
15	{
16	/// ////////////////////// Dfinitions ////////////////////// ///
17	CNc4DataOutput::CNc4DataOutput
18	(CFile* file, const StdString & filename, bool exist)
19	: SuperClass()
20	, SuperClassWriter(filename, exist)
21	, filename(filename)
22	, file(file),hasTimeInstant(false),hasTimeCentered(false), timeCounterType(none)
23	{
24	SuperClass::type = MULTI_FILE;
25	compressionLevel= file->compression_level.isEmpty() ? 0 :file->compression_level ;
26	}
27
28	CNc4DataOutput::CNc4DataOutput
29	(CFile* file, const StdString & filename, bool exist, bool useClassicFormat, bool useCFConvention,
30	MPI_Comm comm_file, bool multifile, bool isCollective, const StdString& timeCounterName)
31	: SuperClass()
32	, SuperClassWriter(filename, exist, useClassicFormat, useCFConvention, &comm_file, multifile, timeCounterName)
33	, comm_file(comm_file)
34	, filename(filename)
35	, isCollective(isCollective)
36	, file(file),hasTimeInstant(false),hasTimeCentered(false), timeCounterType(none)
37	{
38	SuperClass::type = (multifile) ? MULTI_FILE : ONE_FILE;
39	if (file==NULL) compressionLevel = 0 ;
40	else compressionLevel= file->compression_level.isEmpty() ? 0 :file->compression_level ;
41	}
42
43	CNc4DataOutput::~CNc4DataOutput(void)
44	{ /* Ne rien faire de plus */ }
45
46	///--------------------------------------------------------------
47
48	const StdString & CNc4DataOutput::getFileName(void) const
49	{
50	return (this->filename);
51	}
52
53	//---------------------------------------------------------------
54
55	void CNc4DataOutput::writeDomain_(CDomain* domain)
56	TRY
57	{
58	StdString lonName,latName ;
59
60	domain->computeWrittenIndex();
61	domain->computeWrittenCompressedIndex(comm_file);
62
63	if (domain->type == CDomain::type_attr::unstructured)
64	{
65	if (SuperClassWriter::useCFConvention)
66	writeUnstructuredDomain(domain) ;
67	else
68	writeUnstructuredDomainUgrid(domain) ;
69	return ;
70	}
71
72	CContext* context = CContext::getCurrent() ;
73	CContextServer* server=context->server ;
74
75	if (domain->IsWritten(this->filename)) return;
76	domain->checkAttributes();
77
78	if (domain->isEmpty())
79	if (SuperClass::type==MULTI_FILE) return;
80
81	std::vector<StdString> dim0, dim1;
82	StdString domid = domain->getDomainOutputName();
83	StdString appendDomid = (singleDomain) ? "" : "_"+domid ;
84	if (isWrittenDomain(domid)) return ;
85	else setWrittenDomain(domid);
86
87	int nvertex = (domain->nvertex.isEmpty()) ? 0 : domain->nvertex;
88
89
90	StdString dimXid, dimYid ;
91
92	nc_type typePrec ;
93	if (domain->prec.isEmpty()) typePrec = NC_FLOAT ;
94	else if (domain->prec==4) typePrec = NC_FLOAT ;
95	else if (domain->prec==8) typePrec = NC_DOUBLE ;
96
97	bool isRegularDomain = (domain->type == CDomain::type_attr::rectilinear);
98	switch (domain->type)
99	{
100	case CDomain::type_attr::curvilinear :
101
102	if (domain->lon_name.isEmpty()) lonName = "nav_lon";
103	else lonName = domain->lon_name;
104
105	if (domain->lat_name.isEmpty()) latName = "nav_lat";
106	else latName = domain->lat_name;
107
108	if (domain->dim_i_name.isEmpty()) dimXid=StdString("x").append(appendDomid);
109	else dimXid=domain->dim_i_name.getValue() + appendDomid;
110
111	if (domain->dim_j_name.isEmpty()) dimYid=StdString("y").append(appendDomid);
112	else dimYid=domain->dim_j_name.getValue() + appendDomid;
113
114	break ;
115
116	case CDomain::type_attr::rectilinear :
117
118	if (domain->lon_name.isEmpty())
119	{
120	if (domain->dim_i_name.isEmpty())
121	lonName = "lon";
122	else
123	lonName = domain->dim_i_name.getValue();
124	}
125	else lonName = domain->lon_name;
126
127	if (domain->lat_name.isEmpty())
128	{
129	if (domain->dim_j_name.isEmpty())
130	latName = "lat";
131	else
132	latName = domain->dim_j_name.getValue();
133	}
134	else latName = domain->lat_name;
135
136	if (domain->dim_i_name.isEmpty()) dimXid = lonName+appendDomid;
137	else dimXid = domain->dim_i_name.getValue()+appendDomid;
138
139	if (domain->dim_j_name.isEmpty()) dimYid = latName+appendDomid;
140	else dimYid = domain->dim_j_name.getValue()+appendDomid;
141	break;
142	}
143
144	StdString dimVertId = StdString("nvertex").append(appendDomid);
145
146	string lonid,latid,bounds_lonid,bounds_latid ;
147	string areaId = "area" + appendDomid;
148	/*
149	StdString lonid_loc = (server->intraCommSize > 1)
150	? StdString("lon").append(appendDomid).append("_local")
151	: lonid;
152	StdString latid_loc = (server->intraCommSize > 1)
153	? StdString("lat").append(appendDomid).append("_local")
154	: latid;
155	*/
156
157	CArray<int, 1>& indexToWrite = domain->localIndexToWriteOnServer;
158	int nbWritten = indexToWrite.numElements();
159	CArray<double,1> writtenLat, writtenLon;
160	CArray<double,2> writtenBndsLat, writtenBndsLon;
161	CArray<double,1> writtenArea;
162
163	if (domain->hasLonLat)
164	{
165	writtenLat.resize(nbWritten);
166	writtenLon.resize(nbWritten);
167	for (int idx = 0; idx < nbWritten; ++idx)
168	{
169	if (indexToWrite(idx) < 0)
170	{
171	writtenLat(idx) = -1.; // hole
172	writtenLon(idx) = -1.;
173	}
174	else
175	{
176	writtenLat(idx) = domain->latvalue(indexToWrite(idx));
177	writtenLon(idx) = domain->lonvalue(indexToWrite(idx));
178	}
179	}
180
181	if (domain->hasBounds)
182	{
183	int nvertex = domain->nvertex, idx;
184	writtenBndsLat.resize(nvertex, nbWritten);
185	writtenBndsLon.resize(nvertex, nbWritten);
186	CArray<double,2>& boundslat = domain->bounds_latvalue;
187	CArray<double,2>& boundslon = domain->bounds_lonvalue;
188	for (idx = 0; idx < nbWritten; ++idx)
189	for (int nv = 0; nv < nvertex; ++nv)
190	{
191	if (indexToWrite(idx) < 0)
192	{
193	writtenBndsLat(nv, idx) = -1.; // hole
194	writtenBndsLon(nv, idx) = -1.;
195	}
196	else
197	{
198	writtenBndsLat(nv, idx) = boundslat(nv, int(indexToWrite(idx)));
199	writtenBndsLon(nv, idx) = boundslon(nv, int(indexToWrite(idx)));
200	}
201	}
202	}
203	}
204
205	if (domain->hasArea)
206	{
207	writtenArea.resize(nbWritten);
208	for (int idx = 0; idx < nbWritten; ++idx)
209	{
210	if (indexToWrite(idx) < 0)
211	writtenArea(idx) = -1.;
212	else
213	writtenArea(idx) = domain->areavalue(indexToWrite(idx));
214	}
215	}
216
217	try
218	{
219	switch (SuperClass::type)
220	{
221	case (MULTI_FILE) :
222	{
223	switch (domain->type)
224	{
225	case CDomain::type_attr::curvilinear :
226	dim0.push_back(dimYid); dim0.push_back(dimXid);
227	lonid = lonName+appendDomid;
228	latid = latName+appendDomid;
229	break ;
230	case CDomain::type_attr::rectilinear :
231	lonid = lonName+appendDomid;
232	latid = latName+appendDomid;
233	dim0.push_back(dimYid);
234	dim1.push_back(dimXid);
235	break;
236	}
237	if (!domain->bounds_lon_name.isEmpty()) bounds_lonid = domain->bounds_lon_name;
238	else bounds_lonid = "bounds_"+lonName+appendDomid;
239	if (!domain->bounds_lat_name.isEmpty()) bounds_latid = domain->bounds_lat_name;
240	else bounds_latid = "bounds_"+latName+appendDomid;
241
242	SuperClassWriter::addDimension(dimXid, domain->ni);
243	SuperClassWriter::addDimension(dimYid, domain->nj);
244
245	if (domain->hasBounds)
246	SuperClassWriter::addDimension(dimVertId, domain->nvertex);
247
248	int commRank ;
249	int commSize ;
250	MPI_Comm_rank(comm_file,&commRank) ;
251	MPI_Comm_size(comm_file,&commSize) ;
252	if (commSize > 1)
253	{
254	this->writeLocalAttributes(domain->ibegin,
255	domain->ni,
256	domain->jbegin,
257	domain->nj,
258	appendDomid);
259
260	if (singleDomain)
261	this->writeLocalAttributes_IOIPSL(dimXid, dimYid,
262	domain->ibegin,
263	domain->ni,
264	domain->jbegin,
265	domain->nj,
266	domain->ni_glo,domain->nj_glo,
267	commRank,commSize);
268	}
269
270	if (domain->hasLonLat)
271	{
272	switch (domain->type)
273	{
274	case CDomain::type_attr::curvilinear :
275	SuperClassWriter::addVariable(latid, typePrec, dim0, compressionLevel);
276	SuperClassWriter::addVariable(lonid, typePrec, dim0, compressionLevel);
277	break ;
278	case CDomain::type_attr::rectilinear :
279	SuperClassWriter::addVariable(latid, typePrec, dim0, compressionLevel);
280	SuperClassWriter::addVariable(lonid, typePrec, dim1, compressionLevel);
281	break ;
282	}
283
284	this->writeAxisAttributes(lonid, isRegularDomain ? "X" : "", "longitude", "Longitude", "degrees_east", domid);
285	this->writeAxisAttributes(latid, isRegularDomain ? "Y" : "", "latitude", "Latitude", "degrees_north", domid);
286
287	if (domain->hasBounds)
288	{
289	SuperClassWriter::addAttribute("bounds", bounds_lonid, &lonid);
290	SuperClassWriter::addAttribute("bounds", bounds_latid, &latid);
291
292	dim0.clear();
293	dim0.push_back(dimYid);
294	dim0.push_back(dimXid);
295	dim0.push_back(dimVertId);
296	SuperClassWriter::addVariable(bounds_lonid, typePrec, dim0, compressionLevel);
297	SuperClassWriter::addVariable(bounds_latid, typePrec, dim0, compressionLevel);
298	}
299	}
300
301	dim0.clear();
302	dim0.push_back(dimYid);
303	dim0.push_back(dimXid);
304
305
306	// supress mask if (server->intraCommSize > 1)
307	// supress mask {
308	// supress mask SuperClassWriter::addVariable(maskid, NC_INT, dim0);
309	// supress mask
310	// supress mask this->writeMaskAttributes(maskid,
311	// supress mask domain->data_dim.getValue()/*,
312	// supress mask domain->data_ni.getValue(),
313	// supress mask domain->data_nj.getValue(),
314	// supress mask domain->data_ibegin.getValue(),
315	// supress mask domain->data_jbegin.getValue()*/);
316	// supress mask }
317
318	//SuperClassWriter::setDefaultValue(maskid, &dvm);
319
320	if (domain->hasArea)
321	{
322	SuperClassWriter::addVariable(areaId, typePrec, dim0, compressionLevel);
323	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
324	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
325	}
326
327	SuperClassWriter::definition_end();
328
329	if (domain->hasLonLat)
330	{
331	switch (domain->type)
332	{
333	case CDomain::type_attr::curvilinear :
334	SuperClassWriter::writeData(writtenLat, latid, isCollective, 0);
335	SuperClassWriter::writeData(writtenLon, lonid, isCollective, 0);
336	break;
337	case CDomain::type_attr::rectilinear :
338	CArray<double,1> lat = writtenLat(Range(fromStart,toEnd,domain->ni)) ;
339	SuperClassWriter::writeData(CArray<double,1>(lat.copy()), latid, isCollective, 0);
340	CArray<double,1> lon = writtenLon(Range(0,domain->ni-1)) ;
341	SuperClassWriter::writeData(CArray<double,1>(lon.copy()), lonid, isCollective, 0);
342	break;
343	}
344
345	if (domain->hasBounds)
346	{
347	SuperClassWriter::writeData(writtenBndsLon, bounds_lonid, isCollective, 0);
348	SuperClassWriter::writeData(writtenBndsLat, bounds_latid, isCollective, 0);
349	}
350	}
351
352	if (domain->hasArea)
353	{
354	SuperClassWriter::writeData(writtenArea, areaId, isCollective, 0);
355	}
356
357	SuperClassWriter::definition_start();
358
359	break;
360	}
361	case (ONE_FILE) :
362	{
363	SuperClassWriter::addDimension(dimXid, domain->ni_glo);
364	SuperClassWriter::addDimension(dimYid, domain->nj_glo);
365
366	if (domain->hasBounds)
367	SuperClassWriter::addDimension(dimVertId, domain->nvertex);
368
369	if (domain->hasLonLat)
370	{
371	switch (domain->type)
372	{
373	case CDomain::type_attr::curvilinear :
374	dim0.push_back(dimYid); dim0.push_back(dimXid);
375	lonid = lonName+appendDomid;
376	latid = latName+appendDomid;
377	SuperClassWriter::addVariable(latid, typePrec, dim0, compressionLevel);
378	SuperClassWriter::addVariable(lonid, typePrec, dim0, compressionLevel);
379	break;
380
381	case CDomain::type_attr::rectilinear :
382	dim0.push_back(dimYid);
383	dim1.push_back(dimXid);
384	lonid = lonName+appendDomid;
385	latid = latName+appendDomid;
386	SuperClassWriter::addVariable(latid, typePrec, dim0, compressionLevel);
387	SuperClassWriter::addVariable(lonid, typePrec, dim1, compressionLevel);
388	break;
389	}
390	if (!domain->bounds_lon_name.isEmpty()) bounds_lonid = domain->bounds_lon_name;
391	else bounds_lonid = "bounds_"+lonName+appendDomid;
392	if (!domain->bounds_lat_name.isEmpty()) bounds_latid = domain->bounds_lat_name;
393	else bounds_latid = "bounds_"+latName+appendDomid;
394
395	this->writeAxisAttributes
396	(lonid, isRegularDomain ? "X" : "", "longitude", "Longitude", "degrees_east", domid);
397	this->writeAxisAttributes
398	(latid, isRegularDomain ? "Y" : "", "latitude", "Latitude", "degrees_north", domid);
399
400	if (domain->hasBounds)
401	{
402	SuperClassWriter::addAttribute("bounds", bounds_lonid, &lonid);
403	SuperClassWriter::addAttribute("bounds", bounds_latid, &latid);
404
405	dim0.clear();
406	dim0.push_back(dimYid);
407	dim0.push_back(dimXid);
408	dim0.push_back(dimVertId);
409	SuperClassWriter::addVariable(bounds_lonid, typePrec, dim0, compressionLevel);
410	SuperClassWriter::addVariable(bounds_latid, typePrec, dim0, compressionLevel);
411	}
412	}
413
414	if (domain->hasArea)
415	{
416	dim0.clear();
417	dim0.push_back(dimYid); dim0.push_back(dimXid);
418	SuperClassWriter::addVariable(areaId, typePrec, dim0, compressionLevel);
419	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
420	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
421	dim0.clear();
422	}
423
424	SuperClassWriter::definition_end();
425
426	switch (domain->type)
427	{
428	case CDomain::type_attr::curvilinear :
429	{
430	std::vector<StdSize> start(2) ;
431	std::vector<StdSize> count(2) ;
432	// Comment out: it is not working for a hole
433	// if (domain->isEmpty())
434	// {
435	// start[0]=0 ; start[1]=0 ;
436	// count[0]=0 ; count[1]=0 ;
437	// }
438	// else
439	{
440	start[1]=domain->ibegin;
441	start[0]=domain->jbegin;
442	count[1]=domain->ni ; count[0]=domain->nj ;
443	}
444
445	if (domain->hasLonLat)
446	{
447	SuperClassWriter::writeData(writtenLat, latid, isCollective, 0,&start,&count);
448	SuperClassWriter::writeData(writtenLon, lonid, isCollective, 0,&start,&count);
449	}
450	break;
451	}
452	case CDomain::type_attr::rectilinear :
453	{
454	if (domain->hasLonLat)
455	{
456	std::vector<StdSize> start(1) ;
457	std::vector<StdSize> count(1) ;
458	if (domain->isEmpty())
459	{
460	start[0]=0 ;
461	count[0]=0 ;
462	SuperClassWriter::writeData(writtenLat, latid, isCollective, 0,&start,&count);
463	SuperClassWriter::writeData(writtenLon, lonid, isCollective, 0,&start,&count);
464	}
465	else
466	{
467	start[0]=domain->jbegin;
468	count[0]=domain->nj;
469	CArray<double,1> lat = writtenLat(Range(fromStart,toEnd,domain->ni));
470	SuperClassWriter::writeData(CArray<double,1>(lat.copy()), latid, isCollective, 0,&start,&count);
471
472	start[0]=domain->ibegin;
473	count[0]=domain->ni;
474	CArray<double,1> lon = writtenLon(Range(0,domain->ni-1));
475	SuperClassWriter::writeData(CArray<double,1>(lon.copy()), lonid, isCollective, 0,&start,&count);
476	}
477	}
478	break;
479	}
480	}
481
482	if (domain->hasBounds)
483	{
484	std::vector<StdSize> start(3);
485	std::vector<StdSize> count(3);
486	if (domain->isEmpty())
487	{
488	start[2] = start[1] = start[0] = 0;
489	count[2] = count[1] = count[0] = 0;
490	}
491	else
492	{
493	start[2] = 0;
494	start[1] = domain->ibegin;
495	start[0] = domain->jbegin;
496	count[2] = domain->nvertex;
497	count[1] = domain->ni;
498	count[0] = domain->nj;
499	}
500
501	SuperClassWriter::writeData(writtenBndsLon, bounds_lonid, isCollective, 0, &start, &count);
502	SuperClassWriter::writeData(writtenBndsLat, bounds_latid, isCollective, 0, &start, &count);
503	}
504
505	if (domain->hasArea)
506	{
507	std::vector<StdSize> start(2);
508	std::vector<StdSize> count(2);
509
510	if (domain->isEmpty())
511	{
512	start[0] = 0; start[1] = 0;
513	count[0] = 0; count[1] = 0;
514	}
515	else
516	{
517	start[1] = domain->ibegin;
518	start[0] = domain->jbegin;
519	count[1] = domain->ni;
520	count[0] = domain->nj;
521	}
522
523	SuperClassWriter::writeData(writtenArea, areaId, isCollective, 0, &start, &count);
524	}
525
526	SuperClassWriter::definition_start();
527	break;
528	}
529	default :
530	ERROR("CNc4DataOutput::writeDomain(domain)",
531	<< "[ type = " << SuperClass::type << "]"
532	<< " not implemented yet !");
533	}
534	}
535	catch (CNetCdfException& e)
536	{
537	StdString msg("On writing the domain : ");
538	msg.append(domid); msg.append("\n");
539	msg.append("In the context : ");
540	msg.append(context->getId()); msg.append("\n");
541	msg.append(e.what());
542	ERROR("CNc4DataOutput::writeDomain_(CDomain* domain)", << msg);
543	}
544
545	domain->addRelFile(this->filename);
546	}
547	CATCH
548
549	//--------------------------------------------------------------
550
551	void CNc4DataOutput::writeUnstructuredDomainUgrid(CDomain* domain)
552	{
553	CContext* context = CContext::getCurrent() ;
554	CContextServer* server=context->server ;
555
556	if (domain->IsWritten(this->filename)) return;
557
558	StdString domid = domain->getDomainOutputName();
559
560	// The first domain for the same mesh that will be written is that with the highest value of nvertex.
561	// Thus the entire mesh connectivity will be generated at once.
562
563	if (isWrittenDomain(domid)) return ;
564	else setWrittenDomain(domid);
565
566	domain->checkAttributes();
567	if (domain->isEmpty())
568	if (SuperClass::type==MULTI_FILE) return ;
569
570	nc_type typePrec ;
571	if (domain->prec.isEmpty()) typePrec = NC_FLOAT ;
572	else if (domain->prec==4) typePrec = NC_FLOAT ;
573	else if (domain->prec==8) typePrec = NC_DOUBLE ;
574
575	std::vector<StdString> dim0;
576	StdString domainName = domain->name;
577
578	StdString node_x = domainName + "_node_x";
579	StdString node_y = domainName + "_node_y";
580
581	StdString edge_x = domainName + "_edge_x";
582	StdString edge_y = domainName + "_edge_y";
583	StdString edge_nodes = domainName + "_edge_nodes";
584
585	StdString face_x = domainName + "_face_x";
586	StdString face_y = domainName + "_face_y";
587	StdString face_nodes = domainName + "_face_nodes";
588	StdString face_edges = domainName + "_face_edges";
589	StdString edge_faces = domainName + "_edge_face_links";
590	StdString face_faces = domainName + "_face_links";
591
592	StdString dimNode = "n" + domainName + "_node";
593	StdString dimEdge = "n" + domainName + "_edge";
594	StdString dimFace = "n" + domainName + "_face";
595	StdString dimVertex = "n" + domainName + "_vertex";
596	StdString dimTwo = "Two";
597
598	if (!SuperClassWriter::dimExist(dimTwo)) SuperClassWriter::addDimension(dimTwo, 2);
599	dim0.clear();
600	SuperClassWriter::addVariable(domainName, NC_INT, dim0, compressionLevel);
601	SuperClassWriter::addAttribute("cf_role", StdString("mesh_topology"), &domainName);
602	SuperClassWriter::addAttribute("long_name", StdString("Topology data of 2D unstructured mesh"), &domainName);
603	SuperClassWriter::addAttribute("topology_dimension", 2, &domainName);
604	SuperClassWriter::addAttribute("node_coordinates", node_x + " " + node_y, &domainName);
605
606
607	try
608	{
609	switch (SuperClass::type)
610	{
611	case (ONE_FILE) :
612	{
613	// Adding nodes
614	if (domain->nvertex == 1)
615	{
616	if (!SuperClassWriter::varExist(node_x) \|\| !SuperClassWriter::varExist(node_y))
617	{
618	SuperClassWriter::addDimension(dimNode, domain->ni_glo);
619	dim0.clear();
620	dim0.push_back(dimNode);
621	SuperClassWriter::addVariable(node_x, typePrec, dim0, compressionLevel);
622	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &node_x);
623	SuperClassWriter::addAttribute("long_name", StdString("Longitude of mesh nodes."), &node_x);
624	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &node_x);
625	SuperClassWriter::addVariable(node_y, typePrec, dim0, compressionLevel);
626	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &node_y);
627	SuperClassWriter::addAttribute("long_name", StdString("Latitude of mesh nodes."), &node_y);
628	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &node_y);
629	}
630	} // domain->nvertex == 1
631
632	// Adding edges and nodes, if nodes have not been defined previously
633	if (domain->nvertex == 2)
634	{
635	if (!SuperClassWriter::varExist(node_x) \|\| !SuperClassWriter::varExist(node_y))
636	{
637	SuperClassWriter::addDimension(dimNode, domain->mesh->nbNodesGlo);
638	dim0.clear();
639	dim0.push_back(dimNode);
640	SuperClassWriter::addVariable(node_x, typePrec, dim0, compressionLevel);
641	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &node_x);
642	SuperClassWriter::addAttribute("long_name", StdString("Longitude of mesh nodes."), &node_x);
643	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &node_x);
644	SuperClassWriter::addVariable(node_y, typePrec, dim0, compressionLevel);
645	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &node_y);
646	SuperClassWriter::addAttribute("long_name", StdString("Latitude of mesh nodes."), &node_y);
647	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &node_y);
648	}
649	SuperClassWriter::addAttribute("edge_node_connectivity", edge_nodes, &domainName);
650	SuperClassWriter::addAttribute("edge_coordinates", edge_x + " " + edge_y, &domainName);
651	SuperClassWriter::addDimension(dimEdge, domain->ni_glo);
652	dim0.clear();
653	dim0.push_back(dimEdge);
654	SuperClassWriter::addVariable(edge_x, typePrec, dim0, compressionLevel);
655	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &edge_x);
656	SuperClassWriter::addAttribute("long_name", StdString("Characteristic longitude of mesh edges."), &edge_x);
657	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &edge_x);
658	SuperClassWriter::addVariable(edge_y, typePrec, dim0, compressionLevel);
659	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &edge_y);
660	SuperClassWriter::addAttribute("long_name", StdString("Characteristic latitude of mesh edges."), &edge_y);
661	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &edge_y);
662	dim0.clear();
663	dim0.push_back(dimEdge);
664	dim0.push_back(dimTwo);
665	SuperClassWriter::addVariable(edge_nodes, NC_INT, dim0, compressionLevel);
666	SuperClassWriter::addAttribute("cf_role", StdString("edge_node_connectivity"), &edge_nodes);
667	SuperClassWriter::addAttribute("long_name", StdString("Maps every edge/link to two nodes that it connects."), &edge_nodes);
668	SuperClassWriter::addAttribute("start_index", 0, &edge_nodes);
669	} // domain->nvertex == 2
670
671	// Adding faces, edges, and nodes, if edges and nodes have not been defined previously
672	if (domain->nvertex > 2)
673	{
674	// Nodes
675	if (!SuperClassWriter::varExist(node_x) \|\| !SuperClassWriter::varExist(node_y))
676	{
677	SuperClassWriter::addDimension(dimNode, domain->mesh->nbNodesGlo);
678	dim0.clear();
679	dim0.push_back(dimNode);
680	SuperClassWriter::addVariable(node_x, typePrec, dim0, compressionLevel);
681	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &node_x);
682	SuperClassWriter::addAttribute("long_name", StdString("Longitude of mesh nodes."), &node_x);
683	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &node_x);
684	SuperClassWriter::addVariable(node_y, typePrec, dim0, compressionLevel);
685	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &node_y);
686	SuperClassWriter::addAttribute("long_name", StdString("Latitude of mesh nodes."), &node_y);
687	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &node_y);
688	}
689	if (!SuperClassWriter::varExist(edge_x) \|\| !SuperClassWriter::varExist(edge_y))
690	{
691	SuperClassWriter::addAttribute("edge_coordinates", edge_x + " " + edge_y, &domainName);
692	SuperClassWriter::addAttribute("edge_node_connectivity", edge_nodes, &domainName);
693	SuperClassWriter::addAttribute("face_edge_connectivity", face_edges, &domainName);
694	SuperClassWriter::addAttribute("edge_face_connectivity", edge_faces, &domainName);
695	SuperClassWriter::addDimension(dimEdge, domain->mesh->nbEdgesGlo);
696	dim0.clear();
697	dim0.push_back(dimEdge);
698	SuperClassWriter::addVariable(edge_x, typePrec, dim0, compressionLevel);
699	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &edge_x);
700	SuperClassWriter::addAttribute("long_name", StdString("Characteristic longitude of mesh edges."), &edge_x);
701	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &edge_x);
702	SuperClassWriter::addVariable(edge_y, typePrec, dim0, compressionLevel);
703	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &edge_y);
704	SuperClassWriter::addAttribute("long_name", StdString("Characteristic latitude of mesh edges."), &edge_y);
705	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &edge_y);
706	dim0.clear();
707	dim0.push_back(dimEdge);
708	dim0.push_back(dimTwo);
709	SuperClassWriter::addVariable(edge_nodes, NC_INT, dim0, compressionLevel);
710	SuperClassWriter::addAttribute("cf_role", StdString("edge_node_connectivity"), &edge_nodes);
711	SuperClassWriter::addAttribute("long_name", StdString("Maps every edge/link to two nodes that it connects."), &edge_nodes);
712	SuperClassWriter::addAttribute("start_index", 0, &edge_nodes);
713	}
714	SuperClassWriter::addAttribute("face_face_connectivity", face_faces, &domainName);
715	SuperClassWriter::addAttribute("face_coordinates", face_x + " " + face_y, &domainName);
716	SuperClassWriter::addAttribute("face_node_connectivity", face_nodes, &domainName);
717	SuperClassWriter::addDimension(dimFace, domain->ni_glo);
718	SuperClassWriter::addDimension(dimVertex, domain->nvertex);
719	dim0.clear();
720	dim0.push_back(dimFace);
721	SuperClassWriter::addVariable(face_x, typePrec, dim0, compressionLevel);
722	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &face_x);
723	SuperClassWriter::addAttribute("long_name", StdString("Characteristic longitude of mesh faces."), &face_x);
724	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &face_x);
725	SuperClassWriter::addVariable(face_y, typePrec, dim0, compressionLevel);
726	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &face_y);
727	SuperClassWriter::addAttribute("long_name", StdString("Characteristic latitude of mesh faces."), &face_y);
728	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &face_y);
729	dim0.clear();
730	dim0.push_back(dimFace);
731	dim0.push_back(dimVertex);
732	SuperClassWriter::addVariable(face_nodes, NC_INT, dim0, compressionLevel);
733	SuperClassWriter::addAttribute("cf_role", StdString("face_node_connectivity"), &face_nodes);
734	SuperClassWriter::addAttribute("long_name", StdString("Maps every face to its corner nodes."), &face_nodes);
735	SuperClassWriter::addAttribute("start_index", 0, &face_nodes);
736	dim0.clear();
737	dim0.push_back(dimFace);
738	dim0.push_back(dimVertex);
739	SuperClassWriter::addVariable(face_edges, NC_INT, dim0, compressionLevel);
740	SuperClassWriter::addAttribute("cf_role", StdString("face_edge_connectivity"), &face_edges);
741	SuperClassWriter::addAttribute("long_name", StdString("Maps every face to its edges."), &face_edges);
742	SuperClassWriter::addAttribute("start_index", 0, &face_edges);
743	SuperClassWriter::addAttribute("_FillValue", 999999, &face_edges);
744	dim0.clear();
745	dim0.push_back(dimEdge);
746	dim0.push_back(dimTwo);
747	SuperClassWriter::addVariable(edge_faces, NC_INT, dim0, compressionLevel);
748	SuperClassWriter::addAttribute("cf_role", StdString("edge_face_connectivity"), &edge_faces);
749	SuperClassWriter::addAttribute("long_name", StdString("neighbor faces for edges"), &edge_faces);
750	SuperClassWriter::addAttribute("start_index", 0, &edge_faces);
751	SuperClassWriter::addAttribute("_FillValue", -999, &edge_faces);
752	SuperClassWriter::addAttribute("comment", StdString("missing neighbor faces are indicated using _FillValue"), &edge_faces);
753	dim0.clear();
754	dim0.push_back(dimFace);
755	dim0.push_back(dimVertex);
756	SuperClassWriter::addVariable(face_faces, NC_INT, dim0, compressionLevel);
757	SuperClassWriter::addAttribute("cf_role", StdString("face_face_connectivity"), &face_faces);
758	SuperClassWriter::addAttribute("long_name", StdString("Indicates which other faces neighbor each face"), &face_faces);
759	SuperClassWriter::addAttribute("start_index", 0, &face_faces);
760	SuperClassWriter::addAttribute("_FillValue", 999999, &face_faces);
761	SuperClassWriter::addAttribute("flag_values", -1, &face_faces);
762	SuperClassWriter::addAttribute("flag_meanings", StdString("out_of_mesh"), &face_faces);
763	} // domain->nvertex > 2
764
765	SuperClassWriter::definition_end();
766
767	std::vector<StdSize> startEdges(1) ;
768	std::vector<StdSize> countEdges(1) ;
769	std::vector<StdSize> startNodes(1) ;
770	std::vector<StdSize> countNodes(1) ;
771	std::vector<StdSize> startFaces(1) ;
772	std::vector<StdSize> countFaces(1) ;
773	std::vector<StdSize> startEdgeNodes(2) ;
774	std::vector<StdSize> countEdgeNodes(2) ;
775	std::vector<StdSize> startEdgeFaces(2) ;
776	std::vector<StdSize> countEdgeFaces(2) ;
777	std::vector<StdSize> startFaceConctv(2) ;
778	std::vector<StdSize> countFaceConctv(2) ;
779
780	if (domain->nvertex == 1)
781	{
782	if (domain->isEmpty())
783	{
784	startNodes[0]=0 ;
785	countNodes[0]=0 ;
786	}
787	else
788	{
789	startNodes[0] = domain->ibegin;
790	countNodes[0] = domain->ni ;
791	}
792
793	SuperClassWriter::writeData(domain->mesh->node_lat, node_y, isCollective, 0, &startNodes, &countNodes);
794	SuperClassWriter::writeData(domain->mesh->node_lon, node_x, isCollective, 0, &startNodes, &countNodes);
795	}
796	else if (domain->nvertex == 2)
797	{
798	if (domain->isEmpty())
799	{
800	startEdges[0]=0 ;
801	countEdges[0]=0 ;
802	startNodes[0]=0 ;
803	countNodes[0]=0 ;
804	startEdgeNodes[0]=0;
805	startEdgeNodes[1]=0;
806	countEdgeNodes[0]=0;
807	countEdgeNodes[1]=0;
808
809	}
810	else
811	{
812	startEdges[0] = domain->ibegin;
813	countEdges[0] = domain->ni;
814	startNodes[0] = domain->mesh->node_start;
815	countNodes[0] = domain->mesh->node_count;
816	if (countNodes[0]==0) startNodes[0]=0 ; // for netcdf error
817	startEdgeNodes[0] = domain->ibegin;
818	startEdgeNodes[1] = 0;
819	countEdgeNodes[0] = domain->ni;
820	countEdgeNodes[1] = 2;
821	}
822	SuperClassWriter::writeData(domain->mesh->node_lat, node_y, isCollective, 0, &startNodes, &countNodes);
823	SuperClassWriter::writeData(domain->mesh->node_lon, node_x, isCollective, 0, &startNodes, &countNodes);
824	SuperClassWriter::writeData(domain->mesh->edge_lat, edge_y, isCollective, 0, &startEdges, &countEdges);
825	SuperClassWriter::writeData(domain->mesh->edge_lon, edge_x, isCollective, 0, &startEdges, &countEdges);
826	SuperClassWriter::writeData(domain->mesh->edge_nodes, edge_nodes, isCollective, 0, &startEdgeNodes, &countEdgeNodes);
827	}
828	else
829	{
830	if (domain->isEmpty())
831	{
832	startFaces[0] = 0 ;
833	countFaces[0] = 0 ;
834	startNodes[0] = 0;
835	countNodes[0] = 0;
836	startEdges[0] = 0;
837	countEdges[0] = 0;
838	startEdgeFaces[0] = 0;
839	startEdgeFaces[1] = 0;
840	countEdgeFaces[0] = 0;
841	countEdgeFaces[1] = 0;
842	startFaceConctv[0] = 0;
843	startFaceConctv[1] = 0;
844	countFaceConctv[0] = 0;
845	countFaceConctv[1] = 0;
846	}
847	else
848	{
849	startFaces[0] = domain->ibegin;
850	countFaces[0] = domain->ni ;
851	startNodes[0] = domain->mesh->node_start;
852	countNodes[0] = domain->mesh->node_count;
853	if (countNodes[0]==0) startNodes[0]=0;
854
855	startEdges[0] = domain->mesh->edge_start;
856	countEdges[0] = domain->mesh->edge_count;
857	if (countEdges[0]==0) startEdges[0]=0 ; // for netcdf error
858
859	startEdgeNodes[0] = domain->mesh->edge_start;
860	countEdgeNodes[0] = domain->mesh->edge_count;
861	if (countEdgeNodes[0]==0) startEdgeNodes[0]=0; // for netcdf error
862	startEdgeNodes[1] = 0;
863	countEdgeNodes[1]= 2;
864
865	startEdgeFaces[0] = domain->mesh->edge_start;
866	countEdgeFaces[0] = domain->mesh->edge_count;
867	if (countEdgeFaces[0]==0) startEdgeFaces[0]=0 ; // for netcdf error
868	startEdgeFaces[1]= 0;
869	countEdgeFaces[1]= 2;
870
871	startFaceConctv[0] = domain->ibegin;
872	countFaceConctv[0] = domain->ni;
873	startFaceConctv[1] = 0;
874	countFaceConctv[1] = domain->nvertex;
875	}
876	SuperClassWriter::writeData(domain->mesh->node_lat, node_y, isCollective, 0, &startNodes, &countNodes);
877	SuperClassWriter::writeData(domain->mesh->node_lon, node_x, isCollective, 0, &startNodes, &countNodes);
878	SuperClassWriter::writeData(domain->mesh->edge_lat, edge_y, isCollective, 0, &startEdges, &countEdges);
879	SuperClassWriter::writeData(domain->mesh->edge_lon, edge_x, isCollective, 0, &startEdges, &countEdges);
880	SuperClassWriter::writeData(domain->mesh->edge_nodes, edge_nodes, isCollective, 0, &startEdgeNodes, &countEdgeNodes);
881	SuperClassWriter::writeData(domain->mesh->face_lat, face_y, isCollective, 0, &startFaces, &countFaces);
882	SuperClassWriter::writeData(domain->mesh->face_lon, face_x, isCollective, 0, &startFaces, &countFaces);
883	SuperClassWriter::writeData(domain->mesh->face_nodes, face_nodes, isCollective, 0, &startFaceConctv, &countFaceConctv);
884	SuperClassWriter::writeData(domain->mesh->face_edges, face_edges, isCollective, 0, &startFaceConctv, &countFaceConctv);
885	SuperClassWriter::writeData(domain->mesh->edge_faces, edge_faces, isCollective, 0, &startEdgeFaces, &countEdgeFaces);
886	SuperClassWriter::writeData(domain->mesh->face_faces, face_faces, isCollective, 0, &startFaceConctv, &countFaceConctv);
887	}
888	SuperClassWriter::definition_start();
889
890	break;
891	} // ONE_FILE
892
893	case (MULTI_FILE) :
894	{
895	ERROR("CNc4DataOutput::writeDomain(domain)",
896	<< "[ type = multiple_file ]"
897	<< " is not yet implemented for UGRID files !");
898	break;
899	}
900
901	default :
902	ERROR("CNc4DataOutput::writeDomain(domain)",
903	<< "[ type = " << SuperClass::type << "]"
904	<< " not implemented yet !");
905	} // switch
906	} // try
907
908	catch (CNetCdfException& e)
909	{
910	StdString msg("On writing the domain : ");
911	msg.append(domid); msg.append("\n");
912	msg.append("In the context : ");
913	msg.append(context->getId()); msg.append("\n");
914	msg.append(e.what());
915	ERROR("CNc4DataOutput::writeUnstructuredDomainUgrid(CDomain* domain)", << msg);
916	}
917
918	domain->addRelFile(this->filename);
919	}
920
921	//--------------------------------------------------------------
922
923	void CNc4DataOutput::writeUnstructuredDomain(CDomain* domain)
924	{
925	CContext* context = CContext::getCurrent() ;
926	CContextServer* server=context->server ;
927
928	if (domain->IsWritten(this->filename)) return;
929	domain->checkAttributes();
930
931	if (domain->isEmpty())
932	if (SuperClass::type==MULTI_FILE) return ;
933
934	std::vector<StdString> dim0, dim1;
935	StdString domid = domain->getDomainOutputName();
936	if (isWrittenDomain(domid)) return ;
937	else setWrittenDomain(domid);
938
939	StdString appendDomid = (singleDomain) ? "" : "_"+domid ;
940
941	StdString lonName,latName, cellName ;
942	if (domain->lon_name.isEmpty()) lonName = "lon";
943	else lonName = domain->lon_name;
944
945	if (domain->lat_name.isEmpty()) latName = "lat";
946	else latName = domain->lat_name;
947
948	if (!domain->dim_i_name.isEmpty()) cellName=domain->dim_i_name;
949	else cellName="cell";
950	StdString dimXid = cellName+appendDomid;
951	StdString dimVertId = StdString("nvertex").append(appendDomid);
952
953	string lonid,latid,bounds_lonid,bounds_latid ;
954	string areaId = "area" + appendDomid;
955
956	nc_type typePrec ;
957	if (domain->prec.isEmpty()) typePrec = NC_FLOAT ;
958	else if (domain->prec==4) typePrec = NC_FLOAT ;
959	else if (domain->prec==8) typePrec = NC_DOUBLE ;
960
961	int nvertex = (domain->nvertex.isEmpty()) ? 0 : domain->nvertex;
962
963	CArray<int, 1>& indexToWrite = domain->localIndexToWriteOnServer;
964	int nbWritten = indexToWrite.numElements();
965	CArray<double,1> writtenLat, writtenLon;
966	CArray<double,2> writtenBndsLat, writtenBndsLon;
967	CArray<double,1> writtenArea;
968
969	if (domain->hasLonLat)
970	{
971	writtenLat.resize(nbWritten);
972	writtenLon.resize(nbWritten);
973	for (int idx = 0; idx < nbWritten; ++idx)
974	{
975	if (indexToWrite(idx) < 0)
976	{
977	writtenLat(idx) = -1.;
978	writtenLon(idx) = -1.;
979	}
980	else
981	{
982	writtenLat(idx) = domain->latvalue(indexToWrite(idx));
983	writtenLon(idx) = domain->lonvalue(indexToWrite(idx));
984	}
985	}
986	}
987
988	if (domain->hasBounds)
989	{
990	int nvertex = domain->nvertex, idx;
991	writtenBndsLat.resize(nvertex, nbWritten);
992	writtenBndsLon.resize(nvertex, nbWritten);
993	CArray<double,2>& boundslat = domain->bounds_latvalue;
994	CArray<double,2>& boundslon = domain->bounds_lonvalue;
995	for (idx = 0; idx < nbWritten; ++idx)
996	{
997	for (int nv = 0; nv < nvertex; ++nv)
998	{
999	if (indexToWrite(idx) < 0)
1000	{
1001	writtenBndsLat(nv, idx) = -1.;
1002	writtenBndsLon(nv, idx) = -1.;
1003	}
1004	else
1005	{
1006	writtenBndsLat(nv, idx) = boundslat(nv, int(indexToWrite(idx)));
1007	writtenBndsLon(nv, idx) = boundslon(nv, int(indexToWrite(idx)));
1008	}
1009	}
1010	}
1011	}
1012
1013	if (domain->hasArea)
1014	{
1015	writtenArea.resize(nbWritten);
1016	for (int idx = 0; idx < nbWritten; ++idx)
1017	{
1018	if (indexToWrite(idx) < 0)
1019	writtenArea(idx) = -1.;
1020	else
1021	writtenArea(idx) = domain->areavalue(indexToWrite(idx));
1022	}
1023	}
1024
1025	try
1026	{
1027	switch (SuperClass::type)
1028	{
1029	case (MULTI_FILE) :
1030	{
1031	dim0.push_back(dimXid);
1032	SuperClassWriter::addDimension(dimXid, domain->ni);
1033
1034	lonid = lonName+appendDomid;
1035	latid = latName+appendDomid;
1036	if (!domain->bounds_lon_name.isEmpty()) bounds_lonid = domain->bounds_lon_name;
1037	else bounds_lonid = "bounds_"+lonName+appendDomid;
1038	if (!domain->bounds_lat_name.isEmpty()) bounds_latid = domain->bounds_lat_name;
1039	else bounds_latid = "bounds_"+latName+appendDomid;
1040
1041	if (domain->hasLonLat)
1042	{
1043	SuperClassWriter::addVariable(latid, typePrec, dim0, compressionLevel);
1044	SuperClassWriter::addVariable(lonid, typePrec, dim0, compressionLevel);
1045	this->writeAxisAttributes(lonid, "", "longitude", "Longitude", "degrees_east", domid);
1046	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_lonid, &lonid);
1047	this->writeAxisAttributes(latid, "", "latitude", "Latitude", "degrees_north", domid);
1048	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_latid, &latid);
1049	if (domain->hasBounds) SuperClassWriter::addDimension(dimVertId, domain->nvertex);
1050	}
1051	dim0.clear();
1052	if (domain->hasBounds)
1053	{
1054	dim0.push_back(dimXid);
1055	dim0.push_back(dimVertId);
1056	SuperClassWriter::addVariable(bounds_lonid, typePrec, dim0, compressionLevel);
1057	SuperClassWriter::addVariable(bounds_latid, typePrec, dim0, compressionLevel);
1058	}
1059
1060	dim0.clear();
1061	dim0.push_back(dimXid);
1062	if (domain->hasArea)
1063	{
1064	SuperClassWriter::addVariable(areaId, typePrec, dim0, compressionLevel);
1065	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
1066	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
1067	}
1068
1069	SuperClassWriter::definition_end();
1070
1071	if (domain->hasLonLat)
1072	{
1073	SuperClassWriter::writeData(writtenLat, latid, isCollective, 0);
1074	SuperClassWriter::writeData(writtenLon, lonid, isCollective, 0);
1075	if (domain->hasBounds)
1076	{
1077	SuperClassWriter::writeData(writtenBndsLon, bounds_lonid, isCollective, 0);
1078	SuperClassWriter::writeData(writtenBndsLat, bounds_latid, isCollective, 0);
1079	}
1080	}
1081
1082	if (domain->hasArea)
1083	SuperClassWriter::writeData(writtenArea, areaId, isCollective, 0);
1084
1085	SuperClassWriter::definition_start();
1086	break ;
1087	}
1088
1089	case (ONE_FILE) :
1090	{
1091	lonid = lonName+appendDomid;
1092	latid = latName+appendDomid;
1093	if (!domain->bounds_lon_name.isEmpty()) bounds_lonid = domain->bounds_lon_name;
1094	else bounds_lonid = "bounds_"+lonName+appendDomid;
1095	if (!domain->bounds_lat_name.isEmpty()) bounds_latid = domain->bounds_lat_name;
1096	else bounds_latid = "bounds_"+latName+appendDomid;
1097
1098	dim0.push_back(dimXid);
1099	SuperClassWriter::addDimension(dimXid, domain->ni_glo);
1100	if (domain->hasLonLat)
1101	{
1102	SuperClassWriter::addVariable(latid, typePrec, dim0, compressionLevel);
1103	SuperClassWriter::addVariable(lonid, typePrec, dim0, compressionLevel);
1104
1105	this->writeAxisAttributes(lonid, "", "longitude", "Longitude", "degrees_east", domid);
1106	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_lonid, &lonid);
1107	this->writeAxisAttributes(latid, "", "latitude", "Latitude", "degrees_north", domid);
1108	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_latid, &latid);
1109	if (domain->hasBounds) SuperClassWriter::addDimension(dimVertId, nvertex);
1110	}
1111	dim0.clear();
1112
1113	if (domain->hasBounds)
1114	{
1115	dim0.push_back(dimXid);
1116	dim0.push_back(dimVertId);
1117	SuperClassWriter::addVariable(bounds_lonid, typePrec, dim0, compressionLevel);
1118	SuperClassWriter::addVariable(bounds_latid, typePrec, dim0, compressionLevel);
1119	}
1120
1121	if (domain->hasArea)
1122	{
1123	dim0.clear();
1124	dim0.push_back(dimXid);
1125	SuperClassWriter::addVariable(areaId, typePrec, dim0, compressionLevel);
1126	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
1127	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
1128	}
1129
1130	SuperClassWriter::definition_end();
1131
1132	std::vector<StdSize> start(1), startBounds(2) ;
1133	std::vector<StdSize> count(1), countBounds(2) ;
1134	if (domain->isEmpty())
1135	{
1136	start[0]=0 ;
1137	count[0]=0 ;
1138	startBounds[1]=0 ;
1139	countBounds[1]=nvertex ;
1140	startBounds[0]=0 ;
1141	countBounds[0]=0 ;
1142	}
1143	else
1144	{
1145	start[0]=domain->ibegin;
1146	count[0]=domain->ni;
1147	startBounds[0]=domain->ibegin;
1148	startBounds[1]=0 ;
1149	countBounds[0]=domain->ni;
1150	countBounds[1]=nvertex ;
1151	}
1152
1153	if (domain->hasLonLat)
1154	{
1155	SuperClassWriter::writeData(writtenLat, latid, isCollective, 0,&start,&count);
1156	SuperClassWriter::writeData(writtenLon, lonid, isCollective, 0,&start,&count);
1157	if (domain->hasBounds)
1158	{
1159	SuperClassWriter::writeData(writtenBndsLon, bounds_lonid, isCollective, 0,&startBounds,&countBounds);
1160	SuperClassWriter::writeData(writtenBndsLat, bounds_latid, isCollective, 0,&startBounds,&countBounds);
1161	}
1162	}
1163
1164	if (domain->hasArea)
1165	SuperClassWriter::writeData(writtenArea, areaId, isCollective, 0, &start, &count);
1166
1167	SuperClassWriter::definition_start();
1168
1169	break;
1170	}
1171	default :
1172	ERROR("CNc4DataOutput::writeDomain(domain)",
1173	<< "[ type = " << SuperClass::type << "]"
1174	<< " not implemented yet !");
1175	}
1176	}
1177	catch (CNetCdfException& e)
1178	{
1179	StdString msg("On writing the domain : ");
1180	msg.append(domid); msg.append("\n");
1181	msg.append("In the context : ");
1182	msg.append(context->getId()); msg.append("\n");
1183	msg.append(e.what());
1184	ERROR("CNc4DataOutput::writeUnstructuredDomain(CDomain* domain)", << msg);
1185	}
1186	domain->addRelFile(this->filename);
1187	}
1188	//--------------------------------------------------------------
1189
1190	void CNc4DataOutput::writeAxis_(CAxis* axis)
1191	{
1192	if (axis->IsWritten(this->filename)) return;
1193	axis->checkAttributes();
1194
1195	axis->computeWrittenIndex();
1196	axis->computeWrittenCompressedIndex(comm_file);
1197
1198	int size = (MULTI_FILE == SuperClass::type) ? axis->n.getValue()
1199	: axis->n_glo.getValue();
1200
1201	if ((0 == axis->n) && (MULTI_FILE == SuperClass::type)) return;
1202
1203	std::vector<StdString> dims;
1204	StdString axisid = axis->getAxisOutputName();
1205	StdString axisDim, axisBoundsId;
1206	if (isWrittenAxis(axisid)) return ;
1207	else setWrittenAxis(axisid);
1208
1209	nc_type typePrec ;
1210	if (axis->prec.isEmpty()) typePrec = NC_FLOAT ;
1211	else if (axis->prec==4) typePrec = NC_FLOAT ;
1212	else if (axis->prec==8) typePrec = NC_DOUBLE ;
1213
1214	if (!axis->label.isEmpty()) typePrec = NC_CHAR ;
1215	string strId="str_len" ;
1216	try
1217	{
1218	if (axis->dim_name.isEmpty()) axisDim = axisid;
1219	else axisDim=axis->dim_name.getValue();
1220	SuperClassWriter::addDimension(axisDim, size);
1221	dims.push_back(axisDim);
1222
1223	if (!axis->label.isEmpty() && !SuperClassWriter::dimExist(strId)) SuperClassWriter::addDimension(strId, stringArrayLen);
1224
1225	if (axis->hasValue \|\| !axis->label.isEmpty())
1226	{
1227	if (!axis->label.isEmpty()) dims.push_back(strId);
1228
1229	SuperClassWriter::addVariable(axisid, typePrec, dims, compressionLevel);
1230
1231	if (!axis->name.isEmpty())
1232	SuperClassWriter::addAttribute("name", axis->name.getValue(), &axisid);
1233
1234	if (!axis->standard_name.isEmpty())
1235	SuperClassWriter::addAttribute("standard_name", axis->standard_name.getValue(), &axisid);
1236
1237	if (!axis->long_name.isEmpty())
1238	SuperClassWriter::addAttribute("long_name", axis->long_name.getValue(), &axisid);
1239
1240	if (!axis->unit.isEmpty())
1241	SuperClassWriter::addAttribute("units", axis->unit.getValue(), &axisid);
1242
1243	if (!axis->axis_type.isEmpty())
1244	{
1245	switch(axis->axis_type)
1246	{
1247	case CAxis::axis_type_attr::X :
1248	SuperClassWriter::addAttribute("axis", string("X"), &axisid);
1249	break;
1250	case CAxis::axis_type_attr::Y :
1251	SuperClassWriter::addAttribute("axis", string("Y"), &axisid);
1252	break;
1253	case CAxis::axis_type_attr::Z :
1254	SuperClassWriter::addAttribute("axis", string("Z"), &axisid);
1255	break;
1256	case CAxis::axis_type_attr::T :
1257	SuperClassWriter::addAttribute("axis", string("T"), &axisid);
1258	break;
1259	}
1260	}
1261
1262	if (!axis->positive.isEmpty())
1263	{
1264	SuperClassWriter::addAttribute("positive",
1265	(axis->positive == CAxis::positive_attr::up) ? string("up") : string("down"),
1266	&axisid);
1267	}
1268
1269	if (!axis->formula.isEmpty())
1270	SuperClassWriter::addAttribute("formula", axis->formula.getValue(), &axisid);
1271
1272	if (!axis->formula_term.isEmpty())
1273	SuperClassWriter::addAttribute("formula_terms", axis->formula_term.getValue(), &axisid);
1274
1275	axisBoundsId = (axis->bounds_name.isEmpty()) ? axisid + "_bounds" : axis->bounds_name;
1276	if (!axis->bounds.isEmpty() && axis->label.isEmpty())
1277	{
1278	dims.push_back("axis_nbounds");
1279	SuperClassWriter::addVariable(axisBoundsId, typePrec, dims, compressionLevel);
1280	SuperClassWriter::addAttribute("bounds", axisBoundsId, &axisid);
1281
1282	if (!axis->standard_name.isEmpty())
1283	SuperClassWriter::addAttribute("standard_name", axis->standard_name.getValue(), &axisBoundsId);
1284
1285	if (!axis->unit.isEmpty())
1286	SuperClassWriter::addAttribute("units", axis->unit.getValue(), &axisBoundsId);
1287
1288	if (!axis->formula_bounds.isEmpty())
1289	SuperClassWriter::addAttribute("formula", axis->formula_bounds.getValue(), &axisBoundsId);
1290
1291	if (!axis->formula_term_bounds.isEmpty())
1292	SuperClassWriter::addAttribute("formula_terms", axis->formula_term_bounds.getValue(), &axisBoundsId);
1293	}
1294	}
1295
1296	SuperClassWriter::definition_end();
1297
1298	CArray<int, 1>& indexToWrite = axis->localIndexToWriteOnServer;
1299	int nbWritten = indexToWrite.numElements();
1300	CArray<double,1> axis_value(indexToWrite.numElements());
1301	if (!axis->value.isEmpty())
1302	{
1303	for (int i = 0; i < nbWritten; i++)
1304	{
1305	if (indexToWrite(i) < 0)
1306	axis_value(i) = -1; // Some value in case of a hole
1307	else
1308	axis_value(i) = axis->value(indexToWrite(i));
1309	}
1310	}
1311	CArray<double,2> axis_bounds;
1312	CArray<string,1> axis_label;
1313	if (!axis->label.isEmpty())
1314	{
1315	axis_label.resize(indexToWrite.numElements());
1316	for (int i = 0; i < nbWritten; i++)
1317	{
1318	if (indexToWrite(i) < 0)
1319	axis_label(i) = boost::lexical_cast<string>(-1); // Some value in case of a hole
1320	else
1321	axis_label(i) = axis->label(indexToWrite(i));
1322	}
1323	}
1324
1325	switch (SuperClass::type)
1326	{
1327	case MULTI_FILE:
1328	{
1329	if (axis->label.isEmpty())
1330	{
1331	if (!axis->value.isEmpty())
1332	SuperClassWriter::writeData(axis_value, axisid, isCollective, 0);
1333
1334	if (!axis->bounds.isEmpty())
1335	{
1336	axis_bounds.resize(2, indexToWrite.numElements());
1337	for (int i = 0; i < nbWritten; ++i)
1338	{
1339	if (indexToWrite(i) < 0)
1340	{
1341	axis_bounds(0, i) = -1.; // Some value in case of a hole
1342	axis_bounds(1, i) = -1.;
1343	}
1344	else
1345	{
1346	axis_bounds(0, i) = axis->bounds(0, int(indexToWrite(i)));
1347	axis_bounds(1, i) = axis->bounds(1, int(indexToWrite(i)));
1348	}
1349	}
1350	SuperClassWriter::writeData(axis_bounds, axisBoundsId, isCollective, 0);
1351	}
1352	}
1353	else
1354	SuperClassWriter::writeData(axis_label, axisid, isCollective, 0);
1355
1356	SuperClassWriter::definition_start();
1357	break;
1358	}
1359	case ONE_FILE:
1360	{
1361	std::vector<StdSize> start(1), startBounds(2) ;
1362	std::vector<StdSize> count(1), countBounds(2) ;
1363	start[0] = startBounds[0] = axis->begin;
1364	count[0] = countBounds[0] = axis->n;
1365	startBounds[1] = 0;
1366	countBounds[1] = 2;
1367
1368	if (axis->label.isEmpty())
1369	{
1370	if (!axis->value.isEmpty())
1371	SuperClassWriter::writeData(axis_value, axisid, isCollective, 0, &start, &count);
1372
1373	if (!axis->bounds.isEmpty())
1374	{
1375	axis_bounds.resize(2, indexToWrite.numElements());
1376	for (int i = 0; i < nbWritten; ++i)
1377	{
1378	if (indexToWrite(i) < 0)
1379	{
1380	axis_bounds(0, i) = -1.;
1381	axis_bounds(1, i) = -1.;
1382	}
1383	else
1384	{
1385	axis_bounds(0, i) = axis->bounds(0, int(indexToWrite(i)));
1386	axis_bounds(1, i) = axis->bounds(1, int(indexToWrite(i)));
1387	}
1388	}
1389	SuperClassWriter::writeData(axis_bounds, axisBoundsId, isCollective, 0, &startBounds, &countBounds);
1390	}
1391	}
1392	else
1393	{
1394	std::vector<StdSize> startLabel(2), countLabel(2);
1395	startLabel[0] = start[0]; startLabel[1] = 0;
1396	countLabel[0] = count[0]; countLabel[1] = stringArrayLen;
1397	SuperClassWriter::writeData(axis_label, axisid, isCollective, 0, &startLabel, &countLabel);
1398	}
1399
1400	SuperClassWriter::definition_start();
1401
1402	break;
1403	}
1404	default :
1405	ERROR("CNc4DataOutput::writeAxis_(CAxis* axis)",
1406	<< "[ type = " << SuperClass::type << "]"
1407	<< " not implemented yet !");
1408	}
1409	}
1410	catch (CNetCdfException& e)
1411	{
1412	StdString msg("On writing the axis : ");
1413	msg.append(axisid); msg.append("\n");
1414	msg.append("In the context : ");
1415	CContext* context = CContext::getCurrent() ;
1416	msg.append(context->getId()); msg.append("\n");
1417	msg.append(e.what());
1418	ERROR("CNc4DataOutput::writeAxis_(CAxis* axis)", << msg);
1419	}
1420	axis->addRelFile(this->filename);
1421	}
1422
1423	void CNc4DataOutput::writeScalar_(CScalar* scalar)
1424	{
1425	if (scalar->IsWritten(this->filename)) return;
1426	scalar->checkAttributes();
1427	int scalarSize = 1;
1428
1429	StdString scalaId = scalar->getScalarOutputName();
1430	StdString boundsId;
1431	if (isWrittenAxis(scalaId)) return ;
1432	else setWrittenAxis(scalaId);
1433
1434	nc_type typePrec ;
1435	if (scalar->prec.isEmpty()) typePrec = NC_FLOAT ;
1436	else if (scalar->prec==4) typePrec = NC_FLOAT ;
1437	else if (scalar->prec==8) typePrec = NC_DOUBLE ;
1438
1439	if (!scalar->label.isEmpty()) typePrec = NC_CHAR ;
1440	string strId="str_len" ;
1441
1442	try
1443	{
1444	if (!scalar->label.isEmpty() && !SuperClassWriter::dimExist(strId)) SuperClassWriter::addDimension(strId, stringArrayLen);
1445
1446	if (!scalar->value.isEmpty() \|\| !scalar->label.isEmpty())
1447	{
1448	std::vector<StdString> dims;
1449	StdString scalarDim = scalaId;
1450
1451	if (!scalar->label.isEmpty()) dims.push_back(strId);
1452
1453	SuperClassWriter::addVariable(scalaId, typePrec, dims);
1454
1455	if (!scalar->name.isEmpty())
1456	SuperClassWriter::addAttribute("name", scalar->name.getValue(), &scalaId);
1457
1458	if (!scalar->standard_name.isEmpty())
1459	SuperClassWriter::addAttribute("standard_name", scalar->standard_name.getValue(), &scalaId);
1460
1461	if (!scalar->long_name.isEmpty())
1462	SuperClassWriter::addAttribute("long_name", scalar->long_name.getValue(), &scalaId);
1463
1464	if (!scalar->unit.isEmpty())
1465	SuperClassWriter::addAttribute("units", scalar->unit.getValue(), &scalaId);
1466
1467	if (!scalar->axis_type.isEmpty())
1468	{
1469	switch(scalar->axis_type)
1470	{
1471	case CScalar::axis_type_attr::X :
1472	SuperClassWriter::addAttribute("axis", string("X"), &scalaId);
1473	break;
1474	case CScalar::axis_type_attr::Y :
1475	SuperClassWriter::addAttribute("axis", string("Y"), &scalaId);
1476	break;
1477	case CScalar::axis_type_attr::Z :
1478	SuperClassWriter::addAttribute("axis", string("Z"), &scalaId);
1479	break;
1480	case CScalar::axis_type_attr::T :
1481	SuperClassWriter::addAttribute("axis", string("T"), &scalaId);
1482	break;
1483	}
1484	}
1485
1486	if (!scalar->positive.isEmpty())
1487	{
1488	SuperClassWriter::addAttribute("positive",
1489	(scalar->positive == CScalar::positive_attr::up) ? string("up") : string("down"),
1490	&scalaId);
1491	}
1492
1493	if (!scalar->bounds.isEmpty() && scalar->label.isEmpty())
1494	{
1495	dims.clear();
1496	dims.push_back("axis_nbounds");
1497	boundsId = (scalar->bounds_name.isEmpty()) ? (scalaId + "_bounds") : scalar->bounds_name.getValue();
1498	SuperClassWriter::addVariable(boundsId, typePrec, dims);
1499	SuperClassWriter::addAttribute("bounds", boundsId, &scalaId);
1500	}
1501
1502	SuperClassWriter::definition_end();
1503
1504	switch (SuperClass::type)
1505	{
1506	case MULTI_FILE:
1507	{
1508	CArray<double,1> scalarValue(scalarSize);
1509	CArray<string,1> scalarLabel(scalarSize);
1510	CArray<double,1> scalarBounds(scalarSize*2);
1511
1512	if (!scalar->value.isEmpty() && scalar->label.isEmpty())
1513	{
1514	scalarValue(0) = scalar->value;
1515	SuperClassWriter::writeData(scalarValue, scalaId, isCollective, 0);
1516	}
1517
1518	if (!scalar->bounds.isEmpty() && scalar->label.isEmpty())
1519	{
1520	scalarBounds(0) = scalar->bounds(0);
1521	scalarBounds(1) = scalar->bounds(1);
1522	SuperClassWriter::writeData(scalarBounds, boundsId, isCollective, 0);
1523	}
1524
1525	if (!scalar->label.isEmpty())
1526	{
1527	scalarLabel(0) = scalar->label;
1528	SuperClassWriter::writeData(scalarLabel, scalaId, isCollective, 0);
1529	}
1530
1531	SuperClassWriter::definition_start();
1532
1533	break;
1534	}
1535	case ONE_FILE:
1536	{
1537	CArray<double,1> scalarValue(scalarSize);
1538	CArray<string,1> scalarLabel(scalarSize);
1539	CArray<double,1> scalarBounds(scalarSize*2);
1540
1541	std::vector<StdSize> start(1);
1542	std::vector<StdSize> count(1);
1543	start[0] = 0;
1544	count[0] = 1;
1545	if (!scalar->value.isEmpty() && scalar->label.isEmpty())
1546	{
1547	scalarValue(0) = scalar->value;
1548	SuperClassWriter::writeData(scalarValue, scalaId, isCollective, 0, &start, &count);
1549	}
1550	if (!scalar->bounds.isEmpty() && scalar->label.isEmpty())
1551	{
1552	scalarBounds(0) = scalar->bounds(0);
1553	scalarBounds(1) = scalar->bounds(1);
1554	count[0] = 2;
1555	SuperClassWriter::writeData(scalarBounds, boundsId, isCollective, 0, &start, &count);
1556	}
1557	if (!scalar->label.isEmpty())
1558	{
1559	scalarLabel(0) = scalar->label;
1560	count[0] = stringArrayLen;
1561	SuperClassWriter::writeData(scalarLabel, scalaId, isCollective, 0, &start, &count);
1562	}
1563
1564	SuperClassWriter::definition_start();
1565
1566	break;
1567	}
1568	default :
1569	ERROR("CNc4DataOutput::writeAxis_(CAxis* scalar)",
1570	<< "[ type = " << SuperClass::type << "]"
1571	<< " not implemented yet !");
1572	}
1573	}
1574	}
1575	catch (CNetCdfException& e)
1576	{
1577	StdString msg("On writing the scalar : ");
1578	msg.append(scalaId); msg.append("\n");
1579	msg.append("In the context : ");
1580	CContext* context = CContext::getCurrent() ;
1581	msg.append(context->getId()); msg.append("\n");
1582	msg.append(e.what());
1583	ERROR("CNc4DataOutput::writeScalar_(CScalar* scalar)", << msg);
1584	}
1585	scalar->addRelFile(this->filename);
1586	}
1587
1588	//--------------------------------------------------------------
1589
1590	void CNc4DataOutput::writeGridCompressed_(CGrid* grid)
1591	{
1592	if (grid->isScalarGrid() \|\| grid->isWrittenCompressed(this->filename)) return;
1593
1594	try
1595	{
1596	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
1597	std::vector<StdString> domainList = grid->getDomainList();
1598	std::vector<StdString> axisList = grid->getAxisList();
1599	std::vector<StdString> scalarList = grid->getScalarList();
1600	int numElement = axisDomainOrder.numElements(), idxDomain = 0, idxAxis = 0, idxScalar = 0;
1601
1602	std::vector<StdString> dims;
1603
1604	if (grid->isCompressible())
1605	{
1606	StdString varId = grid->getId() + "_points";
1607
1608	int nbIndexes = (SuperClass::type == MULTI_FILE) ? grid->getNumberWrittenIndexes() : grid->getTotalNumberWrittenIndexes();
1609	SuperClassWriter::addDimension(varId, nbIndexes);
1610
1611	dims.push_back(varId);
1612	SuperClassWriter::addVariable(varId, NC_INT, dims);
1613
1614	StdOStringStream compress;
1615	for (int i = numElement - 1; i >= 0; --i)
1616	{
1617	if (2 == axisDomainOrder(i))
1618	{
1619	CDomain* domain = CDomain::get(domainList[domainList.size() - idxDomain - 1]);
1620	StdString domId = domain->getDomainOutputName();
1621	StdString appendDomId = singleDomain ? "" : "_" + domId;
1622
1623	switch (domain->type)
1624	{
1625	case CDomain::type_attr::curvilinear:
1626	compress << "y" << appendDomId << " x" << appendDomId;
1627	break;
1628	case CDomain::type_attr::rectilinear:
1629	compress << "lat" << appendDomId << " lon" << appendDomId;
1630	break;
1631	case CDomain::type_attr::unstructured:
1632	StdString cellName = (!domain->dim_i_name.isEmpty()) ? cellName=domain->dim_i_name : "cell";
1633	compress << cellName << appendDomId;
1634	// compress << "cell" << appendDomId;
1635	break;
1636	}
1637	++idxDomain;
1638	}
1639	else if (1 == axisDomainOrder(i))
1640	{
1641	CAxis* axis = CAxis::get(axisList[axisList.size() - idxAxis - 1]);
1642	compress << axis->getAxisOutputName();
1643	++idxAxis;
1644	}
1645	else
1646	{
1647	CScalar* scalar = CScalar::get(scalarList[scalarList.size() - idxScalar - 1]);
1648	compress << scalar->getScalarOutputName();
1649	++idxScalar;
1650	}
1651
1652	if (i != 0) compress << ' ';
1653	}
1654	SuperClassWriter::addAttribute("compress", compress.str(), &varId);
1655
1656	CArray<int, 1> indexes(grid->getNumberWrittenIndexes());
1657	indexes = grid->localIndexToWriteOnServer;
1658
1659	switch (SuperClass::type)
1660	{
1661	case (MULTI_FILE):
1662	{
1663	SuperClassWriter::writeData(indexes, varId, isCollective, 0);
1664	break;
1665	}
1666	case (ONE_FILE):
1667	{
1668	if (grid->doGridHaveDataDistributed())
1669	grid->getDistributionServer()->computeGlobalIndex(indexes);
1670
1671	std::vector<StdSize> start, count;
1672	start.push_back(grid->getOffsetWrittenIndexes());
1673	count.push_back(grid->getNumberWrittenIndexes());
1674
1675	SuperClassWriter::writeData(indexes, varId, isCollective, 0, &start, &count);
1676	break;
1677	}
1678	}
1679	}
1680	else
1681	{
1682	for (int i = 0; i < numElement; ++i)
1683	{
1684	StdString varId, compress;
1685	CArray<int, 1> indexes;
1686	bool isDistributed;
1687	StdSize nbIndexes, totalNbIndexes, offset;
1688	int firstGlobalIndex;
1689
1690	if (2 == axisDomainOrder(i))
1691	{
1692	CDomain* domain = CDomain::get(domainList[idxDomain]);
1693	StdString domId = domain->getDomainOutputName();
1694
1695	if (!domain->isCompressible()
1696	\|\| domain->type == CDomain::type_attr::unstructured
1697	\|\| domain->isWrittenCompressed(this->filename)
1698	\|\| isWrittenCompressedDomain(domId))
1699	continue;
1700
1701	StdString appendDomId = singleDomain ? "" : "_" + domId;
1702
1703	varId = domId + "_points";
1704	switch (domain->type)
1705	{
1706	case CDomain::type_attr::curvilinear:
1707	compress = "y" + appendDomId + " x" + appendDomId;
1708	break;
1709	case CDomain::type_attr::rectilinear:
1710	compress = "lat" + appendDomId + " lon" + appendDomId;
1711	break;
1712	}
1713
1714	// indexes.resize(domain->compressedIndexToWriteOnServer[comm_file].numElements());
1715	// indexes = domain->compressedIndexToWriteOnServer[com_file];
1716	indexes.resize(domain->getCompressedIndexToWriteOnServer(comm_file).numElements());
1717	indexes = domain->getCompressedIndexToWriteOnServer(comm_file);
1718
1719	isDistributed = domain->isDistributed();
1720	nbIndexes = domain->getNumberWrittenIndexes(comm_file);
1721	totalNbIndexes = domain->getTotalNumberWrittenIndexes(comm_file);
1722	offset = domain->getOffsetWrittenIndexes(comm_file);
1723	firstGlobalIndex = domain->ibegin + domain->jbegin * domain->ni_glo;
1724
1725	domain->addRelFileCompressed(this->filename);
1726	setWrittenCompressedDomain(domId);
1727	++idxDomain;
1728	}
1729	else if (1 == axisDomainOrder(i))
1730	{
1731	CAxis* axis = CAxis::get(axisList[idxAxis]);
1732	StdString axisId = axis->getAxisOutputName();
1733
1734	if (!axis->isCompressible()
1735	\|\| axis->isWrittenCompressed(this->filename)
1736	\|\| isWrittenCompressedAxis(axisId))
1737	continue;
1738
1739	varId = axisId + "_points";
1740	compress = axisId;
1741
1742	// indexes.resize(axis->compressedIndexToWriteOnServer.numElements());
1743	// indexes = axis->compressedIndexToWriteOnServer;
1744
1745	indexes.resize(axis->getCompressedIndexToWriteOnServer(comm_file).numElements());
1746	indexes = axis->getCompressedIndexToWriteOnServer(comm_file);
1747
1748	isDistributed = axis->isDistributed();
1749	nbIndexes = axis->getNumberWrittenIndexes(comm_file);
1750	totalNbIndexes = axis->getTotalNumberWrittenIndexes(comm_file);
1751	offset = axis->getOffsetWrittenIndexes(comm_file);
1752	firstGlobalIndex = axis->begin;
1753
1754	axis->addRelFileCompressed(this->filename);
1755	setWrittenCompressedAxis(axisId);
1756	++idxAxis;
1757	}
1758	else
1759	{
1760	}
1761
1762	if (!varId.empty())
1763	{
1764	SuperClassWriter::addDimension(varId, (SuperClass::type == MULTI_FILE) ? nbIndexes : totalNbIndexes);
1765
1766	dims.clear();
1767	dims.push_back(varId);
1768	SuperClassWriter::addVariable(varId, NC_INT, dims);
1769
1770	SuperClassWriter::addAttribute("compress", compress, &varId);
1771
1772	switch (SuperClass::type)
1773	{
1774	case (MULTI_FILE):
1775	{
1776	indexes -= firstGlobalIndex;
1777	SuperClassWriter::writeData(indexes, varId, isCollective, 0);
1778	break;
1779	}
1780	case (ONE_FILE):
1781	{
1782	std::vector<StdSize> start, count;
1783	start.push_back(offset);
1784	count.push_back(nbIndexes);
1785
1786	SuperClassWriter::writeData(indexes, varId, isCollective, 0, &start, &count);
1787	break;
1788	}
1789	}
1790	}
1791	}
1792	}
1793
1794	grid->addRelFileCompressed(this->filename);
1795	}
1796	catch (CNetCdfException& e)
1797	{
1798	StdString msg("On writing compressed grid : ");
1799	msg.append(grid->getId()); msg.append("\n");
1800	msg.append("In the context : ");
1801	CContext* context = CContext::getCurrent();
1802	msg.append(context->getId()); msg.append("\n");
1803	msg.append(e.what());
1804	ERROR("CNc4DataOutput::writeGridCompressed_(CGrid* grid)", << msg);
1805	}
1806	}
1807
1808	//--------------------------------------------------------------
1809
1810	void CNc4DataOutput::writeTimeDimension_(void)
1811	{
1812	try
1813	{
1814	SuperClassWriter::addDimension(getTimeCounterName());
1815	}
1816	catch (CNetCdfException& e)
1817	{
1818	StdString msg("On writing time dimension : time_couter\n");
1819	msg.append("In the context : ");
1820	CContext* context = CContext::getCurrent() ;
1821	msg.append(context->getId()); msg.append("\n");
1822	msg.append(e.what());
1823	ERROR("CNc4DataOutput::writeTimeDimension_(void)", << msg);
1824	}
1825	}
1826
1827	//--------------------------------------------------------------
1828
1829	void CNc4DataOutput::writeField_(CField* field)
1830	{
1831	CContext* context = CContext::getCurrent() ;
1832	CContextServer* server=context->server ;
1833
1834	std::vector<StdString> dims, coodinates;
1835	CGrid* grid = field->grid;
1836	if (!grid->doGridHaveDataToWrite())
1837	if (SuperClass::type==MULTI_FILE) return ;
1838
1839	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
1840	int numElement = axisDomainOrder.numElements(), idxDomain = 0, idxAxis = 0, idxScalar = 0;
1841	std::vector<StdString> domainList = grid->getDomainList();
1842	std::vector<StdString> axisList = grid->getAxisList();
1843	std::vector<StdString> scalarList = grid->getScalarList();
1844
1845	StdString timeid = getTimeCounterName();
1846	StdString dimXid,dimYid;
1847	std::deque<StdString> dimIdList, dimCoordList;
1848	bool hasArea = false;
1849	StdString cellMeasures = "area:";
1850	bool compressedOutput = !field->indexed_output.isEmpty() && field->indexed_output;
1851
1852	for (int i = 0; i < numElement; ++i)
1853	{
1854	if (2 == axisDomainOrder(i))
1855	{
1856	CDomain* domain = CDomain::get(domainList[idxDomain]);
1857	StdString domId = domain->getDomainOutputName();
1858	StdString appendDomId = singleDomain ? "" : "_" + domId ;
1859	StdString lonName,latName ;
1860	StdString dimIname,dimJname ;
1861
1862	if (domain->lon_name.isEmpty())
1863	{
1864	if (domain->type==CDomain::type_attr::curvilinear) lonName = "nav_lon";
1865	else lonName = "lon";
1866	}
1867	else lonName = domain->lon_name;
1868
1869	if (domain->lat_name.isEmpty())
1870	{
1871	if (domain->type==CDomain::type_attr::curvilinear) latName = "nav_lat";
1872	else latName = "lat";
1873	}
1874	else latName = domain->lat_name;
1875
1876	if (domain->dim_i_name.isEmpty())
1877	{
1878	if (domain->type==CDomain::type_attr::curvilinear) dimIname = "x";
1879	else if (domain->type==CDomain::type_attr::unstructured) dimIname = "cell";
1880	else dimIname = lonName;
1881	}
1882	else dimIname = domain->dim_i_name;
1883
1884	if (domain->dim_j_name.isEmpty())
1885	{
1886	if (domain->type==CDomain::type_attr::curvilinear) dimJname = "y";
1887	else dimJname = latName;
1888	}
1889	else dimJname = domain->dim_j_name;
1890
1891	if (compressedOutput && domain->isCompressible() && domain->type != CDomain::type_attr::unstructured)
1892	{
1893	dimIdList.push_back(domId + "_points");
1894	field->setUseCompressedOutput();
1895	}
1896
1897	switch (domain->type)
1898	{
1899	case CDomain::type_attr::curvilinear:
1900	if (!compressedOutput \|\| !domain->isCompressible())
1901	{
1902	dimXid=dimIname+appendDomId;
1903	dimYid=dimJname+appendDomId;
1904	dimIdList.push_back(dimXid);
1905	dimIdList.push_back(dimYid);
1906	}
1907	dimCoordList.push_back(lonName+appendDomId);
1908	dimCoordList.push_back(latName+appendDomId);
1909	break ;
1910	case CDomain::type_attr::rectilinear:
1911	if (!compressedOutput \|\| !domain->isCompressible())
1912	{
1913	dimXid = dimIname+appendDomId;
1914	dimYid = dimJname+appendDomId;
1915	dimIdList.push_back(dimXid);
1916	dimIdList.push_back(dimYid);
1917	}
1918	if (lonName != dimIname) dimCoordList.push_back(lonName+appendDomId);
1919	if (latName != dimJname) dimCoordList.push_back(latName+appendDomId);
1920
1921	break ;
1922	case CDomain::type_attr::unstructured:
1923	{
1924	if (SuperClassWriter::useCFConvention)
1925	{
1926	dimXid = dimIname + appendDomId;
1927	dimIdList.push_back(dimXid);
1928	dimCoordList.push_back(lonName+appendDomId);
1929	dimCoordList.push_back(latName+appendDomId);
1930	}
1931	else
1932	{
1933	StdString domainName = domain->name;
1934	if (domain->nvertex == 1)
1935	{
1936	dimXid = "n" + domainName + "_node";
1937	dimIdList.push_back(dimXid);
1938	dimCoordList.push_back(StdString(domainName + "_node_x"));
1939	dimCoordList.push_back(StdString(domainName + "_node_y"));
1940	}
1941	else if (domain->nvertex == 2)
1942	{
1943	dimXid = "n" + domainName + "_edge";
1944	dimIdList.push_back(dimXid);
1945	dimCoordList.push_back(StdString(domainName + "_edge_x"));
1946	dimCoordList.push_back(StdString(domainName + "_edge_y"));
1947	}
1948	else
1949	{
1950	dimXid = "n" + domainName + "_face";
1951	dimIdList.push_back(dimXid);
1952	dimCoordList.push_back(StdString(domainName + "_face_x"));
1953	dimCoordList.push_back(StdString(domainName + "_face_y"));
1954	}
1955	} // ugrid convention
1956	} // case unstructured domain
1957	}
1958
1959	if (domain->hasArea)
1960	{
1961	hasArea = true;
1962	cellMeasures += " area" + appendDomId;
1963	}
1964	++idxDomain;
1965	}
1966	else if (1 == axisDomainOrder(i))
1967	{
1968	CAxis* axis = CAxis::get(axisList[idxAxis]);
1969	StdString axisId = axis->getAxisOutputName();
1970	StdString axisDim;
1971
1972	if (axis->dim_name.isEmpty()) axisDim = axisId;
1973	else axisDim=axis->dim_name.getValue();
1974
1975	if (compressedOutput && axis->isCompressible())
1976	{
1977	dimIdList.push_back(axisDim + "_points");
1978	field->setUseCompressedOutput();
1979	}
1980	else
1981	dimIdList.push_back(axisDim);
1982
1983	if (axisDim != axisId) dimCoordList.push_back(axisId);
1984	++idxAxis;
1985	}
1986	else
1987	{
1988	CScalar* scalar = CScalar::get(scalarList[idxScalar]);
1989	StdString scalarId = scalar->getScalarOutputName();
1990	if (!scalar->value.isEmpty() \|\| !scalar->label.isEmpty())
1991	dimCoordList.push_back(scalarId);
1992	++idxScalar;
1993	}
1994	}
1995
1996	StdString fieldid = field->getFieldOutputName();
1997
1998	nc_type type ;
1999	if (field->prec.isEmpty()) type = NC_FLOAT ;
2000	else
2001	{
2002	if (field->prec==2) type = NC_SHORT ;
2003	else if (field->prec==4) type = NC_FLOAT ;
2004	else if (field->prec==8) type = NC_DOUBLE ;
2005	}
2006
2007	bool wtime = !(!field->operation.isEmpty() && field->getOperationTimeType() == func::CFunctor::once);
2008
2009	if (wtime)
2010	{
2011	if (field->hasTimeInstant && hasTimeInstant) coodinates.push_back(string("time_instant"));
2012	else if (field->hasTimeCentered && hasTimeCentered) coodinates.push_back(string("time_centered"));
2013	dims.push_back(timeid);
2014	}
2015
2016	if (compressedOutput && grid->isCompressible())
2017	{
2018	dims.push_back(grid->getId() + "_points");
2019	field->setUseCompressedOutput();
2020	}
2021	else
2022	{
2023	while (!dimIdList.empty())
2024	{
2025	dims.push_back(dimIdList.back());
2026	dimIdList.pop_back();
2027	}
2028	}
2029
2030	while (!dimCoordList.empty())
2031	{
2032	coodinates.push_back(dimCoordList.back());
2033	dimCoordList.pop_back();
2034	}
2035
2036	try
2037	{
2038	SuperClassWriter::addVariable(fieldid, type, dims);
2039
2040	if (!field->standard_name.isEmpty())
2041	SuperClassWriter::addAttribute
2042	("standard_name", field->standard_name.getValue(), &fieldid);
2043
2044	if (!field->long_name.isEmpty())
2045	SuperClassWriter::addAttribute
2046	("long_name", field->long_name.getValue(), &fieldid);
2047
2048	if (!field->unit.isEmpty())
2049	SuperClassWriter::addAttribute
2050	("units", field->unit.getValue(), &fieldid);
2051
2052	// Ugrid field attributes "mesh" and "location"
2053	if (!SuperClassWriter::useCFConvention)
2054	{
2055	if (!domainList.empty())
2056	{
2057	CDomain* domain = CDomain::get(domainList[0]); // Suppose that we have only domain
2058	StdString mesh = domain->name;
2059	SuperClassWriter::addAttribute("mesh", mesh, &fieldid);
2060	StdString location;
2061	if (domain->nvertex == 1)
2062	location = "node";
2063	else if (domain->nvertex == 2)
2064	location = "edge";
2065	else if (domain->nvertex > 2)
2066	location = "face";
2067	SuperClassWriter::addAttribute("location", location, &fieldid);
2068	}
2069
2070	}
2071
2072	if (!field->valid_min.isEmpty())
2073	SuperClassWriter::addAttribute
2074	("valid_min", field->valid_min.getValue(), &fieldid);
2075
2076	if (!field->valid_max.isEmpty())
2077	SuperClassWriter::addAttribute
2078	("valid_max", field->valid_max.getValue(), &fieldid);
2079
2080	if (!field->scale_factor.isEmpty())
2081	SuperClassWriter::addAttribute
2082	("scale_factor", field->scale_factor.getValue(), &fieldid);
2083
2084	if (!field->add_offset.isEmpty())
2085	SuperClassWriter::addAttribute
2086	("add_offset", field->add_offset.getValue(), &fieldid);
2087
2088	SuperClassWriter::addAttribute
2089	("online_operation", field->operation.getValue(), &fieldid);
2090
2091	// write child variables as attributes
2092
2093
2094	bool alreadyAddCellMethod = false;
2095	StdString cellMethodsPrefix(""), cellMethodsSuffix("");
2096	if (!field->cell_methods.isEmpty())
2097	{
2098	StdString cellMethodString = field->cell_methods;
2099	if (field->cell_methods_mode.isEmpty() \|\|
2100	(CField::cell_methods_mode_attr::overwrite == field->cell_methods_mode))
2101	{
2102	SuperClassWriter::addAttribute("cell_methods", cellMethodString, &fieldid);
2103	alreadyAddCellMethod = true;
2104	}
2105	else
2106	{
2107	switch (field->cell_methods_mode)
2108	{
2109	case (CField::cell_methods_mode_attr::prefix):
2110	cellMethodsPrefix = cellMethodString;
2111	cellMethodsPrefix += " ";
2112	break;
2113	case (CField::cell_methods_mode_attr::suffix):
2114	cellMethodsSuffix = " ";
2115	cellMethodsSuffix += cellMethodString;
2116	break;
2117	case (CField::cell_methods_mode_attr::none):
2118	break;
2119	default:
2120	break;
2121	}
2122	}
2123	}
2124
2125
2126	if (wtime)
2127	{
2128	CDuration freqOp = field->freq_op.getValue();
2129	freqOp.solveTimeStep(*context->calendar);
2130	StdString freqOpStr = freqOp.toStringUDUnits();
2131	SuperClassWriter::addAttribute("interval_operation", freqOpStr, &fieldid);
2132
2133	CDuration freqOut = field->getRelFile()->output_freq.getValue();
2134	freqOut.solveTimeStep(*context->calendar);
2135	SuperClassWriter::addAttribute("interval_write", freqOut.toStringUDUnits(), &fieldid);
2136
2137	StdString cellMethods(cellMethodsPrefix + "time: ");
2138	if (field->operation.getValue() == "instant") cellMethods += "point";
2139	else if (field->operation.getValue() == "average") cellMethods += "mean";
2140	else if (field->operation.getValue() == "accumulate") cellMethods += "sum";
2141	else cellMethods += field->operation;
2142	if (freqOp.resolve(context->calendar) != freqOut.resolve(context->calendar))
2143	cellMethods += " (interval: " + freqOpStr + ")";
2144	cellMethods += cellMethodsSuffix;
2145	if (!alreadyAddCellMethod)
2146	SuperClassWriter::addAttribute("cell_methods", cellMethods, &fieldid);
2147	}
2148
2149	if (hasArea)
2150	SuperClassWriter::addAttribute("cell_measures", cellMeasures, &fieldid);
2151
2152	if (!field->default_value.isEmpty())
2153	{
2154	double default_value = field->default_value.getValue();
2155	if (type == NC_DOUBLE)
2156	{
2157	SuperClassWriter::setDefaultValue(fieldid, &default_value);
2158	}
2159	else if (type == NC_SHORT)
2160	{
2161	short sdefault_value = (short)default_value;
2162	SuperClassWriter::setDefaultValue(fieldid, &sdefault_value);
2163	}
2164	else
2165	{
2166	float fdefault_value = (float)default_value;
2167	SuperClassWriter::setDefaultValue(fieldid, &fdefault_value);
2168	}
2169	}
2170	else
2171	SuperClassWriter::setDefaultValue(fieldid, (double*)NULL);
2172
2173	if (field->compression_level.isEmpty())
2174	field->compression_level = field->file->compression_level.isEmpty() ? 0 : field->file->compression_level;
2175	SuperClassWriter::setCompressionLevel(fieldid, field->compression_level);
2176
2177	{ // Ecriture des coordonnes
2178
2179	StdString coordstr; //boost::algorithm::join(coodinates, " ")
2180	std::vector<StdString>::iterator
2181	itc = coodinates.begin(), endc = coodinates.end();
2182
2183	for (; itc!= endc; itc++)
2184	{
2185	StdString & coord = *itc;
2186	if (itc+1 != endc)
2187	coordstr.append(coord).append(" ");
2188	else coordstr.append(coord);
2189	}
2190
2191	SuperClassWriter::addAttribute("coordinates", coordstr, &fieldid);
2192
2193	}
2194
2195	vector<CVariable*> listVars = field->getAllVariables() ;
2196	for (vector<CVariable>::iterator it = listVars.begin() ;it != listVars.end(); it++) writeAttribute_(it, fieldid) ;
2197
2198	}
2199	catch (CNetCdfException& e)
2200	{
2201	StdString msg("On writing field : ");
2202	msg.append(fieldid); msg.append("\n");
2203	msg.append("In the context : ");
2204	msg.append(context->getId()); msg.append("\n");
2205	msg.append(e.what());
2206	ERROR("CNc4DataOutput::writeField_(CField* field)", << msg);
2207	}
2208	} // writeField_()
2209
2210	//--------------------------------------------------------------
2211
2212	void CNc4DataOutput::writeFile_ (CFile* file)
2213	{
2214	StdString filename = file->getFileOutputName();
2215	StdString description = (!file->description.isEmpty())
2216	? file->description.getValue()
2217	: StdString("Created by xios");
2218
2219	singleDomain = (file->nbDomains == 1);
2220
2221	StdString conv_str ;
2222	if (file->convention_str.isEmpty())
2223	{
2224	if (SuperClassWriter::useCFConvention) conv_str="CF-1.6" ;
2225	else conv_str="UGRID" ;
2226	}
2227	else conv_str=file->convention_str ;
2228
2229	try
2230	{
2231	if (!appendMode) this->writeFileAttributes(filename, description,
2232	conv_str,
2233	StdString("An IPSL model"),
2234	this->getTimeStamp());
2235
2236	if (!appendMode)
2237	SuperClassWriter::addDimension("axis_nbounds", 2);
2238	}
2239	catch (CNetCdfException& e)
2240	{
2241	StdString msg("On writing file : ");
2242	msg.append(filename); msg.append("\n");
2243	msg.append("In the context : ");
2244	CContext* context = CContext::getCurrent() ;
2245	msg.append(context->getId()); msg.append("\n");
2246	msg.append(e.what());
2247	ERROR("CNc4DataOutput::writeFile_ (CFile* file)", << msg);
2248	}
2249	}
2250
2251	void CNc4DataOutput::writeAttribute_ (CVariable* var, const string& fieldId)
2252	{
2253	StdString name = var->getVariableOutputName();
2254
2255	try
2256	{
2257	if (var->type.getValue() == CVariable::type_attr::t_int \|\| var->type.getValue() == CVariable::type_attr::t_int32)
2258	addAttribute(name, var->getData<int>(), &fieldId);
2259	else if (var->type.getValue() == CVariable::type_attr::t_int16)
2260	addAttribute(name, var->getData<short int>(), &fieldId);
2261	else if (var->type.getValue() == CVariable::type_attr::t_float)
2262	addAttribute(name, var->getData<float>(), &fieldId);
2263	else if (var->type.getValue() == CVariable::type_attr::t_double)
2264	addAttribute(name, var->getData<double>(), &fieldId);
2265	else if (var->type.getValue() == CVariable::type_attr::t_string)
2266	addAttribute(name, var->getData<string>(), &fieldId);
2267	else
2268	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var, const string& fieldId)",
2269	<< "Unsupported variable of type " << var->type.getStringValue());
2270	}
2271	catch (CNetCdfException& e)
2272	{
2273	StdString msg("On writing attributes of variable with name : ");
2274	msg.append(name); msg.append("in the field "); msg.append(fieldId); msg.append("\n");
2275	msg.append("In the context : ");
2276	CContext* context = CContext::getCurrent() ;
2277	msg.append(context->getId()); msg.append("\n");
2278	msg.append(e.what());
2279	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var, const string& fieldId)", << msg);
2280	}
2281	}
2282
2283	void CNc4DataOutput::writeAttribute_ (CVariable* var)
2284	{
2285	StdString name = var->getVariableOutputName();
2286
2287	try
2288	{
2289	if (var->type.getValue() == CVariable::type_attr::t_int \|\| var->type.getValue() == CVariable::type_attr::t_int32)
2290	addAttribute(name, var->getData<int>());
2291	else if (var->type.getValue() == CVariable::type_attr::t_int16)
2292	addAttribute(name, var->getData<short int>());
2293	else if (var->type.getValue() == CVariable::type_attr::t_float)
2294	addAttribute(name, var->getData<float>());
2295	else if (var->type.getValue() == CVariable::type_attr::t_double)
2296	addAttribute(name, var->getData<double>());
2297	else if (var->type.getValue() == CVariable::type_attr::t_string)
2298	addAttribute(name, var->getData<string>());
2299	else
2300	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var)",
2301	<< "Unsupported variable of type " << var->type.getStringValue());
2302	}
2303	catch (CNetCdfException& e)
2304	{
2305	StdString msg("On writing attributes of variable with name : ");
2306	msg.append(name); msg.append("\n");
2307	msg.append("In the context : ");
2308	CContext* context = CContext::getCurrent() ;
2309	msg.append(context->getId()); msg.append("\n");
2310	msg.append(e.what());
2311	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var)", << msg);
2312	}
2313	}
2314
2315	void CNc4DataOutput::syncFile_ (void)
2316	{
2317	try
2318	{
2319	SuperClassWriter::sync() ;
2320	}
2321	catch (CNetCdfException& e)
2322	{
2323	StdString msg("On synchronizing the write among processes");
2324	msg.append("In the context : ");
2325	CContext* context = CContext::getCurrent() ;
2326	msg.append(context->getId()); msg.append("\n");
2327	msg.append(e.what());
2328	ERROR("CNc4DataOutput::syncFile_ (void)", << msg);
2329	}
2330	}
2331
2332	void CNc4DataOutput::closeFile_ (void)
2333	{
2334	try
2335	{
2336	SuperClassWriter::close() ;
2337	}
2338	catch (CNetCdfException& e)
2339	{
2340	StdString msg("On closing file");
2341	msg.append("In the context : ");
2342	CContext* context = CContext::getCurrent() ;
2343	msg.append(context->getId()); msg.append("\n");
2344	msg.append(e.what());
2345	ERROR("CNc4DataOutput::syncFile_ (void)", << msg);
2346	}
2347
2348	}
2349
2350	//---------------------------------------------------------------
2351
2352	StdString CNc4DataOutput::getTimeStamp(void) const
2353	{
2354	const int buffer_size = 100;
2355	time_t rawtime;
2356	struct tm * timeinfo = NULL;
2357	char buffer [buffer_size];
2358	StdString formatStr;
2359	if (file->time_stamp_format.isEmpty()) formatStr="%Y-%b-%d %H:%M:%S %Z" ;
2360	else formatStr=file->time_stamp_format;
2361
2362	// time ( &rawtime );
2363	// timeinfo = localtime ( &rawtime );
2364	time ( &rawtime );
2365	timeinfo = gmtime ( &rawtime );
2366	strftime (buffer, buffer_size, formatStr.c_str(), timeinfo);
2367
2368	return (StdString(buffer));
2369	}
2370
2371	//---------------------------------------------------------------
2372
2373	void CNc4DataOutput::writeFieldData_ (CField* field)
2374	{
2375	CContext* context = CContext::getCurrent();
2376	CContextServer* server = context->server;
2377	CGrid* grid = field->grid;
2378
2379	if (field->getNStep()<1)
2380	{
2381	return;
2382	}
2383
2384	if (!grid->doGridHaveDataToWrite())
2385	if (SuperClass::type == MULTI_FILE \|\| !isCollective)
2386	{
2387	return;
2388	}
2389
2390	StdString fieldid = field->getFieldOutputName();
2391
2392	StdOStringStream oss;
2393	string timeAxisId;
2394	if (field->hasTimeInstant) timeAxisId = "time_instant";
2395	else if (field->hasTimeCentered) timeAxisId = "time_centered";
2396
2397	StdString timeBoundId = getTimeCounterName() + "_bounds";
2398
2399	StdString timeAxisBoundId;
2400	if (field->hasTimeInstant) timeAxisBoundId = "time_instant_bounds";
2401	else if (field->hasTimeCentered) timeAxisBoundId = "time_centered_bounds";
2402
2403	if (!field->wasWritten())
2404	{
2405	if (appendMode && field->file->record_offset.isEmpty() &&
2406	field->getOperationTimeType() != func::CFunctor::once)
2407	{
2408	double factorUnit;
2409	if (!field->file->time_units.isEmpty() && field->file->time_units==CFile::time_units_attr::days)
2410	factorUnit=context->getCalendar()->getDayLengthInSeconds() ;
2411	else factorUnit=1 ;
2412	field->resetNStep(getRecordFromTime(field->last_Write_srv,factorUnit) + 1);
2413	}
2414
2415	field->setWritten();
2416	}
2417
2418
2419	CArray<double,1> time_data(1);
2420	CArray<double,1> time_data_bound(2);
2421	CArray<double,1> time_counter(1);
2422	CArray<double,1> time_counter_bound(2);
2423
2424	bool wtime = (field->getOperationTimeType() != func::CFunctor::once);
2425	bool wtimeCounter =false ;
2426	bool wtimeData =false ;
2427
2428
2429	if (wtime)
2430	{
2431	Time lastWrite = field->last_Write_srv;
2432	Time lastLastWrite = field->lastlast_Write_srv;
2433
2434
2435	if (field->hasTimeInstant)
2436	{
2437	time_data(0) = time_data_bound(1) = lastWrite;
2438	time_data_bound(0) = time_data_bound(1) = lastWrite;
2439	if (timeCounterType==instant)
2440	{
2441	time_counter(0) = time_data(0);
2442	time_counter_bound(0) = time_data_bound(0);
2443	time_counter_bound(1) = time_data_bound(1);
2444	wtimeCounter=true ;
2445	}
2446	if (hasTimeInstant) wtimeData=true ;
2447	}
2448	else if (field->hasTimeCentered)
2449	{
2450	time_data(0) = (lastWrite + lastLastWrite) / 2;
2451	time_data_bound(0) = lastLastWrite;
2452	time_data_bound(1) = lastWrite;
2453	if (timeCounterType==centered)
2454	{
2455	time_counter(0) = time_data(0) ;
2456	time_counter_bound(0) = time_data_bound(0) ;
2457	time_counter_bound(1) = time_data_bound(1) ;
2458	wtimeCounter=true ;
2459	}
2460	if (hasTimeCentered) wtimeData=true ;
2461	}
2462
2463	if (timeCounterType==record)
2464	{
2465	time_counter(0) = field->getNStep() - 1;
2466	time_counter_bound(0) = time_counter_bound(1) = field->getNStep() - 1;
2467	wtimeCounter=true ;
2468	}
2469
2470	if (!field->file->time_units.isEmpty() && field->file->time_units==CFile::time_units_attr::days)
2471	{
2472	double secByDay=context->getCalendar()->getDayLengthInSeconds() ;
2473	time_data/=secByDay;
2474	time_data_bound/=secByDay;
2475	time_counter/=secByDay;
2476	time_counter_bound/=secByDay;
2477	}
2478	}
2479
2480	int commRank ;
2481	MPI_Comm_rank(comm_file,&commRank) ;
2482	bool isRoot = (commRank == 0);
2483
2484	if (!field->scale_factor.isEmpty() \|\| !field->add_offset.isEmpty())
2485	{
2486	double scaleFactor = 1.0;
2487	double addOffset = 0.0;
2488	if (!field->scale_factor.isEmpty()) scaleFactor = field->scale_factor;
2489	if (!field->add_offset.isEmpty()) addOffset = field->add_offset;
2490	field->scaleFactorAddOffset(scaleFactor, addOffset);
2491	}
2492
2493	try
2494	{
2495	size_t writtenSize;
2496	if (field->getUseCompressedOutput())
2497	writtenSize = grid->getNumberWrittenIndexes();
2498	else
2499	writtenSize = grid->getWrittenDataSize();
2500
2501	CArray<double,1> fieldData(writtenSize);
2502	if (!field->default_value.isEmpty()) fieldData = field->default_value;
2503
2504	if (field->getUseCompressedOutput())
2505	field->outputCompressedField(fieldData);
2506	else
2507	field->outputField(fieldData);
2508
2509	if (!field->prec.isEmpty() && field->prec == 2) fieldData = round(fieldData);
2510
2511	switch (SuperClass::type)
2512	{
2513	case (MULTI_FILE) :
2514	{
2515	CTimer::get("Files : writing data").resume();
2516	SuperClassWriter::writeData(fieldData, fieldid, isCollective, field->getNStep() - 1);
2517	CTimer::get("Files : writing data").suspend();
2518	if (wtime)
2519	{
2520	CTimer::get("Files : writing time axis").resume();
2521	if ( wtimeData)
2522	{
2523	SuperClassWriter::writeTimeAxisData(time_data, timeAxisId, isCollective, field->getNStep() - 1, isRoot);
2524	SuperClassWriter::writeTimeAxisDataBounds(time_data_bound, timeAxisBoundId, isCollective, field->getNStep() - 1, isRoot);
2525	}
2526	if (wtimeCounter)
2527	{
2528	SuperClassWriter::writeTimeAxisData(time_counter, getTimeCounterName(), isCollective, field->getNStep() - 1,isRoot);
2529	if (timeCounterType!=record) SuperClassWriter::writeTimeAxisDataBounds(time_counter_bound, timeBoundId, isCollective, field->getNStep() - 1, isRoot);
2530	}
2531	CTimer::get("Files : writing time axis").suspend();
2532	}
2533	break;
2534	}
2535	case (ONE_FILE) :
2536	{
2537
2538	std::vector<StdSize> start, count;
2539
2540	if (field->getUseCompressedOutput())
2541	{
2542	if (grid->isCompressible())
2543	{
2544	start.push_back(grid->getOffsetWrittenIndexes());
2545	count.push_back(grid->getNumberWrittenIndexes());
2546	}
2547	else
2548	{
2549	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
2550	std::vector<StdString> domainList = grid->getDomainList();
2551	std::vector<StdString> axisList = grid->getAxisList();
2552	int numElement = axisDomainOrder.numElements();
2553	int idxDomain = domainList.size() - 1, idxAxis = axisList.size() - 1;
2554	int idx = domainList.size() * 2 + axisList.size() - 1;
2555
2556	start.reserve(idx+1);
2557	count.reserve(idx+1);
2558
2559	for (int i = numElement - 1; i >= 0; --i)
2560	{
2561	if (2 == axisDomainOrder(i))
2562	{
2563	CDomain* domain = CDomain::get(domainList[idxDomain]);
2564
2565	if (domain->isCompressible())
2566	{
2567	start.push_back(domain->getOffsetWrittenIndexes(comm_file));
2568	count.push_back(domain->getNumberWrittenIndexes(comm_file));
2569	idx -= 2;
2570	}
2571	else
2572	{
2573	if ((domain->type) != CDomain::type_attr::unstructured)
2574	{
2575	start.push_back(domain->jbegin);
2576	count.push_back(domain->nj);
2577	}
2578	--idx;
2579	start.push_back(domain->ibegin);
2580	count.push_back(domain->ni);
2581	--idx;
2582	}
2583	--idxDomain;
2584	}
2585	else if (1 == axisDomainOrder(i))
2586	{
2587	CAxis* axis = CAxis::get(axisList[idxAxis]);
2588
2589	if (axis->isCompressible())
2590	{
2591	start.push_back(axis->getOffsetWrittenIndexes(comm_file));
2592	count.push_back(axis->getNumberWrittenIndexes(comm_file));
2593	}
2594	else
2595	{
2596	start.push_back(axis->begin);
2597	count.push_back(axis->n);
2598	}
2599	--idxAxis;
2600	--idx;
2601	}
2602	}
2603	}
2604	}
2605	else
2606	{
2607	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
2608	std::vector<StdString> domainList = grid->getDomainList();
2609	std::vector<StdString> axisList = grid->getAxisList();
2610	int numElement = axisDomainOrder.numElements();
2611	int idxDomain = domainList.size() - 1, idxAxis = axisList.size() - 1;
2612	int idx = domainList.size() * 2 + axisList.size() - 1;
2613
2614	start.reserve(idx+1);
2615	count.reserve(idx+1);
2616
2617	for (int i = numElement - 1; i >= 0; --i)
2618	{
2619	if (2 == axisDomainOrder(i))
2620	{
2621	CDomain* domain = CDomain::get(domainList[idxDomain]);
2622	if ((domain->type) != CDomain::type_attr::unstructured)
2623	{
2624	start.push_back(domain->jbegin);
2625	count.push_back(domain->nj);
2626	}
2627	--idx ;
2628
2629	start.push_back(domain->ibegin);
2630	count.push_back(domain->ni);
2631	--idx ;
2632	--idxDomain;
2633	}
2634	else if (1 == axisDomainOrder(i))
2635	{
2636	CAxis* axis = CAxis::get(axisList[idxAxis]);
2637	start.push_back(axis->begin);
2638	count.push_back(axis->n);
2639	--idx;
2640	--idxAxis;
2641	}
2642	else
2643	{
2644	if (1 == axisDomainOrder.numElements())
2645	{
2646	start.push_back(0);
2647	count.push_back(1);
2648	}
2649	--idx;
2650	}
2651	}
2652	}
2653
2654
2655	CTimer::get("Files : writing data").resume();
2656	SuperClassWriter::writeData(fieldData, fieldid, isCollective, field->getNStep() - 1, &start, &count);
2657	CTimer::get("Files : writing data").suspend();
2658
2659	if (wtime)
2660	{
2661	CTimer::get("Files : writing time axis").resume();
2662	if ( wtimeData)
2663	{
2664	SuperClassWriter::writeTimeAxisData(time_data, timeAxisId, isCollective, field->getNStep() - 1, isRoot);
2665	SuperClassWriter::writeTimeAxisDataBounds(time_data_bound, timeAxisBoundId, isCollective, field->getNStep() - 1, isRoot);
2666	}
2667	if (wtimeCounter)
2668	{
2669	SuperClassWriter::writeTimeAxisData(time_counter, getTimeCounterName(), isCollective, field->getNStep() - 1,isRoot);
2670	if (timeCounterType!=record) SuperClassWriter::writeTimeAxisDataBounds(time_counter_bound, timeBoundId, isCollective, field->getNStep() - 1, isRoot);
2671
2672	}
2673	CTimer::get("Files : writing time axis").suspend();
2674	}
2675
2676	break;
2677	}
2678	}
2679	}
2680	catch (CNetCdfException& e)
2681	{
2682	StdString msg("On writing field data: ");
2683	msg.append(fieldid); msg.append("\n");
2684	msg.append("In the context : ");
2685	msg.append(context->getId()); msg.append("\n");
2686	msg.append(e.what());
2687	ERROR("CNc4DataOutput::writeFieldData_ (CField* field)", << msg);
2688	}
2689	}
2690
2691	//---------------------------------------------------------------
2692
2693	void CNc4DataOutput::writeTimeAxis_
2694	(CField* field,
2695	const std::shared_ptr<CCalendar> cal)
2696	{
2697	StdOStringStream oss;
2698	bool createInstantAxis=false ;
2699	bool createCenteredAxis=false ;
2700	bool createTimeCounterAxis=false ;
2701
2702	if (field->getOperationTimeType() == func::CFunctor::once) return ;
2703
2704
2705	StdString axisId ;
2706	StdString axisBoundId;
2707	StdString timeid(getTimeCounterName());
2708	StdString timeBoundId("axis_nbounds");
2709
2710	StdString strTimeUnits ;
2711	if (!field->file->time_units.isEmpty() && field->file->time_units==CFile::time_units_attr::days) strTimeUnits="days since " ;
2712	else strTimeUnits="seconds since " ;
2713
2714	if (field->getOperationTimeType() == func::CFunctor::instant) field->hasTimeInstant = true;
2715	if (field->getOperationTimeType() == func::CFunctor::centered) field->hasTimeCentered = true;
2716
2717
2718	if (field->file->time_counter.isEmpty())
2719	{
2720	if (timeCounterType==none) createTimeCounterAxis=true ;
2721	if (field->hasTimeCentered)
2722	{
2723	timeCounterType=centered ;
2724	if (!hasTimeCentered) createCenteredAxis=true ;
2725	}
2726	if (field->hasTimeInstant)
2727	{
2728	if (timeCounterType==none) timeCounterType=instant ;
2729	if (!hasTimeInstant) createInstantAxis=true ;
2730	}
2731	}
2732	else if (field->file->time_counter==CFile::time_counter_attr::instant)
2733	{
2734	if (field->hasTimeCentered)
2735	{
2736	if (!hasTimeCentered) createCenteredAxis=true ;
2737	}
2738	if (field->hasTimeInstant)
2739	{
2740	if (timeCounterType==none) createTimeCounterAxis=true ;
2741	timeCounterType=instant ;
2742	if (!hasTimeInstant) createInstantAxis=true ;
2743	}
2744	}
2745	else if (field->file->time_counter==CFile::time_counter_attr::centered)
2746	{
2747	if (field->hasTimeCentered)
2748	{
2749	if (timeCounterType==none) createTimeCounterAxis=true ;
2750	timeCounterType=centered ;
2751	if (!hasTimeCentered) createCenteredAxis=true ;
2752	}
2753	if (field->hasTimeInstant)
2754	{
2755	if (!hasTimeInstant) createInstantAxis=true ;
2756	}
2757	}
2758	else if (field->file->time_counter==CFile::time_counter_attr::instant_exclusive)
2759	{
2760	if (field->hasTimeCentered)
2761	{
2762	if (!hasTimeCentered) createCenteredAxis=true ;
2763	}
2764	if (field->hasTimeInstant)
2765	{
2766	if (timeCounterType==none) createTimeCounterAxis=true ;
2767	timeCounterType=instant ;
2768	}
2769	}
2770	else if (field->file->time_counter==CFile::time_counter_attr::centered_exclusive)
2771	{
2772	if (field->hasTimeCentered)
2773	{
2774	if (timeCounterType==none) createTimeCounterAxis=true ;
2775	timeCounterType=centered ;
2776	}
2777	if (field->hasTimeInstant)
2778	{
2779	if (!hasTimeInstant) createInstantAxis=true ;
2780	}
2781	}
2782	else if (field->file->time_counter==CFile::time_counter_attr::exclusive)
2783	{
2784	if (field->hasTimeCentered)
2785	{
2786	if (timeCounterType==none) createTimeCounterAxis=true ;
2787	if (timeCounterType==instant) createInstantAxis=true ;
2788	timeCounterType=centered ;
2789	}
2790	if (field->hasTimeInstant)
2791	{
2792	if (timeCounterType==none)
2793	{
2794	createTimeCounterAxis=true ;
2795	timeCounterType=instant ;
2796	}
2797	if (timeCounterType==centered)
2798	{
2799	if (!hasTimeInstant) createInstantAxis=true ;
2800	}
2801	}
2802	}
2803	else if (field->file->time_counter==CFile::time_counter_attr::none)
2804	{
2805	if (field->hasTimeCentered)
2806	{
2807	if (!hasTimeCentered) createCenteredAxis=true ;
2808	}
2809	if (field->hasTimeInstant)
2810	{
2811	if (!hasTimeInstant) createInstantAxis=true ;
2812	}
2813	}
2814	else if (field->file->time_counter==CFile::time_counter_attr::record)
2815	{
2816	if (timeCounterType==none) createTimeCounterAxis=true ;
2817	timeCounterType=record ;
2818	if (field->hasTimeCentered)
2819	{
2820	if (!hasTimeCentered) createCenteredAxis=true ;
2821	}
2822	if (field->hasTimeInstant)
2823	{
2824	if (!hasTimeInstant) createInstantAxis=true ;
2825	}
2826	}
2827
2828	if (createInstantAxis)
2829	{
2830	axisId="time_instant" ;
2831	axisBoundId="time_instant_bounds";
2832	hasTimeInstant=true ;
2833	}
2834
2835	if (createCenteredAxis)
2836	{
2837	axisId="time_centered" ;
2838	axisBoundId="time_centered_bounds";
2839	hasTimeCentered=true ;
2840	}
2841
2842
2843	try
2844	{
2845	std::vector<StdString> dims;
2846
2847	if (createInstantAxis \|\| createCenteredAxis)
2848	{
2849	// Adding time_instant or time_centered
2850	dims.push_back(timeid);
2851	if (!SuperClassWriter::varExist(axisId))
2852	{
2853	SuperClassWriter::addVariable(axisId, NC_DOUBLE, dims);
2854
2855	CDate timeOrigin=cal->getTimeOrigin() ;
2856	StdOStringStream oss2;
2857	StdString strInitdate=oss2.str() ;
2858	StdString strTimeOrigin=timeOrigin.toString() ;
2859	this->writeTimeAxisAttributes(axisId, cal->getType(),strTimeUnits+strTimeOrigin,
2860	strTimeOrigin, axisBoundId);
2861	}
2862
2863	// Adding time_instant_bounds or time_centered_bounds variables
2864	if (!SuperClassWriter::varExist(axisBoundId))
2865	{
2866	dims.clear() ;
2867	dims.push_back(timeid);
2868	dims.push_back(timeBoundId);
2869	SuperClassWriter::addVariable(axisBoundId, NC_DOUBLE, dims);
2870	}
2871	}
2872
2873	if (createTimeCounterAxis)
2874	{
2875	// Adding time_counter
2876	axisId = getTimeCounterName();
2877	axisBoundId = getTimeCounterName() + "_bounds";
2878	dims.clear();
2879	dims.push_back(timeid);
2880	if (!SuperClassWriter::varExist(axisId))
2881	{
2882	SuperClassWriter::addVariable(axisId, NC_DOUBLE, dims);
2883	SuperClassWriter::addAttribute("axis", string("T"), &axisId);
2884
2885	if (field->file->time_counter.isEmpty() \|\|
2886	(field->file->time_counter != CFile::time_counter_attr::record))
2887	{
2888	CDate timeOrigin = cal->getTimeOrigin();
2889	StdString strTimeOrigin = timeOrigin.toString();
2890
2891	this->writeTimeAxisAttributes(axisId, cal->getType(),
2892	strTimeUnits+strTimeOrigin,
2893	strTimeOrigin, axisBoundId);
2894	}
2895	}
2896
2897	// Adding time_counter_bound dimension
2898	if (field->file->time_counter.isEmpty() \|\| (field->file->time_counter != CFile::time_counter_attr::record))
2899	{
2900	if (!SuperClassWriter::varExist(axisBoundId))
2901	{
2902	dims.clear();
2903	dims.push_back(timeid);
2904	dims.push_back(timeBoundId);
2905	SuperClassWriter::addVariable(axisBoundId, NC_DOUBLE, dims);
2906	}
2907	}
2908	}
2909	}
2910	catch (CNetCdfException& e)
2911	{
2912	StdString msg("On writing time axis data: ");
2913	msg.append("In the context : ");
2914	CContext* context = CContext::getCurrent() ;
2915	msg.append(context->getId()); msg.append("\n");
2916	msg.append(e.what());
2917	ERROR("CNc4DataOutput::writeTimeAxis_ (CField* field, \
2918	const std::shared_ptr<CCalendar> cal)", << msg);
2919	}
2920	}
2921
2922	//---------------------------------------------------------------
2923
2924	void CNc4DataOutput::writeTimeAxisAttributes(const StdString & axis_name,
2925	const StdString & calendar,
2926	const StdString & units,
2927	const StdString & time_origin,
2928	const StdString & time_bounds,
2929	const StdString & standard_name,
2930	const StdString & long_name)
2931	{
2932	try
2933	{
2934	SuperClassWriter::addAttribute("standard_name", standard_name, &axis_name);
2935	SuperClassWriter::addAttribute("long_name", long_name , &axis_name);
2936	SuperClassWriter::addAttribute("calendar", calendar , &axis_name);
2937	SuperClassWriter::addAttribute("units", units , &axis_name);
2938	SuperClassWriter::addAttribute("time_origin", time_origin , &axis_name);
2939	SuperClassWriter::addAttribute("bounds", time_bounds , &axis_name);
2940	}
2941	catch (CNetCdfException& e)
2942	{
2943	StdString msg("On writing time axis Attribute: ");
2944	msg.append("In the context : ");
2945	CContext* context = CContext::getCurrent() ;
2946	msg.append(context->getId()); msg.append("\n");
2947	msg.append(e.what());
2948	ERROR("CNc4DataOutput::writeTimeAxisAttributes(const StdString & axis_name, \
2949	const StdString & calendar,\
2950	const StdString & units, \
2951	const StdString & time_origin, \
2952	const StdString & time_bounds, \
2953	const StdString & standard_name, \
2954	const StdString & long_name)", << msg);
2955	}
2956	}
2957
2958	//---------------------------------------------------------------
2959
2960	void CNc4DataOutput::writeAxisAttributes(const StdString & axis_name,
2961	const StdString & axis,
2962	const StdString & standard_name,
2963	const StdString & long_name,
2964	const StdString & units,
2965	const StdString & nav_model)
2966	{
2967	try
2968	{
2969	if (!axis.empty())
2970	SuperClassWriter::addAttribute("axis" , axis , &axis_name);
2971
2972	SuperClassWriter::addAttribute("standard_name", standard_name, &axis_name);
2973	SuperClassWriter::addAttribute("long_name" , long_name , &axis_name);
2974	SuperClassWriter::addAttribute("units" , units , &axis_name);
2975	// SuperClassWriter::addAttribute("nav_model" , nav_model , &axis_name);
2976	}
2977	catch (CNetCdfException& e)
2978	{
2979	StdString msg("On writing Axis Attribute: ");
2980	msg.append("In the context : ");
2981	CContext* context = CContext::getCurrent() ;
2982	msg.append(context->getId()); msg.append("\n");
2983	msg.append(e.what());
2984	ERROR("CNc4DataOutput::writeAxisAttributes(const StdString & axis_name, \
2985	const StdString & axis, \
2986	const StdString & standard_name, \
2987	const StdString & long_name, \
2988	const StdString & units, \
2989	const StdString & nav_model)", << msg);
2990	}
2991	}
2992
2993	//---------------------------------------------------------------
2994
2995	void CNc4DataOutput::writeLocalAttributes
2996	(int ibegin, int ni, int jbegin, int nj, StdString domid)
2997	{
2998	try
2999	{
3000	SuperClassWriter::addAttribute(StdString("ibegin").append(domid), ibegin);
3001	SuperClassWriter::addAttribute(StdString("ni" ).append(domid), ni);
3002	SuperClassWriter::addAttribute(StdString("jbegin").append(domid), jbegin);
3003	SuperClassWriter::addAttribute(StdString("nj" ).append(domid), nj);
3004	}
3005	catch (CNetCdfException& e)
3006	{
3007	StdString msg("On writing Local Attributes: ");
3008	msg.append("In the context : ");
3009	CContext* context = CContext::getCurrent() ;
3010	msg.append(context->getId()); msg.append("\n");
3011	msg.append(e.what());
3012	ERROR("CNc4DataOutput::writeLocalAttributes \
3013	(int ibegin, int ni, int jbegin, int nj, StdString domid)", << msg);
3014	}
3015
3016	}
3017
3018	void CNc4DataOutput::writeLocalAttributes_IOIPSL(const StdString& dimXid, const StdString& dimYid,
3019	int ibegin, int ni, int jbegin, int nj, int ni_glo, int nj_glo, int rank, int size)
3020	{
3021	CArray<int,1> array(2) ;
3022
3023	try
3024	{
3025	SuperClassWriter::addAttribute("DOMAIN_number_total",size ) ;
3026	SuperClassWriter::addAttribute("DOMAIN_number", rank) ;
3027	array = SuperClassWriter::getDimension(dimXid) + 1, SuperClassWriter::getDimension(dimYid) + 1;
3028	SuperClassWriter::addAttribute("DOMAIN_dimensions_ids",array) ;
3029	array=ni_glo,nj_glo ;
3030	SuperClassWriter::addAttribute("DOMAIN_size_global", array) ;
3031	array=ni,nj ;
3032	SuperClassWriter::addAttribute("DOMAIN_size_local", array) ;
3033	array=ibegin+1,jbegin+1 ;
3034	SuperClassWriter::addAttribute("DOMAIN_position_first", array) ;
3035	array=ibegin+ni-1+1,jbegin+nj-1+1 ;
3036	SuperClassWriter::addAttribute("DOMAIN_position_last",array) ;
3037	array=0,0 ;
3038	SuperClassWriter::addAttribute("DOMAIN_halo_size_start", array) ;
3039	SuperClassWriter::addAttribute("DOMAIN_halo_size_end", array);
3040	SuperClassWriter::addAttribute("DOMAIN_type",string("box")) ;
3041	/*
3042	SuperClassWriter::addAttribute("DOMAIN_DIM_N001",string("x")) ;
3043	SuperClassWriter::addAttribute("DOMAIN_DIM_N002",string("y")) ;
3044	SuperClassWriter::addAttribute("DOMAIN_DIM_N003",string("axis_A")) ;
3045	SuperClassWriter::addAttribute("DOMAIN_DIM_N004",string("time_counter")) ;
3046	*/
3047	}
3048	catch (CNetCdfException& e)
3049	{
3050	StdString msg("On writing Local Attributes IOIPSL \n");
3051	msg.append("In the context : ");
3052	CContext* context = CContext::getCurrent() ;
3053	msg.append(context->getId()); msg.append("\n");
3054	msg.append(e.what());
3055	ERROR("CNc4DataOutput::writeLocalAttributes_IOIPSL \
3056	(int ibegin, int ni, int jbegin, int nj, int ni_glo, int nj_glo, int rank, int size)", << msg);
3057	}
3058	}
3059	//---------------------------------------------------------------
3060
3061	void CNc4DataOutput:: writeFileAttributes(const StdString & name,
3062	const StdString & description,
3063	const StdString & conventions,
3064	const StdString & production,
3065	const StdString & timeStamp)
3066	{
3067	try
3068	{
3069	SuperClassWriter::addAttribute("name" , name);
3070	SuperClassWriter::addAttribute("description", description);
3071	SuperClassWriter::addAttribute("title" , description);
3072	SuperClassWriter::addAttribute("Conventions", conventions);
3073	// SuperClassWriter::addAttribute("production" , production);
3074
3075	StdString timeStampStr ;
3076	if (file->time_stamp_name.isEmpty()) timeStampStr="timeStamp" ;
3077	else timeStampStr=file->time_stamp_name ;
3078	SuperClassWriter::addAttribute(timeStampStr, timeStamp);
3079
3080	StdString uuidName ;
3081	if (file->uuid_name.isEmpty()) uuidName="uuid" ;
3082	else uuidName=file->uuid_name ;
3083
3084	if (file->uuid_format.isEmpty()) SuperClassWriter::addAttribute(uuidName, getUuidStr());
3085	else SuperClassWriter::addAttribute(uuidName, getUuidStr(file->uuid_format));
3086
3087	}
3088	catch (CNetCdfException& e)
3089	{
3090	StdString msg("On writing File Attributes \n ");
3091	msg.append("In the context : ");
3092	CContext* context = CContext::getCurrent() ;
3093	msg.append(context->getId()); msg.append("\n");
3094	msg.append(e.what());
3095	ERROR("CNc4DataOutput:: writeFileAttributes(const StdString & name, \
3096	const StdString & description, \
3097	const StdString & conventions, \
3098	const StdString & production, \
3099	const StdString & timeStamp)", << msg);
3100	}
3101	}
3102
3103	//---------------------------------------------------------------
3104
3105	void CNc4DataOutput::writeMaskAttributes(const StdString & mask_name,
3106	int data_dim,
3107	int data_ni,
3108	int data_nj,
3109	int data_ibegin,
3110	int data_jbegin)
3111	{
3112	try
3113	{
3114	SuperClassWriter::addAttribute("data_dim" , data_dim , &mask_name);
3115	SuperClassWriter::addAttribute("data_ni" , data_ni , &mask_name);
3116	SuperClassWriter::addAttribute("data_nj" , data_nj , &mask_name);
3117	SuperClassWriter::addAttribute("data_ibegin", data_ibegin, &mask_name);
3118	SuperClassWriter::addAttribute("data_jbegin", data_jbegin, &mask_name);
3119	}
3120	catch (CNetCdfException& e)
3121	{
3122	StdString msg("On writing Mask Attributes \n ");
3123	msg.append("In the context : ");
3124	CContext* context = CContext::getCurrent() ;
3125	msg.append(context->getId()); msg.append("\n");
3126	msg.append(e.what());
3127	ERROR("CNc4DataOutput::writeMaskAttributes(const StdString & mask_name, \
3128	int data_dim, \
3129	int data_ni, \
3130	int data_nj, \
3131	int data_ibegin, \
3132	int data_jbegin)", << msg);
3133	}
3134	}
3135
3136	///--------------------------------------------------------------
3137
3138	StdSize CNc4DataOutput::getRecordFromTime(Time time, double factorUnit)
3139	{
3140	std::map<Time, StdSize>::const_iterator it = timeToRecordCache.find(time);
3141	if (it == timeToRecordCache.end())
3142	{
3143	StdString timeAxisBoundsId(getTimeCounterName() + "_bounds");
3144	if (!SuperClassWriter::varExist(timeAxisBoundsId)) timeAxisBoundsId = "time_centered_bounds";
3145	if (!SuperClassWriter::varExist(timeAxisBoundsId)) timeAxisBoundsId = "time_instant_bounds";
3146
3147	CArray<double,2> timeAxisBounds;
3148	std::vector<StdSize> dimSize(SuperClassWriter::getDimensions(timeAxisBoundsId)) ;
3149
3150	StdSize record = 0;
3151	double dtime(time);
3152	for (int n = dimSize[0] - 1; n >= 0; n--)
3153	{
3154	SuperClassWriter::getTimeAxisBounds(timeAxisBounds, timeAxisBoundsId, isCollective, n);
3155	timeAxisBounds*=factorUnit ;
3156	if (timeAxisBounds(1, 0) < dtime)
3157	{
3158	record = n + 1;
3159	break;
3160	}
3161	}
3162	it = timeToRecordCache.insert(std::make_pair(time, record)).first;
3163	}
3164	return it->second;
3165	}
3166
3167	///--------------------------------------------------------------
3168
3169	bool CNc4DataOutput::isWrittenDomain(const std::string& domainName) const
3170	{
3171	return (this->writtenDomains.find(domainName) != this->writtenDomains.end());
3172	}
3173
3174	bool CNc4DataOutput::isWrittenCompressedDomain(const std::string& domainName) const
3175	{
3176	return (this->writtenCompressedDomains.find(domainName) != this->writtenCompressedDomains.end());
3177	}
3178
3179	bool CNc4DataOutput::isWrittenAxis(const std::string& axisName) const
3180	{
3181	return (this->writtenAxis.find(axisName) != this->writtenAxis.end());
3182	}
3183
3184	bool CNc4DataOutput::isWrittenCompressedAxis(const std::string& axisName) const
3185	{
3186	return (this->writtenCompressedAxis.find(axisName) != this->writtenCompressedAxis.end());
3187	}
3188
3189	bool CNc4DataOutput::isWrittenScalar(const std::string& scalarName) const
3190	{
3191	return (this->writtenScalar.find(scalarName) != this->writtenScalar.end());
3192	}
3193
3194	void CNc4DataOutput::setWrittenDomain(const std::string& domainName)
3195	{
3196	this->writtenDomains.insert(domainName);
3197	}
3198
3199	void CNc4DataOutput::setWrittenCompressedDomain(const std::string& domainName)
3200	{
3201	this->writtenCompressedDomains.insert(domainName);
3202	}
3203
3204	void CNc4DataOutput::setWrittenAxis(const std::string& axisName)
3205	{
3206	this->writtenAxis.insert(axisName);
3207	}
3208
3209	void CNc4DataOutput::setWrittenCompressedAxis(const std::string& axisName)
3210	{
3211	this->writtenCompressedAxis.insert(axisName);
3212	}
3213
3214	void CNc4DataOutput::setWrittenScalar(const std::string& scalarName)
3215	{
3216	this->writtenScalar.insert(scalarName);
3217	}
3218	} // namespace xios

Note: See TracBrowser for help on using the repository browser.

Download in other formats: