/
mnc_assembly.m
536 lines (467 loc) · 15.4 KB
/
mnc_assembly.m
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
function [nt,nf] = mnc_assembly(fpat,vars, fout,fsize)
% Function [nt,nf] = mnc_assembly(fpat,vars, fout,fsize)
%
% INPUTS
% fpat string containing the file pattern
% vars structure array of variable names
%
% fout output file pattern (DEF: "all.%05d.nc")
% fsize max output file size (DEF: 2.0e+9 = +/-2GB)
%
% OUTPUTS
% nt number of usable tiles found
% nf number of output files written
%
% This function "assembles" MNC output. It finds all the per-tile
% NetCDF files that match the input pattern, does some basic "sanity"
% tests to determine whether the files have compatible sizes, and
% then assembles all of the requested data (all of the variables)
% into one or more "global" NetCDF files. The global files have
% the following dimension conventions:
%
% "exch 1": all values are within a global horizontal grid
% and indicies are (X,Y,Z,T)
%
% "exch 2": all values are within one of up to six "faces"
% of a global cube with indicies (Xf,Yf,F,Z,T)
%
% where "X,Y.Z,T" are global space/time indicies, "Xf,Yf" are local
% per-face spatial indicies, and "F" is a face index.
%
% An example of how to use this script is:
%
% vars = struct([]);
% vars(1).name = 'iter';
% vars(2).name = 'U';
% vars(3).name = 'Unk';
% vars(4).name = 'V';
% vars(5).name = 'Temp';
% vars(6).name = 'S';
% fpat = 'exp0_20041126_0001/state.0000.%06d.nc';
% [nt,nf] = mnc_assembly(fpat,vars);
%
% and the resutlt is written as "all.00000.nc"
%===== Argument checking and defaults =====
if nargin < 2
disp('Error: there must be at least 2 arguments!');
return
end
if nargin < 3
fout = 'all.%05d.nc';
end
if nargin < 4
fsize = 2.0e+9;
end
%===== Find and open all the matching files =====
nt = 0;
nf = 0;
all_ncf = struct([]);
% Find all of the files
exch2_msg = 0;
tmax = 200;
frdone = 0;
it = 0;
while frdone == 0
it = it + 1;
fnm = sprintf(fpat,it);
% disp(fnm);
% Check that the file exists
fid = fopen(fnm, 'r');
if fid < 0
if it >= tmax
frdone = 1;
end
continue;
end
% Open the NetCDF file
fnc = netcdf(fnm, 'nowrite');
if length(fnc) == 0
continue;
end
% Check for exch1/exch2 grid
exch = 1;
exch2_myFace = fnc.exch2_myFace(:);
if length(exch2_myFace) ~= 0
exch = 2;
if exch2_msg == 0
exch2_msg = 1;
disp(' Grid type appears to be: "exch2"');
end
end
n = length(all_ncf) + 1;
all_ncf(n).name = fnm;
all_ncf(n).nc = {fnc};
all_ncf(n).exch = exch;
all_ncf(n).tile_number = fnc.tile_number(1);
all_ncf(n).bi = fnc.bi(1);
all_ncf(n).bj = fnc.bj(1);
all_ncf(n).sNx = fnc.sNx(1);
all_ncf(n).sNy = fnc.sNy(1);
all_ncf(n).Nx = fnc.Nx(1);
all_ncf(n).Ny = fnc.Ny(1);
all_ncf(n).Z = fnc.Z(1);
if exch == 2
all_ncf(n).exch2_myFace = exch2_myFace;
all_ncf(n).exch2_tbasex = fnc.exch2_tbasex(1);
all_ncf(n).exch2_tbasey = fnc.exch2_tbasex(1);
end
clear fnc
end
%===== Do some basic sanity checks =====
% check for number of files/tiles found
if length(all_ncf) == 0
disp('Error: no tiles found--no need to do any assembly!');
return
elseif length(all_ncf) == 1
disp('Error: one tile found--no need to do any assembly!');
return
else
disp(sprintf(' Found %d files matching the pattern: "%s"', ...
length(all_ncf), fpat ));
end
% check for consistent "exch" version
if prod(double([all_ncf.exch] == all_ncf(1).exch)) ~= 1
disp('Error: not all the "exch" types of the files match.');
return;
end
% check for consistent sNx,sNy
if (prod(double([all_ncf.sNx] == all_ncf(1).sNx)) ~= 1) ...
| (prod(double([all_ncf.sNy] == all_ncf(1).sNy)) ~= 1)
disp('Error: the "sNx,sNy" values for all the tiles are not');
disp(' uniform. Future versions of this function will be');
disp(' able to handle non-uniform grid sizes but this');
disp(' feature is not yet implemented.');
return;
end
% check for redundant tiles and "time series" output
if length(all_ncf) ~= length(unique([all_ncf.tile_number]))
disp('Error: redundant tiles were found. Please check that');
disp(' the file pattern does not specify output spanning');
disp(' multiple model runs or even multiple time series');
disp(' within a single model run. For multi-time-series');
disp(' data sets, EACH "LEVEL" IN THE OUTPUT SERIES MUST');
disp(' BE ASSEMBLED SEPARATERLY.');
return
end
%===== Get the dims/vars associations =====
mydims = struct('names', {}, 'lens', {});
myvars = struct([]);
clear tncf;
for ivar = 1:length(vars)
mydim_names = {};
mydim_sizes = {};
myatt.names = {};
myatt.types = {};
myatt.data = {};
myname = vars(ivar).name;
disp([' Looking for variable: ' myname]);
itile = 1;
tncf = all_ncf(itile).nc{1};
ncv = tncf{myname};
len = length(ncv);
if length(ncv) == 0
warns = [' Warning: variable "%s" is not defined in "%s"\n' ...
' so it will be ignored.'];
disp(sprintf(warns,myname,all_ncf(itile).name));
continue
end
mytype = datatype(ncv);
tmpdims = dim(ncv);
for inm = 1:length(tmpdims)
mydim_names{inm} = name(tmpdims{inm});
mydim_sizes{inm} = tmpdims{inm}(:);
end
for iat = 1:length(att(ncv))
aaa = att(ncv);
myatt.names(iat) = { name(aaa{iat}) };
myatt.types(iat) = { datatype(aaa{iat}) };
aab = aaa{iat};
myatt.data(iat) = { aab(:) };
end
% confirm: vars have same dim names across all files
ierr = 0;
for itile = 2:length(all_ncf)
tncf = all_ncf(itile).nc{1};
ncv = tncf{myname};
len = length(ncv);
if length(ncv) == 0
warns = [' Warning: variable "%s" is not defined in "%s"\n' ...
' so it will be ignored.'];
disp(sprintf(warns,myname,all_ncf(itile).name));
continue
end
tmpdims = dim(ncv);
for inm = 1:length(tmpdims)
if mydim_names{inm} ~= name(tmpdims{inm})
warns = ...
[' Warning: variable "%s" is not CONSISTENTLY defined.\n' ...
' It has different dimensions in different files so\n' ...
' so it will be ignored.'];
disp(sprintf(warns,myname));
ierr = 1;
break
end
mydim_sizes{inm} = max([ tmpdims{inm}(:) mydim_sizes{inm} ]);
end
end
if ierr == 0
% check: does the variable have a "horizontal" component
has_horiz = 0;
horiz_names = { 'X' 'Y' 'Xp1' 'Yp1' };
for id = 1:length(mydim_names)
if length([intersect(horiz_names,mydim_names{id})]) > 0
has_horiz = 1;
end
end
% disp([ ' ' myname ' ' sprintf('%d',has_horiz) ]);
imy = length(myvars) + 1;
myvars(imy).name = myname;
myvars(imy).type = mytype;
myvars(imy).dim_names = mydim_names;
myvars(imy).dim_sizes = mydim_sizes;
myvars(imy).atts = myatt;
myvars(imy).has_horiz = has_horiz;
% this is necessary to make it work with Matlab 6.5
if isempty([mydims.names])
addl = mydim_names;
else
addl = setdiff(mydim_names,[mydims.names]);
end
for iaddl = 1:length(addl)
np1 = length(mydims) + 1;
mydims(np1).names = addl(iaddl);
mydims(np1).lens = mydim_sizes(find(strcmp(addl(iaddl),mydim_names)));
end
end
end
% For exch == 2, we need to add a "face" dimension
if all_ncf(1).exch == 2
np1 = length(mydims) + 1;
mydims(np1).names = { 'iface' };
mydims(np1).lens = { length(unique([all_ncf.exch2_myFace])) };
end
% myvars.name
% myvars.dim_names
% myvars.dim_sizes
% myvars(2).dim_names
% myvars(2).dim_names(4)
% mydims
% length(mydims)
% [ mydims.names ]
% [ mydims.lens ]
%===== Assemble! =====
if all_ncf(1).exch == 1
% exch "1":
% $$$ bi_max = max([all_ncf.bi]);
% $$$ bj_max = max([all_ncf.bj]);
% $$$ Xmax = bi_max * all_ncf(1).sNx;
% $$$ Ymax = bj_max * all_ncf(1).sNy;
Xmax = all_ncf(1).Nx;
Ymax = all_ncf(1).Ny;
% at this point I have to make some assumptions about the domain
% decomposition
bi_max = Xmax/all_ncf(1).sNx;
bj_max = Ymax/all_ncf(1).sNy;
itile = 0;
for bj=1:bj_max
for bi=1:bi_max
itile = itile+1;
all_ncf(itile).bi=bi;
all_ncf(itile).bj=bj;
end
end
horzdim = struct('names',{},'lens',{});
horzdim(1).names = { 'X' }; horzdim(1).lens = { Xmax };
horzdim(2).names = {'Xp1'}; horzdim(2).lens = { Xmax + 1 };
horzdim(3).names = { 'Y' }; horzdim(3).lens = { Ymax };
horzdim(4).names = {'Yp1'}; horzdim(4).lens = { Ymax + 1 };
horzdim(5).names = { 'T' }; horzdim(5).lens = { 0 };
iseq = 0;
foutnm = sprintf(fout, iseq);
fonc = netcdf(foutnm,'clobber'); % Should append-or-create!
for idim = 1:length(mydims)
dname = mydims(idim).names{1};
ind = find(strcmp(dname,[horzdim.names]));
if length(ind) ~= 0
dlen = horzdim(ind).lens{1};
else
dlen = mydims(idim).lens{1};
end
comm = sprintf('fonc(''%s'') = %d;',dname,dlen);
eval(comm);
end
for ivar = 1:length(myvars)
comm = sprintf('fonc{''%s''} = nc%s( ',myvars(ivar).name,myvars(ivar).type);
id = 1;
comm = [ comm sprintf('''%s''',myvars(ivar).dim_names{id}) ];
for id = 2:length(myvars(ivar).dim_names)
comm = [ comm sprintf(',''%s''',myvars(ivar).dim_names{id}) ];
end
comm = [ comm ' );' ];
eval(comm);
for iat = 1:length(myvars(ivar).atts.names)
comm = sprintf( ...
'fonc{''%s''}.%s = nc%s( myvars(ivar).atts.data{iat} );', ...
myvars(ivar).name, ...
myvars(ivar).atts.names{iat}, ...
myvars(ivar).atts.types{iat} );
eval(comm);
end
end
% for itime = 1:Tmax
% Here is where we need to check the output file size and start
% another file in the sequence, if necessary.
for ivar = 1:length(myvars)
disp(sprintf(' Copying variable: %s',myvars(ivar).name))
for itile = 1:length(all_ncf)
if (myvars(ivar).has_horiz == 1) | (itile == 1)
clear nct;
nct = all_ncf(itile).nc{1};
ox_off = (all_ncf(itile).bi - 1)*all_ncf(itile).sNx;
oy_off = (all_ncf(itile).bj - 1)*all_ncf(itile).sNy;
diml_in = '';
diml_out = '';
for jj = 1:length(myvars(ivar).dim_names)
doff = 1;
if jj > 1
diml_in = sprintf('%s,',diml_in);
diml_out = sprintf('%s,',diml_out);
end
dlen = myvars(ivar).dim_sizes{jj};
diml_in = sprintf('%s%s',diml_in, ':');
fchar = myvars(ivar).dim_names{jj}(1);
% disp([' fchar = ' fchar ' ' myvars(ivar).dim_names{jj}]);
if strcmp(myvars(ivar).dim_names{jj}(1),'X') == 1
doff = ox_off + doff;
dlen = ox_off + dlen;
end
if strcmp(myvars(ivar).dim_names{jj}(1),'Y') == 1
doff = oy_off + doff;
dlen = oy_off + dlen;
end
diml_out = sprintf('%s%d%s%d',diml_out,doff,':',dlen);
end
comm = sprintf( ...
'fonc{''%s''}(%s) = nct{''%s''}(%s);', ...
myvars(ivar).name, diml_out, myvars(ivar).name, diml_in );
% disp([ ' comm: ' comm ]);
eval(comm);
end
end
end
% end
fonc = close(fonc);
elseif all_ncf(1).exch == 2
% exch "2":
Xmax = 0;
Ymax = 0;
for ii = 1:length(all_ncf)
Xmax = max(Xmax, (all_ncf(ii).exch2_tbasex + all_ncf(ii).sNx));
Ymax = max(Ymax, (all_ncf(ii).exch2_tbasey + all_ncf(ii).sNy));
end
horzdim = struct('names',{},'lens',{});
horzdim(1).names = { 'X' }; horzdim(1).lens = { Xmax };
horzdim(2).names = {'Xp1'}; horzdim(2).lens = { Xmax + 1 };
horzdim(3).names = { 'Y' }; horzdim(3).lens = { Ymax };
horzdim(4).names = {'Yp1'}; horzdim(4).lens = { Ymax + 1 };
horzdim(5).names = { 'T' }; horzdim(5).lens = { 0 };
iseq = 0;
foutnm = sprintf(fout, iseq);
fonc = netcdf(foutnm,'clobber'); % Should append-or-create!
for idim = 1:length(mydims)
dname = mydims(idim).names{1};
ind = find(strcmp(dname,[horzdim.names]));
if length(ind) ~= 0
dlen = horzdim(ind).lens{1};
else
dlen = mydims(idim).lens{1};
end
comm = sprintf('fonc(''%s'') = %d;',dname,dlen);
eval(comm);
end
for ivar = 1:length(myvars)
comm = sprintf('fonc{''%s''} = nc%s( ',myvars(ivar).name,myvars(ivar).type);
id = 1;
comm = [ comm sprintf('''%s''',myvars(ivar).dim_names{id}) ];
for id = 2:length(myvars(ivar).dim_names)
dname = myvars(ivar).dim_names{id};
if (dname(1) == 'Y') & (myvars(ivar).has_horiz == 1)
comm = [ comm sprintf(',''%s''','iface') ];
end
comm = [ comm sprintf(',''%s''',dname) ];
end
comm = [ comm ' );' ];
eval(comm);
for iat = 1:length(myvars(ivar).atts.names)
comm = sprintf( ...
'fonc{''%s''}.%s = nc%s( myvars(ivar).atts.data{iat} );', ...
myvars(ivar).name, ...
myvars(ivar).atts.names{iat}, ...
myvars(ivar).atts.types{iat} );
eval(comm);
end
end
% Here is where we need to check the output file size and start
% another file in the sequence, if necessary.
for ivar = 1:length(myvars)
disp(sprintf(' Copying variable: %s',myvars(ivar).name))
for itile = 1:length(all_ncf)
if (myvars(ivar).has_horiz == 1) | (itile == 1)
clear nct;
nct = all_ncf(itile).nc{1};
ox_off = all_ncf(itile).exch2_tbasex;
oy_off = all_ncf(itile).exch2_tbasey;
diml_tin = '';
diml_res = '';
diml_in = '';
diml_out = '';
if length(myvars(ivar).dim_names) < 2
comm = sprintf( ...
'fonc{''%s''}(%s%d) = nct{''%s''}(:);', ...
myvars(ivar).name, '1:', myvars(ivar).dim_sizes{1}, ...
myvars(ivar).name );
% disp([ ' ' comm ]);
eval(comm);
else
for jj = 1:length(myvars(ivar).dim_names)
doff = 1;
if jj > 1
diml_tin = sprintf('%s,',diml_tin);
diml_res = sprintf('%s,',diml_res);
diml_in = sprintf('%s,',diml_in);
diml_out = sprintf('%s,',diml_out);
end
dnam = myvars(ivar).dim_names{jj};
dlen = myvars(ivar).dim_sizes{jj};
dlenr = dlen;
fchar = myvars(ivar).dim_names{jj}(1);
% disp([' fchar = ' fchar ' ' myvars(ivar).dim_names{jj}]);
if strcmp(dnam(1),'X') == 1
doff = ox_off + doff;
dlen = ox_off + dlen;
end
if strcmp(dnam(1),'Y') == 1
diml_res = sprintf('%s%s',diml_res, '[],');
diml_in = sprintf('%s%s',diml_in, ':,');
diml_out = sprintf('%s%d%s',diml_out,all_ncf(itile).exch2_myFace,',');
doff = oy_off + doff;
dlen = oy_off + dlen;
end
diml_tin = sprintf('%s%s',diml_tin, ':');
diml_res = sprintf('%s%d',diml_res, dlenr);
diml_in = sprintf('%s%s',diml_in, ':');
diml_out = sprintf('%s%d%s%d',diml_out,doff,':',dlen);
end
comm = sprintf( ...
'tmp = reshape(nct{''%s''}(%s), %s); fonc{''%s''}(%s) = tmp(%s);', ...
myvars(ivar).name, diml_tin, diml_res, myvars(ivar).name, ...
diml_out, diml_in );
% disp([ ' ' comm ]);
eval(comm);
end
end
end
end
% end
fonc = close(fonc);
end