1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
|
/*********************************************************************
* Copyright 1993, UCAR/Unidata
* See netcdf/COPYRIGHT file for copying and redistribution conditions.
* $Header: /upc/share/CVS/netcdf-3/ncgen/genbin.c,v 1.4 2010/05/27 21:34:17 dmh Exp $
*********************************************************************/
#include "includes.h"
#include <ctype.h> /* for isprint() */
#include "nciter.h"
#include "offsets.h"
#ifdef ENABLE_BINARY
#undef TRACE
extern List* vlenconstants;
/* Forward*/
static void genbin_defineattr(Symbol* asym,Bytebuffer*);
static void genbin_definevardata(Symbol* vsym);
static void genbin_write(Symbol*,Bytebuffer*,Odometer*,int);
#ifdef USE_NETCDF4
static void genbin_deftype(Symbol* tsym);
static void genbin_definespecialattributes(Symbol* var);
#endif
/*
* Generate C code for creating netCDF from in-memory structure.
*/
void
gen_netcdf(const char *filename)
{
int stat, ncid;
int idim, ivar, iatt;
int ndims, nvars, natts, ngatts, ntyps, ngrps;
#ifdef USE_NETCDF4
int igrp;
#endif
Bytebuffer* databuf = bbNew();
ndims = listlength(dimdefs);
nvars = listlength(vardefs);
natts = listlength(attdefs);
ngatts = listlength(gattdefs);
ntyps = listlength(typdefs);
ngrps = listlength(grpdefs);
/* create netCDF file, uses NC_CLOBBER mode */
cmode_modifier |= NC_CLOBBER;
#ifdef USE_NETCDF4
if(!usingclassic)
cmode_modifier |= NC_NETCDF4;
#endif
stat = nc_create(filename, cmode_modifier, &ncid);
check_err(stat,__LINE__,__FILE__);
/* ncid created above is also root group*/
rootgroup->ncid = ncid;
#ifdef USE_NETCDF4
/* Define the group structure */
/* walking grdefs list will do a preorder walk of all defined groups*/
for(igrp=0;igrp<ngrps;igrp++) {
Symbol* gsym = (Symbol*)listget(grpdefs,igrp);
if(gsym == rootgroup) continue; /* ignore root group*/
stat = nc_def_grp(gsym->container->ncid,gsym->name,&gsym->ncid);
check_err(stat,__LINE__,__FILE__);
}
#endif
#ifdef USE_NETCDF4
/* Define the types*/
if (ntyps > 0) {
int ityp;
for(ityp = 0; ityp < ntyps; ityp++) {
Symbol* tsym = (Symbol*)listget(typdefs,ityp);
genbin_deftype(tsym);
}
}
#endif
/* define dimensions from info in dims array */
if (ndims > 0) {
for(idim = 0; idim < ndims; idim++) {
Symbol* dsym = (Symbol*)listget(dimdefs,idim);
stat = nc_def_dim(dsym->container->ncid,
dsym->name,
dsym->dim.declsize,
&dsym->ncid);
check_err(stat,__LINE__,__FILE__);
}
}
/* define variables from info in vars array */
if (nvars > 0) {
for(ivar = 0; ivar < nvars; ivar++) {
Symbol* vsym = (Symbol*)listget(vardefs,ivar);
if (vsym->typ.dimset.ndims > 0) { /* a dimensioned variable */
/* construct a vector of dimension ids*/
int dimids[NC_MAX_VAR_DIMS];
for(idim=0;idim<vsym->typ.dimset.ndims;idim++)
dimids[idim] = vsym->typ.dimset.dimsyms[idim]->ncid;
stat = nc_def_var(vsym->container->ncid,
vsym->name,
vsym->typ.basetype->ncid,
vsym->typ.dimset.ndims,
dimids,
&vsym->ncid);
} else { /* a scalar */
stat = nc_def_var(vsym->container->ncid,
vsym->name,
vsym->typ.basetype->ncid,
vsym->typ.dimset.ndims,
NULL,
&vsym->ncid);
}
check_err(stat,__LINE__,__FILE__);
}
}
#ifdef USE_NETCDF4
/* Collect vlen data*/
bindata_vlenconstants(vlenconstants);
/* define special variable properties */
if(nvars > 0) {
for(ivar = 0; ivar < nvars; ivar++) {
Symbol* var = (Symbol*)listget(vardefs,ivar);
genbin_definespecialattributes(var);
}
}
#endif /*USE_NETCDF4*/
/* define global attributes */
if(ngatts > 0) {
for(iatt = 0; iatt < ngatts; iatt++) {
Symbol* gasym = (Symbol*)listget(gattdefs,iatt);
bbClear(databuf);
genbin_defineattr(gasym,databuf);
}
}
/* define per-variable attributes */
if(natts > 0) {
for(iatt = 0; iatt < natts; iatt++) {
Symbol* asym = (Symbol*)listget(attdefs,iatt);
bbClear(databuf);
genbin_defineattr(asym,databuf);
}
}
if (nofill_flag) {
stat = nc_set_fill(rootgroup->ncid, NC_NOFILL, 0);
check_err(stat,__LINE__,__FILE__);
}
/* leave define mode */
stat = nc_enddef(rootgroup->ncid);
check_err(stat,__LINE__,__FILE__);
/* Load values into those variables with defined data */
if(nvars > 0) {
for(ivar = 0; ivar < nvars; ivar++) {
Symbol* vsym = (Symbol*)listget(vardefs,ivar);
if(vsym->data != NULL) {
bbClear(databuf);
genbin_definevardata(vsym);
}
}
}
bbFree(databuf);
}
#ifdef USE_NETCDF4
static void
genbin_definespecialattributes(Symbol* var)
{
int stat;
Specialdata* special = &var->var.special;
if(special->flags & _STORAGE_FLAG) {
int storage = special->_Storage;
size_t* chunks = special->_ChunkSizes;
if(special->nchunks == 0 || chunks == NULL) chunks = NULL;
stat = nc_def_var_chunking(var->container->ncid,
var->ncid,
(storage == NC_CONTIGUOUS?NC_CONTIGUOUS
:NC_CHUNKED),
chunks);
check_err(stat,__LINE__,__FILE__);
}
if(special->flags & _FLETCHER32_FLAG) {
stat = nc_def_var_fletcher32(var->container->ncid,
var->ncid,
special->_Fletcher32);
check_err(stat,__LINE__,__FILE__);
}
if(special->flags & (_DEFLATE_FLAG | _SHUFFLE_FLAG)) {
stat = nc_def_var_deflate(var->container->ncid,
var->ncid,
(special->_Shuffle == 1?1:0),
(special->_DeflateLevel >= 0?1:0),
(special->_DeflateLevel >= 0?special->_DeflateLevel
:0));
check_err(stat,__LINE__,__FILE__);
}
if(special->flags & _ENDIAN_FLAG) {
stat = nc_def_var_endian(var->container->ncid,
var->ncid,
(special->_Endianness == NC_ENDIAN_LITTLE?
NC_ENDIAN_LITTLE
:NC_ENDIAN_BIG));
check_err(stat,__LINE__,__FILE__);
}
if(special->flags & _NOFILL_FLAG) {
stat = nc_def_var_fill(var->container->ncid,
var->ncid,
(special->_Fill?NC_FILL:NC_NOFILL),
NULL);
check_err(stat,__LINE__,__FILE__);
}
}
#endif /*USE_NETCDF4*/
void
cl_netcdf(void)
{
int stat;
stat = nc_close(rootgroup->ncid);
check_err(stat,__LINE__,__FILE__);
}
#ifdef USE_NETCDF4
/*
Generate type definitions
*/
static void
genbin_deftype(Symbol* tsym)
{
int i,stat;
ASSERT(tsym->objectclass == NC_TYPE);
switch (tsym->subclass) {
case NC_PRIM: break; /* these are already taken care of*/
case NC_OPAQUE:
stat = nc_def_opaque(tsym->container->ncid,
tsym->typ.size,
tsym->name,
&tsym->ncid);
check_err(stat,__LINE__,__FILE__);
break;
case NC_ENUM: {
Bytebuffer* datum;
Datalist* ecdl;
Datasrc* esrc;
stat = nc_def_enum(tsym->container->ncid,
tsym->typ.basetype->typ.typecode,
tsym->name,
&tsym->ncid);
check_err(stat,__LINE__,__FILE__);
datum = bbNew();
ecdl = builddatalist(1);
dlextend(ecdl); /* make room for one constant*/
ecdl->length = 1;
esrc = datalist2src(ecdl);
for(i=0;i<listlength(tsym->subnodes);i++) {
Symbol* econst = (Symbol*)listget(tsym->subnodes,i);
ASSERT(econst->subclass == NC_ECONST);
ecdl->data[0] = econst->typ.econst;
esrc->index = 0;
bbClear(datum);
bindata_basetype(econst->typ.basetype,esrc,datum,NULL);
stat = nc_insert_enum(tsym->container->ncid,
tsym->ncid,
econst->name,
bbContents(datum));
check_err(stat,__LINE__,__FILE__);
}
bbFree(datum);
ecdl->length = 0;
freedatasrc(esrc);
} break;
case NC_VLEN:
stat = nc_def_vlen(tsym->container->ncid,
tsym->name,
tsym->typ.basetype->ncid,
&tsym->ncid);
check_err(stat,__LINE__,__FILE__);
break;
case NC_COMPOUND:
stat = nc_def_compound(tsym->container->ncid,
tsym->typ.size,
tsym->name,
&tsym->ncid);
check_err(stat,__LINE__,__FILE__);
for(i=0;i<listlength(tsym->subnodes);i++) {
Symbol* efield = (Symbol*)listget(tsym->subnodes,i);
ASSERT(efield->subclass == NC_FIELD);
if(efield->typ.dimset.ndims == 0){
stat = nc_insert_compound(
tsym->container->ncid,
tsym->ncid,
efield->name,
efield->typ.offset,
efield->typ.basetype->ncid);
} else {
int j;
Bytebuffer* dimbuf = bbNew();
/* Generate the field dimension constants*/
for(j=0;j<efield->typ.dimset.ndims;j++) {
unsigned int size = efield->typ.dimset.dimsyms[j]->dim.declsize;
bbAppendn(dimbuf,(char*)&size,sizeof(size));
}
stat = nc_insert_array_compound(
tsym->container->ncid,
tsym->ncid,
efield->name,
efield->typ.offset,
efield->typ.basetype->ncid,
efield->typ.dimset.ndims,
(int*)bbContents(dimbuf));
bbFree(dimbuf);
}
check_err(stat,__LINE__,__FILE__);
}
break;
default: panic("definectype: unexpected type subclass");
}
}
#endif /*USE_NETCDF4*/
static void
genbin_defineattr(Symbol* asym,Bytebuffer* databuf)
{
int stat;
size_t len;
Datalist* list;
int varid, grpid, typid;
Symbol* basetype = asym->typ.basetype;
bbClear(databuf);
grpid = asym->container->ncid,
varid = (asym->att.var == NULL?NC_GLOBAL : asym->att.var->ncid);
typid = basetype->ncid;
list = asym->data;
len = list->length;
bindata_attrdata(asym,databuf);
/* Use the specialized put_att_XX routines if possible*/
if(isprim(basetype->typ.typecode)) {
switch (basetype->typ.typecode) {
case NC_BYTE: {
signed char* data = (signed char*)bbContents(databuf);
stat = nc_put_att_schar(grpid,varid,asym->name,typid,len,data);
check_err(stat,__LINE__,__FILE__);
} break;
case NC_CHAR: {
char* data = (char*)bbContents(databuf);
size_t slen = bbLength(databuf);
#ifdef IGNORE
/* Revise length if slen == 0 */
if(slen == 0) {bbAppend(databuf,'\0'); slen++;}
#endif
stat = nc_put_att_text(grpid,varid,asym->name,slen,data);
check_err(stat,__LINE__,__FILE__);
} break;
case NC_SHORT: {
short* data = (short*)bbContents(databuf);
stat = nc_put_att_short(grpid,varid,asym->name,typid,len,data);
check_err(stat,__LINE__,__FILE__);
} break;
case NC_INT: {
int* data = (int*)bbContents(databuf);
stat = nc_put_att_int(grpid,varid,asym->name,typid,len,data);
check_err(stat,__LINE__,__FILE__);
} break;
case NC_FLOAT: {
float* data = (float*)bbContents(databuf);
stat = nc_put_att_float(grpid,varid,asym->name,typid,len,data);
check_err(stat,__LINE__,__FILE__);
} break;
case NC_DOUBLE: {
double* data = (double*)bbContents(databuf);
stat = nc_put_att_double(grpid,varid,asym->name,typid,len,data);
check_err(stat,__LINE__,__FILE__);
} break;
#ifdef USE_NETCDF4
case NC_STRING: {
const char** data;
data = (const char**)bbContents(databuf);
stat = nc_put_att_string(grpid,varid,asym->name,
bbLength(databuf)/sizeof(char*),
data);
} break;
case NC_UBYTE: {
unsigned char* data = (unsigned char*)bbContents(databuf);
stat = nc_put_att_uchar(grpid,varid,asym->name,typid,len,data);
check_err(stat,__LINE__,__FILE__);
} break;
case NC_USHORT: {
unsigned short* data = (unsigned short*)bbContents(databuf);
stat = nc_put_att_ushort(grpid,varid,asym->name,typid,len,data);
check_err(stat,__LINE__,__FILE__);
} break;
case NC_UINT: {
unsigned int* data = (unsigned int*)bbContents(databuf);
stat = nc_put_att_uint(grpid,varid,asym->name,typid,len,data);
check_err(stat,__LINE__,__FILE__);
} break;
case NC_INT64: {
long long* data = (long long*)bbContents(databuf);
stat = nc_put_att_longlong(grpid,varid,asym->name,typid,len,data);
check_err(stat,__LINE__,__FILE__);
} break;
case NC_UINT64: {
unsigned long long* data = (unsigned long long*)bbContents(databuf);
stat = nc_put_att_ulonglong(grpid,varid,asym->name,typid,len,data);
check_err(stat,__LINE__,__FILE__);
} break;
#endif
default: PANIC1("genbin_defineattr: unexpected basetype: %d",basetype->typ.typecode);
}
} else { /* use the generic put_attribute for user defined types*/
const char* data;
char out[4096];
data = (const char*)bbContents(databuf);
stat = nc_put_att(grpid,varid,asym->name,typid,
len,(void*)data);
check_err(stat,__LINE__,__FILE__);
memset(out,0x77,sizeof(out));
stat = nc_get_att(grpid,varid,asym->name,&out);
check_err(stat,__LINE__,__FILE__);
}
}
/* Following is patterned after the walk functions in semantics.c */
static void
genbin_definevardata(Symbol* vsym)
{
int varid, grpid;
int rank;
Bytebuffer* memory;
nciter_t iter;
Odometer* odom = NULL;
size_t nelems;
int chartype = (vsym->typ.basetype->typ.typecode == NC_CHAR);
Datalist* fillsrc = vsym->var.special._Fillvalue;
int isscalar = (vsym->typ.dimset.ndims == 0);
grpid = vsym->container->ncid,
varid = vsym->ncid;
rank = vsym->typ.dimset.ndims;
memory = bbNew();
/* give the buffer a running start to be large enough*/
bbSetalloc(memory, nciterbuffersize);
if(vsym->data == NULL) return;
/* Generate character constants separately */
if(!isscalar && chartype) {
gen_chararray(vsym,memory,fillsrc);
/* generate a corresponding odometer */
odom = newodometer(&vsym->typ.dimset,NULL,NULL);
genbin_write(vsym,memory,odom,0);
} else { /* not character constant */
Datasrc* src = datalist2src(vsym->data);
if(isscalar) { /*scalar */
bindata_basetype(vsym->typ.basetype,src,memory,fillsrc); /*scalar*/
if(bbLength(memory) > 0)
genbin_write(vsym,memory,odom,1);
} else { /* This is the heavy lifing */
/* Create an iterator to generate blocks of data */
nc_get_iter(vsym,nciterbuffersize,&iter);
/* Fill in the local odometer instance */
odom = newodometer(&vsym->typ.dimset,NULL,NULL);
for(;;) {
nelems=nc_next_iter(&iter,odom->start,odom->count);
if(nelems == 0) break;
if(debug > 0) {/*dump the iteration info*/
int i;
fprintf(stderr,"iter: %s->start[",vsym->name);
for(i=0;i<odom->rank;i++)
fprintf(stderr,"%s%lu",(i==0?"":","),(unsigned long)odom->start[i]);
fprintf(stderr,"]\n %s->count[",vsym->name);
for(i=0;i<odom->rank;i++)
fprintf(stderr,"%s%lu",(i==0?"":","),(unsigned long)odom->count[i]);
fprintf(stderr,"]\n");
}
bindata_array(vsym,memory,src,odom,/*index=*/0,fillsrc);
/* Dump this chunk of (non-scalar) memory */
genbin_write(vsym,memory,odom,0);
}
/* Write any residual data */
if(bbLength(memory) > 0)
genbin_write(vsym,memory,odom,0);
}
}
odometerfree(odom);
bbFree(memory);
}
static void
genbin_write(Symbol* vsym, Bytebuffer* memory, Odometer* odom, int scalar)
{
int stat = NC_NOERR;
if(!scalar && debug > 0) {
int i;
fprintf(stderr,"startset = [");
for(i=0;i<odom->rank;i++)
fprintf(stderr,"%s%lu",(i>0?", ":""),(unsigned long)odom->start[i]);
fprintf(stderr,"] ");
fprintf(stderr,"countset = [");
for(i=0;i<odom->rank;i++)
fprintf(stderr,"%s%lu",(i>0?", ":""),(unsigned long)odom->count[i]);
fprintf(stderr,"]\n");
fflush(stderr);
}
if(scalar) {
size_t count[1] = {1};
stat = nc_put_var1(vsym->container->ncid, vsym->ncid, count,
bbContents(memory));
} else {
stat = nc_put_vara(vsym->container->ncid, vsym->ncid,
odom->start, odom->count,
bbContents(memory));
}
check_err(stat,__LINE__,__FILE__);
bbClear(memory);
}
#endif /*ENABLE_BINARY*/
|
