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nc4_data_output.cpp @ 614

Last change on this file since 614 was 614, checked in by rlacroix, 9 years ago

Improve CF compliance: Minor tweaks and improvements.

Bump the CF version to 1.5.
Use the same bounds dimension for all axis, including time axis.
Add a standard_name attribute for cell area variables.
Set the interval part of cell_methods attribute only when the write interval and the operation interval are different.

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

File size: 63.9 KB

Line
1
2	#include "nc4_data_output.hpp"
3
4	#include <boost/lexical_cast.hpp>
5	#include "attribute_template.hpp"
6	#include "group_template.hpp"
7
8	#include "file.hpp"
9	#include "calendar.hpp"
10	#include "context.hpp"
11	#include "context_server.hpp"
12	#include "netCdfException.hpp"
13	#include "exception.hpp"
14
15	namespace xios
16	{
17	/// ////////////////////// DÃ©finitions ////////////////////// ///
18	CNc4DataOutput::CNc4DataOutput
19	(const StdString & filename, bool exist)
20	: SuperClass()
21	, SuperClassWriter(filename, exist)
22	, filename(filename)
23	{
24	StdString timeid = StdString("time_counter");
25	SuperClass::type = MULTI_FILE;
26	// if (!exist)
27	// SuperClassWriter::addDimension(timeid);
28	}
29
30	CNc4DataOutput::CNc4DataOutput
31	(const StdString & filename, bool exist, MPI_Comm comm_file,bool multifile, bool isCollective)
32	: SuperClass()
33	, SuperClassWriter(filename, exist, &comm_file,multifile)
34	, comm_file(comm_file)
35	, filename(filename)
36	, isCollective(isCollective)
37	{
38	StdString timeid = StdString("time_counter");
39
40	SuperClass::type = (multifile) ? MULTI_FILE : ONE_FILE;
41
42	// if (!exist)
43	// SuperClassWriter::addDimension(timeid);
44	}
45
46
47	CNc4DataOutput::~CNc4DataOutput(void)
48	{ /* Ne rien faire de plus */ }
49
50	///--------------------------------------------------------------
51
52	const StdString & CNc4DataOutput::getFileName(void) const
53	{
54	return (this->filename);
55	}
56
57	//---------------------------------------------------------------
58
59	void CNc4DataOutput::writeDomain_(CDomain* domain)
60	{
61	if (domain->type == CDomain::type_attr::unstructured)
62	{
63	writeUnstructuredDomain(domain) ;
64	return ;
65	}
66
67	CContext* context = CContext::getCurrent() ;
68	CContextServer* server=context->server ;
69
70	if (domain->IsWritten(this->filename)) return;
71	domain->checkAttributes();
72
73	if (domain->isEmpty())
74	if (SuperClass::type==MULTI_FILE) return ;
75
76	std::vector<StdString> dim0, dim1;
77	StdString domid = (!domain->name.isEmpty())
78	? domain->name.getValue() : domain->getId();
79	StdString appendDomid = (singleDomain) ? "" : "_"+domid ;
80
81
82	StdString dimXid, dimYid ;
83
84	bool isRegularDomain = (domain->type == CDomain::type_attr::regular);
85	switch (domain->type)
86	{
87	case CDomain::type_attr::curvilinear :
88	dimXid = StdString("x").append(appendDomid);
89	dimYid = StdString("y").append(appendDomid);
90	break ;
91	case CDomain::type_attr::regular :
92	dimXid = StdString("lon").append(appendDomid);
93	dimYid = StdString("lat").append(appendDomid);
94	break;
95	case CDomain::type_attr::unstructured :
96	dimXid = StdString("cell").append(appendDomid);
97	break;
98	}
99
100	string lonid,latid,bounds_lonid,bounds_latid ;
101	string areaId = "area" + appendDomid;
102	/*
103	StdString lonid_loc = (server->intraCommSize > 1)
104	? StdString("lon").append(appendDomid).append("_local")
105	: lonid;
106	StdString latid_loc = (server->intraCommSize > 1)
107	? StdString("lat").append(appendDomid).append("_local")
108	: latid;
109	*/
110
111	try
112	{
113	switch (SuperClass::type)
114	{
115	case (MULTI_FILE) :
116	{
117	// if (domain->isEmpty()) return;
118
119	if (server->intraCommSize > 1)
120	{
121	// SuperClassWriter::addDimension(lonid, domain->zoom_ni.getValue());
122	// SuperClassWriter::addDimension(latid, domain->zoom_nj.getValue());
123	}
124
125	switch (domain->type)
126	{
127	case CDomain::type_attr::curvilinear :
128	dim0.push_back(dimYid); dim0.push_back(dimXid);
129	lonid = StdString("nav_lon").append(appendDomid);
130	latid = StdString("nav_lat").append(appendDomid);
131	break ;
132	case CDomain::type_attr::regular :
133	lonid = StdString("lon").append(appendDomid);
134	latid = StdString("lat").append(appendDomid);
135	dim0.push_back(dimYid);
136	dim1.push_back(dimXid);
137	break;
138	case CDomain::type_attr::unstructured :
139	lonid = StdString("lon").append(appendDomid);
140	latid = StdString("lat").append(appendDomid);
141	bounds_lonid=string("bounds_lon").append(appendDomid);
142	bounds_latid=string("bounds_lat").append(appendDomid);
143	dim0.push_back(dimXid);
144	break;
145	}
146
147	if (domain->type == CDomain::type_attr::unstructured)
148	{
149	SuperClassWriter::addDimension(dimXid, domain->nj_glo);
150	}
151	else
152	{
153	SuperClassWriter::addDimension(dimXid, domain->zoom_ni_srv);
154	SuperClassWriter::addDimension(dimYid, domain->zoom_nj_srv);
155	}
156
157	if (server->intraCommSize > 1)
158	{
159	if (domain->type != CDomain::type_attr::unstructured)
160	{
161	this->writeLocalAttributes(domain->zoom_ibegin_srv,
162	domain->zoom_ni_srv,
163	domain->zoom_jbegin_srv,
164	domain->zoom_nj_srv,
165	appendDomid);
166
167	if (singleDomain) this->writeLocalAttributes_IOIPSL(domain->zoom_ibegin_srv,
168	domain->zoom_ni_srv,
169	domain->zoom_jbegin_srv,
170	domain->zoom_nj_srv,
171	domain->ni_glo,domain->nj_glo,
172	server->intraCommRank,server->intraCommSize);
173	}
174	}
175
176	switch (domain->type)
177	{
178	case CDomain::type_attr::curvilinear :
179	SuperClassWriter::addVariable(latid, NC_FLOAT, dim0);
180	SuperClassWriter::addVariable(lonid, NC_FLOAT, dim0);
181	break ;
182	case CDomain::type_attr::regular :
183	SuperClassWriter::addVariable(latid, NC_FLOAT, dim0);
184	SuperClassWriter::addVariable(lonid, NC_FLOAT, dim1);
185	break ;
186	case CDomain::type_attr::unstructured :
187	SuperClassWriter::addVariable(latid, NC_FLOAT, dim0);
188	SuperClassWriter::addVariable(lonid, NC_FLOAT, dim0);
189	}
190
191	this->writeAxisAttributes(lonid, isRegularDomain ? "X" : "", "longitude", "Longitude", "degrees_east", domid);
192	this->writeAxisAttributes(latid, isRegularDomain ? "Y" : "", "latitude", "Latitude", "degrees_north", domid);
193
194	dim0.clear();
195	if (domain->type != CDomain::type_attr::unstructured) dim0.push_back(dimYid);
196	dim0.push_back(dimXid);
197
198
199	// supress mask if (server->intraCommSize > 1)
200	// supress mask {
201	// supress mask SuperClassWriter::addVariable(maskid, NC_INT, dim0);
202	// supress mask
203	// supress mask this->writeMaskAttributes(maskid,
204	// supress mask domain->data_dim.getValue()/*,
205	// supress mask domain->data_ni.getValue(),
206	// supress mask domain->data_nj.getValue(),
207	// supress mask domain->data_ibegin.getValue(),
208	// supress mask domain->data_jbegin.getValue()*/);
209	// supress mask }
210
211	//SuperClassWriter::setDefaultValue(maskid, &dvm);
212
213	if (domain->hasArea)
214	{
215	SuperClassWriter::addVariable(areaId, NC_FLOAT, dim0);
216	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
217	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
218	}
219
220	SuperClassWriter::definition_end();
221
222	switch (domain->type)
223	{
224	case CDomain::type_attr::curvilinear :
225	SuperClassWriter::writeData(domain->latvalue_srv, latid, isCollective, 0);
226	SuperClassWriter::writeData(domain->lonvalue_srv, lonid, isCollective, 0);
227	break;
228	case CDomain::type_attr::regular :
229	CArray<double,1> lat = domain->latvalue_srv(Range(fromStart,toEnd,domain->zoom_ni_srv)) ;
230	SuperClassWriter::writeData(CArray<double,1>(lat.copy()), latid, isCollective, 0);
231	CArray<double,1> lon=domain->lonvalue_srv(Range(0,domain->zoom_ni_srv-1)) ;
232	SuperClassWriter::writeData(CArray<double,1>(lon.copy()), lonid, isCollective, 0);
233	break;
234	}
235
236	if (domain->hasArea)
237	SuperClassWriter::writeData(domain->area_srv, areaId, isCollective, 0);
238
239	SuperClassWriter::definition_start();
240
241	break;
242	}
243	case (ONE_FILE) :
244	{
245	SuperClassWriter::addDimension(dimXid, domain->zoom_ni.getValue());
246	SuperClassWriter::addDimension(dimYid, domain->zoom_nj.getValue());
247
248	switch (domain->type)
249	{
250	case CDomain::type_attr::curvilinear :
251	dim0.push_back(dimYid); dim0.push_back(dimXid);
252	lonid = StdString("nav_lon").append(appendDomid);
253	latid = StdString("nav_lat").append(appendDomid);
254	SuperClassWriter::addVariable(latid, NC_FLOAT, dim0);
255	SuperClassWriter::addVariable(lonid, NC_FLOAT, dim0);
256	break;
257
258	case CDomain::type_attr::regular :
259	dim0.push_back(dimYid);
260	dim1.push_back(dimXid);
261	lonid = StdString("lon").append(appendDomid);
262	latid = StdString("lat").append(appendDomid);
263	SuperClassWriter::addVariable(latid, NC_FLOAT, dim0);
264	SuperClassWriter::addVariable(lonid, NC_FLOAT, dim1);
265	break;
266	}
267
268	if (domain->hasArea)
269	{
270	dim0.clear();
271	dim0.push_back(dimYid); dim0.push_back(dimXid);
272	SuperClassWriter::addVariable(areaId, NC_FLOAT, dim0);
273	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
274	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
275	dim0.clear();
276	}
277
278	this->writeAxisAttributes
279	(lonid, isRegularDomain ? "X" : "", "longitude", "Longitude", "degrees_east", domid);
280	this->writeAxisAttributes
281	(latid, isRegularDomain ? "Y" : "", "latitude", "Latitude", "degrees_north", domid);
282
283	SuperClassWriter::definition_end();
284
285	switch (domain->type)
286	{
287	case CDomain::type_attr::curvilinear :
288	{
289	std::vector<StdSize> start(2) ;
290	std::vector<StdSize> count(2) ;
291	if (domain->isEmpty())
292	{
293	start[0]=0 ; start[1]=0 ;
294	count[0]=0 ; count[1]=0 ;
295	}
296	else
297	{
298	start[1]=domain->zoom_ibegin_srv-domain->zoom_ibegin.getValue() ; start [0]=domain->zoom_jbegin_srv-domain->zoom_jbegin.getValue() ;
299	count[1]=domain->zoom_ni_srv ; count[0]=domain->zoom_nj_srv ;
300	}
301
302	SuperClassWriter::writeData(domain->latvalue_srv, latid, isCollective, 0,&start,&count);
303	SuperClassWriter::writeData(domain->lonvalue_srv, lonid, isCollective, 0,&start,&count);
304	break;
305	}
306	case CDomain::type_attr::regular :
307	{
308	std::vector<StdSize> start(1) ;
309	std::vector<StdSize> count(1) ;
310	if (domain->isEmpty())
311	{
312	start[0]=0 ;
313	count[0]=0 ;
314	SuperClassWriter::writeData(domain->latvalue_srv, latid, isCollective, 0,&start,&count);
315	SuperClassWriter::writeData(domain->lonvalue_srv, lonid, isCollective, 0,&start,&count); }
316	else
317	{
318	start[0]=domain->zoom_jbegin_srv-domain->zoom_jbegin.getValue() ;
319	count[0]=domain->zoom_nj_srv ;
320	CArray<double,1> lat = domain->latvalue_srv(Range(fromStart,toEnd,domain->zoom_ni_srv)) ;
321	SuperClassWriter::writeData(CArray<double,1>(lat.copy()), latid, isCollective, 0,&start,&count);
322
323	start[0]=domain->zoom_ibegin_srv-domain->zoom_ibegin.getValue() ;
324	count[0]=domain->zoom_ni_srv ;
325	CArray<double,1> lon=domain->lonvalue_srv(Range(0,domain->zoom_ni_srv-1)) ;
326	SuperClassWriter::writeData(CArray<double,1>(lon.copy()), lonid, isCollective, 0,&start,&count);
327	}
328	break;
329	}
330	}
331
332	if (domain->hasArea)
333	{
334	std::vector<StdSize> start(2);
335	std::vector<StdSize> count(2);
336
337	if (domain->isEmpty())
338	{
339	start[0] = 0; start[1] = 0;
340	count[0] = 0; count[1] = 0;
341	}
342	else
343	{
344	start[1] = domain->zoom_ibegin_srv - domain->zoom_ibegin.getValue();
345	start[0] = domain->zoom_jbegin_srv - domain->zoom_jbegin.getValue();
346	count[1] = domain->zoom_ni_srv;
347	count[0] = domain->zoom_nj_srv;
348	}
349
350	SuperClassWriter::writeData(domain->area_srv, areaId, isCollective, 0, &start, &count);
351	}
352
353	SuperClassWriter::definition_start();
354
355	break;
356	}
357	default :
358	ERROR("CNc4DataOutput::writeDomain(domain)",
359	<< "[ type = " << SuperClass::type << "]"
360	<< " not implemented yet !");
361	}
362	}
363	catch (CNetCdfException& e)
364	{
365	StdString msg("On writing the domain : ");
366	msg.append(domid); msg.append("\n");
367	msg.append("In the context : ");
368	msg.append(context->getId()); msg.append("\n");
369	msg.append(e.what());
370	ERROR("CNc4DataOutput::writeDomain_(CDomain* domain)", << msg);
371	}
372
373	domain->addRelFile(this->filename);
374	}
375
376	void CNc4DataOutput::writeUnstructuredDomain(CDomain* domain)
377	{
378	CContext* context = CContext::getCurrent() ;
379	CContextServer* server=context->server ;
380
381	if (domain->IsWritten(this->filename)) return;
382	domain->checkAttributes();
383
384	if (domain->isEmpty())
385	if (SuperClass::type==MULTI_FILE) return ;
386
387	std::vector<StdString> dim0, dim1;
388	StdString domid = (!domain->name.isEmpty())
389	? domain->name.getValue() : domain->getId();
390	StdString appendDomid = (singleDomain) ? "" : "_"+domid ;
391
392
393	StdString dimXid = StdString("cell").append(appendDomid);
394	StdString dimVertId = StdString("nvertex").append(appendDomid);
395
396	string lonid,latid,bounds_lonid,bounds_latid ;
397	string areaId = "area" + appendDomid;
398
399	try
400	{
401	switch (SuperClass::type)
402	{
403	case (MULTI_FILE) :
404	{
405	lonid = StdString("lon").append(appendDomid);
406	latid = StdString("lat").append(appendDomid);
407	dim0.push_back(dimXid);
408
409	SuperClassWriter::addDimension(dimXid, domain->zoom_nj_srv);
410	SuperClassWriter::addVariable(latid, NC_FLOAT, dim0);
411	SuperClassWriter::addVariable(lonid, NC_FLOAT, dim0);
412
413	bounds_lonid = StdString("bounds_lon").append(appendDomid);
414	bounds_latid = StdString("bounds_lat").append(appendDomid);
415
416
417	this->writeAxisAttributes(lonid, "", "longitude", "Longitude", "degrees_east", domid);
418	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_lonid, &lonid);
419	this->writeAxisAttributes(latid, "", "latitude", "Latitude", "degrees_north", domid);
420	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_latid, &latid);
421	if (domain->hasBounds) SuperClassWriter::addDimension(dimVertId, domain->nvertex);
422	dim0.clear();
423	if (domain->hasBounds)
424	{
425	dim0.push_back(dimXid);
426	dim0.push_back(dimVertId);
427	SuperClassWriter::addVariable(bounds_lonid, NC_FLOAT, dim0);
428	SuperClassWriter::addVariable(bounds_latid, NC_FLOAT, dim0);
429	}
430
431	dim0.clear();
432	dim0.push_back(dimXid);
433
434	if (domain->hasArea)
435	{
436	SuperClassWriter::addVariable(areaId, NC_FLOAT, dim0);
437	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
438	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
439	}
440
441	SuperClassWriter::definition_end();
442
443	SuperClassWriter::writeData(domain->latvalue_srv, latid, isCollective, 0);
444	SuperClassWriter::writeData(domain->lonvalue_srv, lonid, isCollective, 0);
445
446	if (domain->hasBounds)
447	{
448	SuperClassWriter::writeData(domain->bounds_lon_srv, bounds_lonid, isCollective, 0);
449	SuperClassWriter::writeData(domain->bounds_lat_srv, bounds_latid, isCollective, 0);
450	}
451
452	if (domain->hasArea)
453	SuperClassWriter::writeData(domain->area_srv, areaId, isCollective, 0);
454
455	SuperClassWriter::definition_start();
456	break ;
457	}
458
459	case (ONE_FILE) :
460	{
461	lonid = StdString("lon").append(appendDomid);
462	latid = StdString("lat").append(appendDomid);
463	bounds_lonid = StdString("bounds_lon").append(appendDomid);
464	bounds_latid = StdString("bounds_lat").append(appendDomid);
465	dim0.push_back(dimXid);
466	SuperClassWriter::addDimension(dimXid, domain->nj_glo);
467	SuperClassWriter::addVariable(latid, NC_FLOAT, dim0);
468	SuperClassWriter::addVariable(lonid, NC_FLOAT, dim0);
469	this->writeAxisAttributes(lonid, "", "longitude", "Longitude", "degrees_east", domid);
470	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_lonid, &lonid);
471	this->writeAxisAttributes(latid, "", "latitude", "Latitude", "degrees_north", domid);
472	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_latid, &latid);
473	if (domain->hasBounds) SuperClassWriter::addDimension(dimVertId, domain->nvertex);
474	dim0.clear();
475
476	if (domain->hasBounds)
477	{
478	dim0.push_back(dimXid);
479	dim0.push_back(dimVertId);
480	SuperClassWriter::addVariable(bounds_lonid, NC_FLOAT, dim0);
481	SuperClassWriter::addVariable(bounds_latid, NC_FLOAT, dim0);
482	}
483
484	if (domain->hasArea)
485	{
486	dim0.clear();
487	dim0.push_back(dimXid);
488	SuperClassWriter::addVariable(areaId, NC_FLOAT, dim0);
489	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
490	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
491	}
492
493	SuperClassWriter::definition_end();
494
495	std::vector<StdSize> start(1), startBounds(2) ;
496	std::vector<StdSize> count(1), countBounds(2) ;
497	if (domain->isEmpty())
498	{
499	start[0]=0 ;
500	count[0]=0 ;
501	startBounds[1]=0 ;
502	countBounds[1]=domain->nvertex ;
503	startBounds[0]=0 ;
504	countBounds[0]=0 ;
505	}
506	else
507	{
508	start[0]=domain->zoom_jbegin_srv-domain->zoom_jbegin ;
509	count[0]=domain->zoom_nj_srv ;
510	startBounds[0]=domain->zoom_jbegin_srv-domain->zoom_jbegin ;
511	startBounds[1]=0 ;
512	countBounds[0]=domain->zoom_nj_srv ;
513	countBounds[1]=domain->nvertex ;
514	}
515	SuperClassWriter::writeData(domain->latvalue_srv, latid, isCollective, 0,&start,&count);
516	SuperClassWriter::writeData(domain->lonvalue_srv, lonid, isCollective, 0,&start,&count);
517	if (domain->hasBounds)
518	{
519	SuperClassWriter::writeData(domain->bounds_lon_srv, bounds_lonid, isCollective, 0,&startBounds,&countBounds);
520	SuperClassWriter::writeData(domain->bounds_lat_srv, bounds_latid, isCollective, 0,&startBounds,&countBounds);
521	}
522
523	if (domain->hasArea)
524	SuperClassWriter::writeData(domain->area_srv, areaId, isCollective, 0, &start, &count);
525
526	SuperClassWriter::definition_start();
527
528	break;
529	}
530	default :
531	ERROR("CNc4DataOutput::writeDomain(domain)",
532	<< "[ type = " << SuperClass::type << "]"
533	<< " not implemented yet !");
534	}
535	}
536	catch (CNetCdfException& e)
537	{
538	StdString msg("On writing the domain : ");
539	msg.append(domid); msg.append("\n");
540	msg.append("In the context : ");
541	msg.append(context->getId()); msg.append("\n");
542	msg.append(e.what());
543	ERROR("CNc4DataOutput::writeUnstructuredDomain(CDomain* domain)", << msg);
544	}
545	domain->addRelFile(this->filename);
546	}
547	//--------------------------------------------------------------
548
549	void CNc4DataOutput::writeAxis_(CAxis* axis)
550	{
551	if (axis->IsWritten(this->filename)) return;
552	axis->checkAttributes();
553	int zoom_size = axis->zoom_size.getValue();
554	int zoom_begin = axis->zoom_begin.getValue() - 1;
555
556
557	std::vector<StdString> dims;
558	StdString axisid = (!axis->name.isEmpty())
559	? axis->name.getValue() : axis->getId();
560	try
561	{
562	SuperClassWriter::addDimension(axisid, zoom_size);
563	dims.push_back(axisid);
564
565	switch (SuperClass::type)
566	{
567	case (MULTI_FILE ) :
568	{}
569	case (ONE_FILE) :
570	{
571	SuperClassWriter::addVariable(axisid, NC_FLOAT, dims);
572
573	if (!axis->standard_name.isEmpty())
574	SuperClassWriter::addAttribute
575	("standard_name", axis->standard_name.getValue(), &axisid);
576
577	if (!axis->long_name.isEmpty())
578	SuperClassWriter::addAttribute
579	("long_name", axis->long_name.getValue(), &axisid);
580
581	if (!axis->unit.isEmpty())
582	SuperClassWriter::addAttribute
583	("units", axis->unit.getValue(), &axisid);
584
585	if (!axis->positive.isEmpty())
586	{
587	SuperClassWriter::addAttribute("axis", string("Z"), &axisid);
588	SuperClassWriter::addAttribute("positive",
589	(axis->positive == CAxis::positive_attr::up) ? string("up") : string("down"),
590	&axisid);
591	}
592
593	StdString axisBoundsId = axisid + "_bounds";
594	if (!axis->bounds.isEmpty())
595	{
596	dims.push_back("axis_nbounds");
597	SuperClassWriter::addVariable(axisBoundsId, NC_FLOAT, dims);
598	SuperClassWriter::addAttribute("bounds", axisBoundsId, &axisid);
599	}
600
601	SuperClassWriter::definition_end();
602
603	CArray<double,1> axis_value(zoom_size);
604	for(int i = 0 ; i < zoom_size; i++) axis_value(i) = axis->value(i+zoom_begin);
605	SuperClassWriter::writeData(axis_value, axisid, isCollective, 0);
606
607	if (!axis->bounds.isEmpty())
608	{
609	CArray<double,2> axisBounds(zoom_size, 2);
610	for (int i = 0; i < zoom_size; i++)
611	{
612	axisBounds(i, 0) = axis->bounds(i + zoom_begin, 0);
613	axisBounds(i, 1) = axis->bounds(i + zoom_begin, 1);
614	}
615	SuperClassWriter::writeData(axisBounds, axisBoundsId, isCollective, 0);
616	}
617
618	SuperClassWriter::definition_start();
619
620	break;
621	}
622	default :
623	ERROR("CNc4DataOutput::writeDomain(domain)",
624	<< "[ type = " << SuperClass::type << "]"
625	<< " not implemented yet !");
626	}
627	}
628	catch (CNetCdfException& e)
629	{
630	StdString msg("On writing the axis : ");
631	msg.append(axisid); msg.append("\n");
632	msg.append("In the context : ");
633	CContext* context = CContext::getCurrent() ;
634	msg.append(context->getId()); msg.append("\n");
635	msg.append(e.what());
636	ERROR("CNc4DataOutput::writeAxis_(CAxis* axis)", << msg);
637	}
638	axis->addRelFile(this->filename);
639	}
640
641	void CNc4DataOutput::writeTimeDimension_(void)
642	{
643	try
644	{
645	SuperClassWriter::addDimension("time_counter");
646	}
647	catch (CNetCdfException& e)
648	{
649	StdString msg("On writing time dimension : time_couter\n");
650	msg.append("In the context : ");
651	CContext* context = CContext::getCurrent() ;
652	msg.append(context->getId()); msg.append("\n");
653	msg.append(e.what());
654	ERROR("CNc4DataOutput::writeTimeDimension_(void)", << msg);
655	}
656	}
657	//--------------------------------------------------------------
658
659	void CNc4DataOutput::writeField_(CField* field)
660	{
661	CContext* context = CContext::getCurrent() ;
662	CContextServer* server=context->server ;
663
664	std::vector<StdString> dims, coodinates;
665	CGrid* grid = field->grid;
666	CDomain* domain = grid->domain;
667
668	if (domain->isEmpty())
669	if (SuperClass::type==MULTI_FILE) return ;
670
671	StdString timeid = StdString("time_counter");
672	StdString domid = (!domain->name.isEmpty())
673	? domain->name.getValue() : domain->getId();
674	StdString appendDomid = (singleDomain) ? "" : "_"+domid ;
675
676	// bool isCurvilinear = domain->isCurvilinear ;
677	// bool isCurvilinear = (domain->type == CDomain::type_attr::curvilinear) ;
678
679	StdString dimXid,dimYid ;
680
681	switch (domain->type)
682	{
683	case CDomain::type_attr::curvilinear :
684	dimXid = StdString("x").append(appendDomid);
685	dimYid = StdString("y").append(appendDomid);
686	break ;
687	case CDomain::type_attr::regular :
688	dimXid = StdString("lon").append(appendDomid);
689	dimYid = StdString("lat").append(appendDomid);
690	break ;
691	case CDomain::type_attr::unstructured :
692	dimXid = StdString("cell").append(appendDomid);
693	break ;
694	}
695
696	/*
697	StdString lonid_loc = (server->intraCommSize > 1)
698	? StdString("lon").append(appendDomid).append("_local")
699	: lonid;
700	StdString latid_loc = (server->intraCommSize > 1)
701	? StdString("lat").append(appendDomid).append("_local")
702	: latid;
703	*/
704	StdString fieldid = (!field->name.isEmpty())
705	? field->name.getValue() : field->getBaseFieldReference()->getId();
706
707	// unsigned int ssize = domain->zoom_ni_loc.getValue() * domain->zoom_nj_loc.getValue();
708	// bool isCurvilinear = (domain->lonvalue.getValue()->size() == ssize);
709	// bool isCurvilinear = domain->isCurvilinear ;
710
711	nc_type type ;
712	if (field->prec.isEmpty()) type = NC_FLOAT ;
713	else
714	{
715	if (field->prec==2) type = NC_SHORT ;
716	else if (field->prec==4) type = NC_FLOAT ;
717	else if (field->prec==8) type = NC_DOUBLE ;
718	}
719
720	bool wtime = !(!field->operation.isEmpty() && field->foperation->timeType() == func::CFunctor::once);
721
722	if (wtime)
723	{
724
725	//StdOStringStream oss;
726	// oss << "time_" << field->operation.getValue()
727	// << "_" << field->getRelFile()->output_freq.getValue();
728	//oss
729	if (field->foperation->timeType() == func::CFunctor::instant) coodinates.push_back(string("time_instant"));
730	else if (field->foperation->timeType() == func::CFunctor::centered) coodinates.push_back(string("time_centered"));
731	dims.push_back(timeid);
732	}
733
734	if (!grid->axis_ref.isEmpty())
735	{
736	CAxis* axis = grid->axis ;
737	StdString axisid = (!axis->name.isEmpty()) ? axis->name.getValue() : axis->getId();
738	dims.push_back(axisid);
739	coodinates.push_back(axisid);
740	}
741
742	switch (domain->type)
743	{
744	case CDomain::type_attr::curvilinear :
745	coodinates.push_back(StdString("nav_lon").append(appendDomid));
746	coodinates.push_back(StdString("nav_lat").append(appendDomid));
747	break;
748	case CDomain::type_attr::regular :
749	case CDomain::type_attr::unstructured :
750	coodinates.push_back(StdString("lon").append(appendDomid));
751	coodinates.push_back(StdString("lat").append(appendDomid));
752	break;
753	}
754
755	if ( domain->type == CDomain::type_attr::curvilinear \|\| domain->type == CDomain::type_attr::regular)dims.push_back(dimYid);
756	dims.push_back(dimXid);
757
758	try
759	{
760	SuperClassWriter::addVariable(fieldid, type, dims);
761
762	if (!field->standard_name.isEmpty())
763	SuperClassWriter::addAttribute
764	("standard_name", field->standard_name.getValue(), &fieldid);
765
766	if (!field->long_name.isEmpty())
767	SuperClassWriter::addAttribute
768	("long_name", field->long_name.getValue(), &fieldid);
769
770	if (!field->unit.isEmpty())
771	SuperClassWriter::addAttribute
772	("units", field->unit.getValue(), &fieldid);
773
774	if (!field->valid_min.isEmpty())
775	SuperClassWriter::addAttribute
776	("valid_min", field->valid_min.getValue(), &fieldid);
777
778	if (!field->valid_max.isEmpty())
779	SuperClassWriter::addAttribute
780	("valid_max", field->valid_max.getValue(), &fieldid);
781
782	if (!field->scale_factor.isEmpty())
783	SuperClassWriter::addAttribute
784	("scale_factor", field->scale_factor.getValue(), &fieldid);
785
786	if (!field->add_offset.isEmpty())
787	SuperClassWriter::addAttribute
788	("add_offset", field->add_offset.getValue(), &fieldid);
789
790	SuperClassWriter::addAttribute
791	("online_operation", field->operation.getValue(), &fieldid);
792
793	// write child variables as attributes
794
795
796	vector<CVariable*> listVars = field->getAllVariables() ;
797	for (vector<CVariable>::iterator it = listVars.begin() ;it != listVars.end(); it++) writeAttribute_(it, fieldid) ;
798
799
800	if (wtime)
801	{
802	CDuration freqOp = CDuration::FromString(field->freq_op);
803	freqOp.solveTimeStep(*context->calendar);
804	StdString freqOpStr = freqOp.toStringUDUnits();
805	SuperClassWriter::addAttribute("interval_operation", freqOpStr, &fieldid);
806
807	CDuration freqOut = CDuration::FromString(field->getRelFile()->output_freq);
808	freqOut.solveTimeStep(*context->calendar);
809	SuperClassWriter::addAttribute("interval_write", freqOut.toStringUDUnits(), &fieldid);
810
811	StdString cellMethods = coodinates.front() + ": ";
812	if (field->operation.getValue() == "instant") cellMethods += "point";
813	else if (field->operation.getValue() == "average") cellMethods += "mean";
814	else if (field->operation.getValue() == "accumulate") cellMethods += "sum";
815	else cellMethods += field->operation;
816	if (freqOp.resolve(context->calendar) != freqOut.resolve(context->calendar))
817	cellMethods += " (interval: " + freqOpStr + ")";
818	SuperClassWriter::addAttribute("cell_methods", cellMethods, &fieldid);
819	}
820
821	if (domain->hasArea)
822	SuperClassWriter::addAttribute("cell_measures", "area: area" + appendDomid, &fieldid);
823
824	if (!field->default_value.isEmpty())
825	{
826	double default_value = field->default_value.getValue();
827	float fdefault_value = (float)default_value;
828	if (type == NC_DOUBLE)
829	SuperClassWriter::setDefaultValue(fieldid, &default_value);
830	else
831	SuperClassWriter::setDefaultValue(fieldid, &fdefault_value);
832	}
833	else
834	{
835	double * default_value = NULL;
836	SuperClassWriter::setDefaultValue(fieldid, default_value);
837	}
838
839	if (field->compression_level.isEmpty())
840	field->compression_level = field->file->compression_level.isEmpty() ? 0 : field->file->compression_level;
841	SuperClassWriter::setCompressionLevel(fieldid, field->compression_level);
842
843	{ // Ecriture des coordonnÃ©es
844
845	StdString coordstr; //boost::algorithm::join(coodinates, " ")
846	std::vector<StdString>::iterator
847	itc = coodinates.begin(), endc = coodinates.end();
848
849	for (; itc!= endc; itc++)
850	{
851	StdString & coord = *itc;
852	if (itc+1 != endc)
853	coordstr.append(coord).append(" ");
854	else coordstr.append(coord);
855	}
856
857	SuperClassWriter::addAttribute("coordinates", coordstr, &fieldid);
858
859	}
860	}
861	catch (CNetCdfException& e)
862	{
863	StdString msg("On writing field : ");
864	msg.append(fieldid); msg.append("\n");
865	msg.append("In the context : ");
866	msg.append(context->getId()); msg.append("\n");
867	msg.append(e.what());
868	ERROR("CNc4DataOutput::writeField_(CField* field)", << msg);
869	}
870	}
871
872	//--------------------------------------------------------------
873
874	void CNc4DataOutput::writeFile_ (CFile* file)
875	{
876	StdString filename = (!file->name.isEmpty())
877	? file->name.getValue() : file->getId();
878	StdString description = (!file->description.isEmpty())
879	? file->description.getValue()
880	: StdString("Created by xios");
881
882	singleDomain = (file->nbDomains == 1);
883
884	try
885	{
886	this->writeFileAttributes(filename, description,
887	StdString("CF-1.5"),
888	StdString("An IPSL model"),
889	this->getTimeStamp());
890
891	SuperClassWriter::addDimension("axis_nbounds", 2);
892	}
893	catch (CNetCdfException& e)
894	{
895	StdString msg("On writing file : ");
896	msg.append(filename); msg.append("\n");
897	msg.append("In the context : ");
898	CContext* context = CContext::getCurrent() ;
899	msg.append(context->getId()); msg.append("\n");
900	msg.append(e.what());
901	ERROR("CNc4DataOutput::writeFile_ (CFile* file)", << msg);
902	}
903	}
904
905	void CNc4DataOutput::writeAttribute_ (CVariable* var, const string& fieldId)
906	{
907	string name ;
908	if (!var->name.isEmpty()) name=var->name ;
909	else if (var->hasId()) name=var->getId() ;
910	else return ;
911
912	try
913	{
914	if (var->getVarType()==CVariable::t_int) addAttribute(name,var->getData<int>(),&fieldId) ;
915	else if (var->getVarType()==CVariable::t_short_int) addAttribute(name,var->getData<short int>(),&fieldId) ;
916	else if (var->getVarType()==CVariable::t_long_int) addAttribute(name,var->getData<long int>(),&fieldId) ;
917	else if (var->getVarType()==CVariable::t_float) addAttribute(name,var->getData<float>(),&fieldId) ;
918	else if (var->getVarType()==CVariable::t_double) addAttribute(name,var->getData<double>(),&fieldId) ;
919	else addAttribute(name,var->getData<string>(),&fieldId) ;
920	}
921	catch (CNetCdfException& e)
922	{
923	StdString msg("On writing attributes of variable with name : ");
924	msg.append(name); msg.append("in the field "); msg.append(fieldId); msg.append("\n");
925	msg.append("In the context : ");
926	CContext* context = CContext::getCurrent() ;
927	msg.append(context->getId()); msg.append("\n");
928	msg.append(e.what());
929	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var, const string& fieldId)", << msg);
930	}
931	}
932
933	void CNc4DataOutput::writeAttribute_ (CVariable* var)
934	{
935	string name ;
936	if (!var->name.isEmpty()) name=var->name ;
937	else if (var->hasId()) name=var->getId() ;
938	else return ;
939	try
940	{
941	if (var->getVarType()==CVariable::t_int) addAttribute(name,var->getData<int>()) ;
942	else if (var->getVarType()==CVariable::t_short_int) addAttribute(name,var->getData<short int>()) ;
943	else if (var->getVarType()==CVariable::t_long_int) addAttribute(name,var->getData<long int>()) ;
944	else if (var->getVarType()==CVariable::t_float) addAttribute(name,var->getData<float>()) ;
945	else if (var->getVarType()==CVariable::t_double) addAttribute(name,var->getData<double>()) ;
946	else addAttribute(name,var->getData<string>()) ;
947	}
948	catch (CNetCdfException& e)
949	{
950	StdString msg("On writing attributes of variable with name : ");
951	msg.append(name); msg.append("\n");
952	msg.append("In the context : ");
953	CContext* context = CContext::getCurrent() ;
954	msg.append(context->getId()); msg.append("\n");
955	msg.append(e.what());
956	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var)", << msg);
957	}
958	}
959
960	void CNc4DataOutput::syncFile_ (void)
961	{
962	try
963	{
964	SuperClassWriter::sync() ;
965	}
966	catch (CNetCdfException& e)
967	{
968	StdString msg("On synchronizing the write among processes");
969	msg.append("In the context : ");
970	CContext* context = CContext::getCurrent() ;
971	msg.append(context->getId()); msg.append("\n");
972	msg.append(e.what());
973	ERROR("CNc4DataOutput::syncFile_ (void)", << msg);
974	}
975	}
976
977	void CNc4DataOutput::closeFile_ (void)
978	{
979	try
980	{
981	SuperClassWriter::close() ;
982	}
983	catch (CNetCdfException& e)
984	{
985	StdString msg("On closing file");
986	msg.append("In the context : ");
987	CContext* context = CContext::getCurrent() ;
988	msg.append(context->getId()); msg.append("\n");
989	msg.append(e.what());
990	ERROR("CNc4DataOutput::syncFile_ (void)", << msg);
991	}
992
993	}
994
995	//---------------------------------------------------------------
996
997	StdString CNc4DataOutput::getTimeStamp(void) const
998	{
999	const int buffer_size = 100;
1000	time_t rawtime;
1001	struct tm * timeinfo = NULL;
1002	char buffer [buffer_size];
1003
1004	time ( &rawtime );
1005	timeinfo = localtime ( &rawtime );
1006	strftime (buffer, buffer_size, "%Y-%b-%d %H:%M:%S %Z", timeinfo);
1007
1008	return (StdString(buffer));
1009	}
1010
1011	//---------------------------------------------------------------
1012
1013	void CNc4DataOutput::writeFieldData_ (CField* field)
1014	{
1015	CContext* context = CContext::getCurrent() ;
1016	// if (field->getRelFile()->isSyncTime()) SuperClassWriter::sync() ;
1017	CContextServer* server=context->server ;
1018
1019	CGrid* grid = field->grid ;
1020	CDomain* domain = grid->domain ;
1021
1022	if(SuperClass::type==MULTI_FILE \|\| !isCollective) if (domain->isEmpty()) return;
1023
1024
1025	StdString fieldid = (!field->name.isEmpty())
1026	? field->name.getValue()
1027	: field->getBaseFieldReference()->getId();
1028
1029	StdOStringStream oss;
1030	string timeAxisId ;
1031	if (field->foperation->timeType() == func::CFunctor::instant) timeAxisId="time_instant" ;
1032	else if (field->foperation->timeType() == func::CFunctor::centered) timeAxisId="time_centered" ;
1033
1034	StdString timeBoundId("time_counter_bounds");
1035
1036	StdString timeAxisBoundId;
1037	if (field->foperation->timeType() == func::CFunctor::instant) timeAxisBoundId="time_instant_bounds" ;
1038	else if (field->foperation->timeType() == func::CFunctor::centered) timeAxisBoundId="time_centered_bounds" ;
1039
1040	CArray<double,1> time_data(1) ;
1041	CArray<double,1> time_counter(1) ;
1042	CArray<double,1> time_counter_bound(2);
1043	CArray<double,1> time_data_bound(2);
1044
1045	bool wtime = !(!field->operation.isEmpty() && (field->foperation->timeType() == func::CFunctor::once));
1046
1047	if (wtime)
1048	{
1049	time_counter(0)= (Time(field->last_Write_srv) + Time(field->lastlast_Write_srv)) / 2;
1050	if (field->foperation->timeType() == func::CFunctor::instant)
1051	time_data(0) = Time(*field->last_Write_srv);
1052	else if (field->foperation->timeType() == func::CFunctor::centered) time_data(0) = time_counter(0);
1053
1054	time_counter_bound(0) = Time(*field->lastlast_Write_srv);
1055	time_counter_bound(1) = Time(*field->last_Write_srv);
1056	if (field->foperation->timeType() == func::CFunctor::instant)
1057	time_data_bound(0) = time_data_bound(1) = Time(*field->last_Write_srv);
1058	else if (field->foperation->timeType() == func::CFunctor::centered)
1059	{
1060	time_data_bound(0) = time_counter_bound(0);
1061	time_data_bound(1) = time_counter_bound(1);
1062	}
1063	}
1064
1065	bool isRoot ;
1066	if (server->intraCommRank==0) isRoot=true ;
1067	else isRoot=false ;
1068
1069	if (!field->scale_factor.isEmpty() \|\| !field->add_offset.isEmpty())
1070	{
1071	double scaleFactor=1. ;
1072	double addOffset=0. ;
1073	if (!field->scale_factor.isEmpty()) scaleFactor=field->scale_factor ;
1074	if (!field->add_offset.isEmpty()) addOffset=field->add_offset ;
1075	field->scaleFactorAddOffset(scaleFactor,addOffset) ;
1076	}
1077
1078	try
1079	{
1080	if (grid->hasAxis()) // 3D
1081	{
1082	CAxis* axis = grid->axis ;
1083	CArray<double,3> field_data3D(domain->zoom_ni_srv,domain->zoom_nj_srv,axis->zoom_size) ;
1084	if (!field->default_value.isEmpty()) field_data3D = field->default_value ;
1085
1086	field->outputField(field_data3D);
1087
1088	if (!field->prec.isEmpty() && field->prec==2) field_data3D=round(field_data3D) ;
1089
1090	switch (SuperClass::type)
1091	{
1092	case (MULTI_FILE) :
1093	{
1094	SuperClassWriter::writeData(field_data3D, fieldid, isCollective, field->getNStep()-1);
1095	if (wtime)
1096	{
1097	SuperClassWriter::writeData(time_data, timeAxisId, isCollective, field->getNStep()-1);
1098	SuperClassWriter::writeData(time_counter, string("time_counter"), isCollective, field->getNStep()-1);
1099	SuperClassWriter::writeData(time_counter_bound, timeBoundId, isCollective, field->getNStep()-1);
1100	SuperClassWriter::writeData(time_data_bound, timeAxisBoundId, isCollective, field->getNStep()-1);
1101	}
1102	break ;
1103	}
1104	case (ONE_FILE) :
1105	{
1106	std::vector<StdSize> start(3) ;
1107	std::vector<StdSize> count(3) ;
1108	if (domain->isEmpty())
1109	{
1110	start[0]=0 ; start[1]=0 ; start[2]=0 ;
1111	count[0]=0 ; count[1]=0 ; start[2]=0 ;
1112	}
1113	else
1114	{
1115	// start[2]=domain->zoom_ibegin_loc.getValue()-domain->zoom_ibegin.getValue() ; start [1]=domain->zoom_jbegin_loc.getValue()-domain->zoom_jbegin.getValue() ; start[0]=0 ;
1116	start[2]=domain->zoom_ibegin_srv-domain->zoom_ibegin.getValue() ; start [1]=domain->zoom_jbegin_srv-domain->zoom_jbegin.getValue() ; start[0]=0 ;
1117	count[2]=domain->zoom_ni_srv ; count[1]=domain->zoom_nj_srv ; count[0] = axis->zoom_size.getValue();
1118	}
1119	SuperClassWriter::writeData(field_data3D, fieldid, isCollective, field->getNStep()-1,&start,&count );
1120	if (wtime)
1121	{
1122	SuperClassWriter::writeTimeAxisData(time_data, timeAxisId, isCollective, field->getNStep()-1,isRoot );
1123	SuperClassWriter::writeTimeAxisData(time_counter, string("time_counter"), isCollective, field->getNStep()-1,isRoot );
1124	SuperClassWriter::writeTimeAxisData(time_counter_bound, timeBoundId, isCollective, field->getNStep()-1, isRoot );
1125	SuperClassWriter::writeTimeAxisData(time_data_bound, timeAxisBoundId, isCollective, field->getNStep()-1, isRoot);
1126	}
1127	break;
1128	}
1129	}
1130
1131	}
1132	else // 2D
1133	{
1134	CArray<double,2> field_data2D(domain->zoom_ni_srv,domain->zoom_nj_srv) ;
1135	if (!field->default_value.isEmpty()) field_data2D = field->default_value ;
1136	field->outputField(field_data2D);
1137	if (!field->prec.isEmpty() && field->prec==2) field_data2D=round(field_data2D) ;
1138	switch (SuperClass::type)
1139	{
1140	case (MULTI_FILE) :
1141	{
1142	SuperClassWriter::writeData(field_data2D, fieldid, isCollective, field->getNStep()-1);
1143	if (wtime)
1144	{
1145	SuperClassWriter::writeData(time_data, timeAxisId, isCollective, field->getNStep()-1);
1146	SuperClassWriter::writeData(time_counter, string("time_counter"), isCollective, field->getNStep()-1);
1147	SuperClassWriter::writeData(time_counter_bound, timeBoundId, isCollective, field->getNStep()-1);
1148	SuperClassWriter::writeData(time_data_bound, timeAxisBoundId, isCollective, field->getNStep()-1);
1149	}
1150	break;
1151	}
1152	case (ONE_FILE) :
1153	{
1154	std::vector<StdSize> start(2) ;
1155	std::vector<StdSize> count(2) ;
1156	if (domain->isEmpty())
1157	{
1158	start[0]=0 ; start[1]=0 ;
1159	count[0]=0 ; count[1]=0 ;
1160	}
1161	else
1162	{
1163	start[1]=domain->zoom_ibegin_srv-domain->zoom_ibegin.getValue() ; start[0]=domain->zoom_jbegin_srv-domain->zoom_jbegin.getValue() ;
1164	count[1]=domain->zoom_ni_srv ; count[0]=domain->zoom_nj_srv ;
1165	}
1166
1167	SuperClassWriter::writeData(field_data2D, fieldid, isCollective, field->getNStep()-1,&start,&count);
1168	if (wtime)
1169	{
1170	SuperClassWriter::writeTimeAxisData(time_data, timeAxisId, isCollective, field->getNStep()-1,isRoot);
1171	SuperClassWriter::writeTimeAxisData(time_counter, string("time_counter"), isCollective, field->getNStep()-1,isRoot);
1172	SuperClassWriter::writeTimeAxisData(time_counter_bound, timeBoundId, isCollective, field->getNStep()-1, isRoot);
1173	SuperClassWriter::writeTimeAxisData(time_data_bound, timeAxisBoundId, isCollective, field->getNStep()-1, isRoot);
1174	}
1175	break;
1176
1177	}
1178	}
1179	}
1180	}
1181	catch (CNetCdfException& e)
1182	{
1183	StdString msg("On writing field data: ");
1184	msg.append(fieldid); msg.append("\n");
1185	msg.append("In the context : ");
1186	msg.append(context->getId()); msg.append("\n");
1187	msg.append(e.what());
1188	ERROR("CNc4DataOutput::writeFieldData_ (CField* field)", << msg);
1189	}
1190	}
1191
1192	//---------------------------------------------------------------
1193
1194	void CNc4DataOutput::writeTimeAxis_
1195	(CField* field,
1196	const boost::shared_ptr<CCalendar> cal)
1197	{
1198	StdOStringStream oss;
1199
1200	// if (field->operation.getValue().compare("once") == 0) return ;
1201	if (field->foperation->timeType() == func::CFunctor::once) return ;
1202
1203	// oss << "time_" << field->operation.getValue()
1204	// << "_" << field->getRelFile()->output_freq.getValue();
1205
1206	// StdString axisid = oss.str();
1207	// if (field->foperation->timeType() == func::CFunctor::centered) axisid="time_centered" ;
1208	// else if (field->foperation->timeType() == func::CFunctor::instant) axisid="time_instant" ;
1209
1210	StdString axisid("time_centered") ;
1211	StdString axisBoundId("time_centered_bounds");
1212	StdString timeid("time_counter");
1213	StdString timeBoundId("axis_nbounds");
1214
1215	if (field->foperation->timeType() == func::CFunctor::instant)
1216	{
1217	axisid = "time_instant";
1218	axisBoundId = "time_instant_bounds";
1219	}
1220
1221	try
1222	{
1223	// Adding time_instant or time_centered
1224	std::vector<StdString> dims;
1225	dims.push_back(timeid);
1226	if (!SuperClassWriter::varExist(axisid))
1227	{
1228	SuperClassWriter::addVariable(axisid, NC_DOUBLE, dims);
1229
1230	CDate timeOrigin=cal->getTimeOrigin() ;
1231	StdOStringStream oss2;
1232	// oss2<<initDate.getYear()<<"-"<<initDate.getMonth()<<"-"<<initDate.getDay()<<" "
1233	// <<initDate.getHour()<<"-"<<initDate.getMinute()<<"-"<<initDate.getSecond() ;
1234	StdString strInitdate=oss2.str() ;
1235	StdString strTimeOrigin=timeOrigin.toString() ;
1236	this->writeTimeAxisAttributes
1237	(axisid, cal->getType(),
1238	StdString("seconds since ").append(strTimeOrigin),
1239	strTimeOrigin, axisBoundId);
1240	}
1241
1242	// Adding time_instant_bounds or time_centered_bounds variables
1243	if (!SuperClassWriter::varExist(axisBoundId))
1244	{
1245	dims.clear() ;
1246	dims.push_back(timeid);
1247	dims.push_back(timeBoundId);
1248	SuperClassWriter::addVariable(axisBoundId, NC_DOUBLE, dims);
1249	}
1250
1251	// Adding time_counter
1252	axisid = "time_counter" ;
1253	axisBoundId = "time_counter_bounds" ;
1254	dims.clear() ;
1255	dims.push_back(timeid);
1256	if (!SuperClassWriter::varExist(axisid))
1257	{
1258	SuperClassWriter::addVariable(axisid, NC_DOUBLE, dims);
1259	SuperClassWriter::addAttribute("axis", string("T"), &axisid);
1260	CDate timeOrigin=cal->getTimeOrigin() ;
1261	StdString strTimeOrigin=timeOrigin.toString() ;
1262
1263	this->writeTimeAxisAttributes
1264	(axisid, cal->getType(),
1265	StdString("seconds since ").append(strTimeOrigin),
1266	strTimeOrigin, axisBoundId);
1267	}
1268
1269	// Adding time_counter_bound dimension
1270	if (!SuperClassWriter::varExist(axisBoundId))
1271	{
1272	dims.clear();
1273	dims.push_back(timeid);
1274	dims.push_back(timeBoundId);
1275	SuperClassWriter::addVariable(axisBoundId, NC_DOUBLE, dims);
1276	}
1277	}
1278	catch (CNetCdfException& e)
1279	{
1280	StdString msg("On writing time axis data: ");
1281	msg.append("In the context : ");
1282	CContext* context = CContext::getCurrent() ;
1283	msg.append(context->getId()); msg.append("\n");
1284	msg.append(e.what());
1285	ERROR("CNc4DataOutput::writeTimeAxis_ (CField* field, \
1286	const boost::shared_ptr<CCalendar> cal)", << msg);
1287	}
1288	}
1289
1290	//---------------------------------------------------------------
1291
1292	void CNc4DataOutput::writeTimeAxisAttributes(const StdString & axis_name,
1293	const StdString & calendar,
1294	const StdString & units,
1295	const StdString & time_origin,
1296	const StdString & time_bounds,
1297	const StdString & standard_name,
1298	const StdString & long_name)
1299	{
1300	try
1301	{
1302	SuperClassWriter::addAttribute("standard_name", standard_name, &axis_name);
1303	SuperClassWriter::addAttribute("long_name", long_name , &axis_name);
1304	SuperClassWriter::addAttribute("calendar", calendar , &axis_name);
1305	SuperClassWriter::addAttribute("units", units , &axis_name);
1306	SuperClassWriter::addAttribute("time_origin", time_origin , &axis_name);
1307	SuperClassWriter::addAttribute("bounds", time_bounds , &axis_name);
1308	}
1309	catch (CNetCdfException& e)
1310	{
1311	StdString msg("On writing time axis Attribute: ");
1312	msg.append("In the context : ");
1313	CContext* context = CContext::getCurrent() ;
1314	msg.append(context->getId()); msg.append("\n");
1315	msg.append(e.what());
1316	ERROR("CNc4DataOutput::writeTimeAxisAttributes(const StdString & axis_name, \
1317	const StdString & calendar,\
1318	const StdString & units, \
1319	const StdString & time_origin, \
1320	const StdString & time_bounds, \
1321	const StdString & standard_name, \
1322	const StdString & long_name)", << msg);
1323	}
1324	}
1325
1326	//---------------------------------------------------------------
1327
1328	void CNc4DataOutput::writeAxisAttributes(const StdString & axis_name,
1329	const StdString & axis,
1330	const StdString & standard_name,
1331	const StdString & long_name,
1332	const StdString & units,
1333	const StdString & nav_model)
1334	{
1335	try
1336	{
1337	if (!axis.empty())
1338	SuperClassWriter::addAttribute("axis" , axis , &axis_name);
1339
1340	SuperClassWriter::addAttribute("standard_name", standard_name, &axis_name);
1341	SuperClassWriter::addAttribute("long_name" , long_name , &axis_name);
1342	SuperClassWriter::addAttribute("units" , units , &axis_name);
1343	SuperClassWriter::addAttribute("nav_model" , nav_model , &axis_name);
1344	}
1345	catch (CNetCdfException& e)
1346	{
1347	StdString msg("On writing Axis Attribute: ");
1348	msg.append("In the context : ");
1349	CContext* context = CContext::getCurrent() ;
1350	msg.append(context->getId()); msg.append("\n");
1351	msg.append(e.what());
1352	ERROR("CNc4DataOutput::writeAxisAttributes(const StdString & axis_name, \
1353	const StdString & axis, \
1354	const StdString & standard_name, \
1355	const StdString & long_name, \
1356	const StdString & units, \
1357	const StdString & nav_model)", << msg);
1358	}
1359	}
1360
1361	//---------------------------------------------------------------
1362
1363	void CNc4DataOutput::writeLocalAttributes
1364	(int ibegin, int ni, int jbegin, int nj, StdString domid)
1365	{
1366	try
1367	{
1368	SuperClassWriter::addAttribute(StdString("ibegin").append(domid), ibegin);
1369	SuperClassWriter::addAttribute(StdString("ni" ).append(domid), ni);
1370	SuperClassWriter::addAttribute(StdString("jbegin").append(domid), jbegin);
1371	SuperClassWriter::addAttribute(StdString("nj" ).append(domid), nj);
1372	}
1373	catch (CNetCdfException& e)
1374	{
1375	StdString msg("On writing Local Attributes: ");
1376	msg.append("In the context : ");
1377	CContext* context = CContext::getCurrent() ;
1378	msg.append(context->getId()); msg.append("\n");
1379	msg.append(e.what());
1380	ERROR("CNc4DataOutput::writeLocalAttributes \
1381	(int ibegin, int ni, int jbegin, int nj, StdString domid)", << msg);
1382	}
1383
1384	}
1385
1386	void CNc4DataOutput::writeLocalAttributes_IOIPSL
1387	(int ibegin, int ni, int jbegin, int nj, int ni_glo, int nj_glo, int rank, int size)
1388	{
1389	CArray<int,1> array(2) ;
1390
1391	try
1392	{
1393	SuperClassWriter::addAttribute("DOMAIN_number_total",size ) ;
1394	SuperClassWriter::addAttribute("DOMAIN_number", rank) ;
1395	array=1,2 ;
1396	SuperClassWriter::addAttribute("DOMAIN_dimensions_ids",array) ;
1397	array=ni_glo,nj_glo ;
1398	SuperClassWriter::addAttribute("DOMAIN_size_global", array) ;
1399	array=ni,nj ;
1400	SuperClassWriter::addAttribute("DOMAIN_size_local", array) ;
1401	array=ibegin,jbegin ;
1402	SuperClassWriter::addAttribute("DOMAIN_position_first", array) ;
1403	array=ibegin+ni-1,jbegin+nj-1 ;
1404	SuperClassWriter::addAttribute("DOMAIN_position_last",array) ;
1405	array=0,0 ;
1406	SuperClassWriter::addAttribute("DOMAIN_halo_size_start", array) ;
1407	SuperClassWriter::addAttribute("DOMAIN_halo_size_end", array);
1408	SuperClassWriter::addAttribute("DOMAIN_type",string("box")) ;
1409	/*
1410	SuperClassWriter::addAttribute("DOMAIN_DIM_N001",string("x")) ;
1411	SuperClassWriter::addAttribute("DOMAIN_DIM_N002",string("y")) ;
1412	SuperClassWriter::addAttribute("DOMAIN_DIM_N003",string("axis_A")) ;
1413	SuperClassWriter::addAttribute("DOMAIN_DIM_N004",string("time_counter")) ;
1414	*/
1415	}
1416	catch (CNetCdfException& e)
1417	{
1418	StdString msg("On writing Local Attributes IOI PSL \n");
1419	msg.append("In the context : ");
1420	CContext* context = CContext::getCurrent() ;
1421	msg.append(context->getId()); msg.append("\n");
1422	msg.append(e.what());
1423	ERROR("CNc4DataOutput::writeLocalAttributes_IOIPSL \
1424	(int ibegin, int ni, int jbegin, int nj, int ni_glo, int nj_glo, int rank, int size)", << msg);
1425	}
1426	}
1427	//---------------------------------------------------------------
1428
1429	void CNc4DataOutput:: writeFileAttributes(const StdString & name,
1430	const StdString & description,
1431	const StdString & conventions,
1432	const StdString & production,
1433	const StdString & timeStamp)
1434	{
1435	try
1436	{
1437	SuperClassWriter::addAttribute("name" , name);
1438	SuperClassWriter::addAttribute("description", description);
1439	SuperClassWriter::addAttribute("title" , description);
1440	SuperClassWriter::addAttribute("Conventions", conventions);
1441	SuperClassWriter::addAttribute("production" , production);
1442	SuperClassWriter::addAttribute("timeStamp" , timeStamp);
1443	}
1444	catch (CNetCdfException& e)
1445	{
1446	StdString msg("On writing File Attributes \n ");
1447	msg.append("In the context : ");
1448	CContext* context = CContext::getCurrent() ;
1449	msg.append(context->getId()); msg.append("\n");
1450	msg.append(e.what());
1451	ERROR("CNc4DataOutput:: writeFileAttributes(const StdString & name, \
1452	const StdString & description, \
1453	const StdString & conventions, \
1454	const StdString & production, \
1455	const StdString & timeStamp)", << msg);
1456	}
1457	}
1458
1459	//---------------------------------------------------------------
1460
1461	void CNc4DataOutput::writeMaskAttributes(const StdString & mask_name,
1462	int data_dim,
1463	int data_ni,
1464	int data_nj,
1465	int data_ibegin,
1466	int data_jbegin)
1467	{
1468	try
1469	{
1470	SuperClassWriter::addAttribute("data_dim" , data_dim , &mask_name);
1471	SuperClassWriter::addAttribute("data_ni" , data_ni , &mask_name);
1472	SuperClassWriter::addAttribute("data_nj" , data_nj , &mask_name);
1473	SuperClassWriter::addAttribute("data_ibegin", data_ibegin, &mask_name);
1474	SuperClassWriter::addAttribute("data_jbegin", data_jbegin, &mask_name);
1475	}
1476	catch (CNetCdfException& e)
1477	{
1478	StdString msg("On writing Mask Attributes \n ");
1479	msg.append("In the context : ");
1480	CContext* context = CContext::getCurrent() ;
1481	msg.append(context->getId()); msg.append("\n");
1482	msg.append(e.what());
1483	ERROR("CNc4DataOutput::writeMaskAttributes(const StdString & mask_name, \
1484	int data_dim, \
1485	int data_ni, \
1486	int data_nj, \
1487	int data_ibegin, \
1488	int data_jbegin)", << msg);
1489	}
1490	}
1491
1492	///--------------------------------------------------------------
1493
1494	} // namespace xios

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source: XIOS/branchs/xios-1.0/src/output/nc4_data_output.cpp @ 614

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