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source: XIOS/trunk/src/io/nc4_data_output.cpp @ 1639

Last change on this file since 1639 was 1639, checked in by yushan, 5 years ago
revert erroneous commit on trunk
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: 132.0 KB

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

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