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nc4_data_output.cpp @ 1048

Last change on this file since 1048 was 1048, checked in by ymipsl, 7 years ago

Xios output now an uuid for each files.
2 new file attribute to parametrize uuid output :
- uuid_name (default is "uuid")
- uuid_format : the substring "%uuid%" will replace by the uuid (default : no format)

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: 117.1 KB

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

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source: XIOS/trunk/src/io/nc4_data_output.cpp @ 1048

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