/[MITgcm]/MITgcm/utils/matlab/rdmds.m
ViewVC logotype

Contents of /MITgcm/utils/matlab/rdmds.m

Parent Directory Parent Directory | Revision Log Revision Log | View Revision Graph Revision Graph


Revision 1.27 - (show annotations) (download)
Wed May 15 23:10:49 2013 UTC (11 years, 1 month ago) by jmc
Branch: MAIN
CVS Tags: checkpoint65z, checkpoint65x, checkpoint65y, checkpoint65r, checkpoint65s, checkpoint65p, checkpoint65q, checkpoint65v, checkpoint65w, checkpoint65t, checkpoint65u, checkpoint65j, checkpoint65k, checkpoint65h, checkpoint65i, checkpoint65n, checkpoint65l, checkpoint65m, checkpoint65b, checkpoint65c, checkpoint65a, checkpoint65f, checkpoint65g, checkpoint65d, checkpoint65e, checkpoint65, checkpoint66g, checkpoint66f, checkpoint66e, checkpoint66d, checkpoint66c, checkpoint66b, checkpoint66a, checkpoint66o, checkpoint66n, checkpoint66m, checkpoint66l, checkpoint66k, checkpoint66j, checkpoint66i, checkpoint66h, checkpoint65o, checkpoint64y, checkpoint64x, checkpoint64z, checkpoint64q, checkpoint64p, checkpoint64s, checkpoint64r, checkpoint64u, checkpoint64t, checkpoint64w, checkpoint64v, checkpoint64i, checkpoint64h, checkpoint64k, checkpoint64j, checkpoint64m, checkpoint64l, checkpoint64o, checkpoint64n, HEAD
Changes since 1.26: +15 -11 lines
- change search for meta-files (in case of sereral set of files with
 same suffix, and read-in without iteration number)
- ignore iteration number argument when value is '-1"

1 function [AA,itrs,MM] = rdmds(fnamearg,varargin)
2 % RDMDS Read MITgcmUV meta/data files
3 %
4 % A = RDMDS(FNAME)
5 % A = RDMDS(FNAME,ITER)
6 % A = RDMDS(FNAME,[ITER1 ITER2 ...])
7 % A = RDMDS(FNAME,NaN)
8 % A = RDMDS(FNAME,Inf)
9 % [A,ITS,M] = RDMDS(FNAME,[...])
10 % A = RDMDS(FNAME,[...],'rec',RECNUM)
11 %
12 % A = RDMDS(FNAME) reads data described by meta/data file format.
13 % FNAME is a string containing the "head" of the file names.
14 %
15 % eg. To load the meta-data files
16 % T.0000002880.000.000.meta, T.0000002880.000.000.data
17 % T.0000002880.001.000.meta, T.0000002880.001.000.data
18 % T.0000002880.002.000.meta, T.0000002880.002.000.data
19 % T.0000002880.003.000.meta, T.0000002880.003.000.data
20 % use
21 % >> A=rdmds('T.0000002880');
22 % >> size(A)
23 % ans =
24 % 64 32 5
25 % eg. To load a multiple record file
26 % >> A=rdmds('pickup.0000002880');
27 % >> size(A)
28 % ans =
29 % 64 32 5 61
30 %
31 %
32 % A = RDMDS(FNAME,ITER) reads data described by meta/data file format.
33 % FNAME is a string containing the "head" of the file name excluding the
34 % 10-digit iterartion number.
35 % ITER is a vector of positive integers that will expand to the 10-digit
36 % number in the file name.
37 % If ITER=NaN, all iterations will be read.
38 % If ITER=Inf, the last (highest) iteration will be read.
39 %
40 % eg. To repeat above operation
41 % >> A=rdmds('T',2880);
42 % eg. To read multiple time steps
43 % >> A=rdmds('T',[0 1440 2880]);
44 % eg. To read all time steps
45 % >> [A,ITS]=rdmds('T',NaN);
46 % eg. To read the last time step
47 % >> [A,IT]=rdmds('T',Inf);
48 % Note: this form can not read files with no iteration count in file name.
49 %
50 %
51 % A = RDMDS(FNAME,[...],'rec',RECNUM) reads individual records from
52 % multiple record files.
53 %
54 % eg. To read a single record from a multi-record file
55 % >> [A,IT]=rdmds('pickup.ckptA',11);
56 % eg. To read several records from a multi-record file
57 % >> [A,IT]=rdmds('pickup',Inf,'rec',[1:5 8 12]);
58 %
59 %
60 % A = RDMDS(FNAME,ITER,MACHINEFORMAT) allows the machine format to be
61 % A = RDMDS(FNAME,MACHINEFORMAT)
62 % specified which MACHINEFORMAT is on of the following strings:
63 % 'n' 'l' 'b' 'd' 'g' 'c' 'a' 's' - see FOPEN for more details
64 %
65
66 % $Header: /u/gcmpack/MITgcm/utils/matlab/rdmds.m,v 1.26 2010/01/10 01:51:03 jmc Exp $
67 % $Name: $
68
69 AA=[];
70 itrs=[];
71 MM=[];
72
73 % Default options
74 ieee='b';
75 fname=fnamearg;
76 userecords=0;
77 recnum=[];
78
79 % Check optional arguments
80 for ind=1:size(varargin,2);
81 arg=varargin{ind};
82 if ischar(arg)
83 if strcmp(arg,'n') | strcmp(arg,'native')
84 ieee='n';
85 elseif strcmp(arg,'l') | strcmp(arg,'ieee-le')
86 ieee='l';
87 elseif strcmp(arg,'b') | strcmp(arg,'ieee-be')
88 ieee='b';
89 elseif strcmp(arg,'c') | strcmp(arg,'cray')
90 ieee='c';
91 elseif strcmp(arg,'a') | strcmp(arg,'ieee-le.l64')
92 ieee='a';
93 elseif strcmp(arg,'s') | strcmp(arg,'ieee-be.l64')
94 ieee='s';
95 elseif strcmp(arg,'rec')
96 userecords=1;
97 else
98 error(['Optional argument ' arg ' is unknown'])
99 end
100 else
101 if userecords==1
102 recnum=arg;
103 elseif isempty(itrs)
104 if isnan(arg)
105 itrs=scanforfiles(fname);
106 disp([ sprintf('Reading %i time levels:',size(itrs,2)) sprintf(' %i',itrs) ]);
107 elseif isinf(arg)
108 itrs=scanforfiles(fname);
109 if isempty(itrs)
110 AA=[];itrs=[];return;
111 end
112 disp([ sprintf('Found %i time levels, reading %i',size(itrs,2),itrs(end)) ]);
113 itrs=itrs(end);
114 % elseif prod(double(arg>=0)) & prod(double(round(arg)==arg))
115 % elseif prod(arg>=0) & prod(round(arg)==arg)
116 elseif min(arg)>=0 & isempty(find(round(arg)~=arg))
117 if arg>=9999999999
118 error(sprintf('Argument %i > 9999999999',arg))
119 end
120 itrs=arg;
121 elseif length(arg) == 1 & arg == -1
122 itrs=arg;
123 else
124 error(sprintf('Argument %i must be a positive integer',arg))
125 end
126 else
127 error('Multiple iterations should be specified as a vector')
128 end
129 end
130 end
131
132 if isempty(itrs)
133 itrs=-1;
134 end
135
136 % Loop over each iteration
137 for iter=1:size(itrs,2);
138 if itrs(iter)>=0
139 fname=sprintf('%s.%10.10i',fnamearg,itrs(iter));
140 end
141
142 % Figure out if there is a path in the filename
143 NS=findstr('/',fname);
144 if size(NS)>0
145 Dir=fname(1:NS(end));
146 else
147 Dir='./';
148 end
149
150 % Match name of all meta-files
151 %fprintf(' search for file "%s".*meta\n',fname);
152 allfiles=dir( sprintf('%s.*meta',fname) );
153
154 if size(allfiles,1)==0
155 disp(sprintf('No files match the search: %s.*meta',fname));
156 %allow partial reads% error('No files found.')
157 end
158
159 % Loop through allfiles
160 for j=1:size(allfiles,1);
161 %fprintf(' file # %3i : %s\n',j,allfiles(j).name);
162
163 % Read meta- and data-file
164 [A,N,M,mG] = localrdmds([Dir allfiles(j).name],ieee,recnum);
165
166 %- Merge local Meta file content (M) to MM string:
167 if j > 0, %- to comment out this block: "if j < 0" (since j is always > 0)
168 ii=findstr(M,' timeStepNumber');
169 if isempty(ii), ii1=0; ii2=0;
170 else ii1=ii; ii2=ii+min(findstr(M(1+ii:end),'];')); end
171 ii=findstr(M,' timeInterval');
172 if isempty(ii), jj1=0; jj2=0;
173 else jj1=ii; jj2=ii+min(findstr(M(1+ii:end),'];')); end
174 if iter==1 & j==1,
175 MM=M; ind1=0; ind2=0; is1=ii1; js1=jj1; M3='';
176 if ii1*jj1 > 0,
177 %ind1=min(ii1,jj1); ind2=max(ii2,jj2);
178 %if ii1 < jj1, ii3=ii2+1; jj3=jj1-1;
179 %else ii3=jj2+1; jj3=ii1-1; end
180 order=sort([ii1 ii2 jj1 jj2]);
181 ind1=order(1); ii3=order(2)+1; jj3=order(3)-1; ind2=order(4);
182 M2=M(ii1:ii2); M4=M(jj1:jj2); M3=M(ii3:jj3);
183 elseif ii1 > 0,
184 ind1=ii1; ind2=ii2;
185 M2=M(ii1:ii2); M4='';
186 elseif jj1 > 0,
187 ind1=jj1; ind2=jj2;
188 M4=M(jj1:jj2); M2='';
189 end
190 M5=M(1+ind2:end);
191 %fprintf(' ii1,ii2 = %i %i ; jj1,jj2= %i %i ;', ii1,ii2, jj1,jj2);
192 %fprintf(' ii3,jj3= %i %i ; ind1,ind2= %i %i\n',ii3,jj3,ind1,ind2);
193 %fprintf('M(1:ind1)=%s<\n',M(1:ind1));
194 %fprintf(' M2=%s<\n',M2);
195 %fprintf(' M3=%s<\n',M3);
196 %fprintf(' M4=%s<\n',M4);
197 %fprintf(' M5=%s<\n',M5);
198 else
199 if ii1*jj1 > 0,
200 order=sort([ii1 ii2 jj1 jj2]);
201 ind=order(1); ii3=order(2)+1; jj3=order(3)-1; ind2=order(4);
202 else ind=max(ii1,jj1); ind2=ii2+jj2; end
203 compar=(ind == ind1); ii=0;
204 if compar & ind1 == 0, ii=1; compar=strcmp (MM,M); end
205 if compar & ind1 > 0, ii=2; compar=strncmp(MM,M,ind1) ; end
206 if compar & ind1 > 0, ii=3; compar=strcmp(M5,M(1+ind2:end)); end
207 if compar & ii1*jj1 > 0, ii=4; compar=strcmp(M3,M(ii3:jj3)); end
208 if ~compar,
209 fprintf('WARNING: Meta file (%s) is different (%i) from 1rst one:\n', ...
210 allfiles(j).name,ii);
211 fprintf(' it=%i :MM:%s\n',itrs(1),MM);
212 fprintf(' it=%i :M :%s\n\n',itrs(iter),M);
213 elseif ind1 > 0,
214 if ii1 > 0,
215 Mj=M(ii1:ii2); ii=findstr(Mj,'['); Mj=Mj(1+ii:end);
216 % add it-number from Mj to M2 (if different):
217 if isempty(findstr(M2,Mj)), M2=[deblank(M2(1:end-1)),Mj]; end
218 end
219 if jj1 > 0,
220 Mj=M(jj1:jj2); ii=findstr(Mj,'['); Mj=Mj(1+ii:end);
221 % add time interval from Mj to M4 (if different):
222 if isempty(findstr(M4,Mj)), M4=[deblank(M4(1:end-1)),' ;',Mj]; end
223 end
224 end
225 end
226 % save modifications:
227 if ind1>0 & j==size(allfiles,1) & iter==size(itrs,2),
228 if ii1 < jj1, MM=[MM(1:ind1-1),M2,M3,M4,M5];
229 else MM=[MM(1:ind1-1),M4,M3,M2,M5]; end
230 end
231 end
232
233 %- put local data file content in global array AA:
234 bdims=N(1,:);
235 r0=N(2,:);
236 rN=N(3,:);
237 ndims=prod(size(bdims));
238 if j==1 & iter==1, AA=zeros([bdims size(itrs,2)]); end
239 if mG(1)==0 & mG(2)==1,
240 if (ndims == 1)
241 AA(r0(1):rN(1),iter)=A;
242 elseif (ndims == 2)
243 AA(r0(1):rN(1),r0(2):rN(2),iter)=A;
244 elseif (ndims == 3)
245 AA(r0(1):rN(1),r0(2):rN(2),r0(3):rN(3),iter)=A;
246 elseif (ndims == 4)
247 AA(r0(1):rN(1),r0(2):rN(2),r0(3):rN(3),r0(4):rN(4),iter)=A;
248 elseif (ndims == 5)
249 AA(r0(1):rN(1),r0(2):rN(2),r0(3):rN(3),r0(4):rN(4),r0(5):rN(5),iter)=A;
250 else
251 error('Dimension of data set is larger than currently coded. Sorry!')
252 end
253 elseif (ndims == 1)
254 AA(r0(1):rN(1),iter)=A;
255 else
256 %- to debug: do simple stransfert (with a loop on 2nd index);
257 % will need to change this later, to improve efficiency:
258 for i=0:rN(2)-r0(2),
259 if (ndims == 2)
260 AA(r0(1)+i*mG(1):rN(1)+i*mG(1),r0(2)+i*mG(2),iter)=A(:,1+i);
261 elseif (ndims == 3)
262 AA(r0(1)+i*mG(1):rN(1)+i*mG(1),r0(2)+i*mG(2), ...
263 r0(3):rN(3),iter)=A(:,1+i,:);
264 elseif (ndims == 4)
265 AA(r0(1)+i*mG(1):rN(1)+i*mG(1),r0(2)+i*mG(2), ...
266 r0(3):rN(3),r0(4):rN(4),iter)=A(:,1+i,:,:);
267 elseif (ndims == 5)
268 AA(r0(1)+i*mG(1):rN(1)+i*mG(1),r0(2)+i*mG(2), ...
269 r0(3):rN(3),r0(4):rN(4),r0(5):rN(5),iter)=A(:,1+i,:,:,:);
270 else
271 error('Dimension of data set is larger than currently coded. Sorry!')
272 end
273 end
274 end
275
276 end % files
277 end % iterations
278
279 %-------------------------------------------------------------------------------
280
281 function [A,N,M,map2glob] = localrdmds(fname,ieee,recnum)
282
283 mname=strrep(fname,' ','');
284 dname=strrep(mname,'.meta','.data');
285
286 %- set default mapping from tile to global file:
287 map2glob=[0 1];
288
289 % Read and interpret Meta file
290 fid = fopen(mname,'r');
291 if (fid == -1)
292 error(['File' mname ' could not be opened'])
293 end
294
295 % Scan each line of the Meta file
296 allstr=' ';
297 keepgoing = 1;
298 while keepgoing > 0,
299 line = fgetl(fid);
300 if (line == -1)
301 keepgoing=-1;
302 else
303 % Strip out "(PID.TID *.*)" by finding first ")"
304 %old ind=findstr([line ')'],')'); line=line(ind(1)+1:end);
305 ind=findstr(line,')');
306 if size(ind) ~= 0
307 line=line(ind(1)+1:end);
308 end
309 % Remove comments of form //
310 line=[line,' //']; ind=findstr(line,'//'); line=line(1:ind(1)-1);
311 % Add to total string (without starting & ending blanks)
312 while line(1:1) == ' ', line=line(2:end); end
313 if strncmp(line,'map2glob',8), eval(line);
314 else allstr=[allstr,deblank(line),' '];
315 end
316 end
317 end
318
319 % Close meta file
320 fclose(fid);
321
322 % Strip out comments of form /* ... */
323 ind1=findstr(allstr,'/*'); ind2=findstr(allstr,'*/');
324 if size(ind1) ~= size(ind2)
325 error('The /* ... */ comments are not properly paired')
326 end
327 while size(ind1,2) > 0
328 allstr=[deblank(allstr(1:ind1(1)-1)) allstr(ind2(1)+2:end)];
329 %allstr=[allstr(1:ind1(1)-1) allstr(ind2(1)+3:end)];
330 ind1=findstr(allstr,'/*'); ind2=findstr(allstr,'*/');
331 end
332
333 % This is a kludge to catch whether the meta-file is of the
334 % old or new type. nrecords does not exist in the old type.
335 nrecords = NaN;
336
337 %- store the full string for output:
338 M=strrep(allstr,'format','dataprec');
339
340 % Everything in lower case
341 allstr=lower(allstr);
342
343 % Fix the unfortunate choice of 'format'
344 allstr=strrep(allstr,'format','dataprec');
345
346 % Evaluate meta information
347 eval(allstr);
348
349 N=reshape( dimlist , 3 , prod(size(dimlist))/3 );
350 rep=[' dimList = [ ',sprintf('%i ',N(1,:)),']'];
351 if ~isnan(nrecords) & nrecords > 1 & isempty(recnum)
352 N=[N,[nrecords 1 nrecords]'];
353 elseif ~isempty(recnum) & recnum>nrecords
354 error('Requested record number is higher than the number of available records')
355 end
356
357 %- make "dimList" shorter (& fit output array size) in output "M":
358 pat=' dimList = \[(\s*\d+\,?)*\s*\]';
359 M=regexprep(M,pat,rep);
360 % and remove double space within sq.brakets:
361 ind1=findstr(M,'['); ind2=findstr(M,']');
362 if length(ind1) == length(ind2),
363 for i=length(ind1):-1:1, if ind1(i) < ind2(i),
364 M=[M(1:ind1(i)),regexprep(M(ind1(i)+1:ind2(i)-1),'(\s+)',' '),M(ind2(i):end)];
365 end; end
366 else error('The [ ... ] brakets are not properly paired')
367 end
368
369 if isempty(recnum)
370 recnum=1;
371 end
372
373 if isnan(nrecords)
374 % This is the old 'meta' method that used sequential access
375
376 A=allstr;
377 % Open data file
378 fid=fopen(dname,'r',ieee);
379
380 % Read record size in bytes
381 recsz=fread(fid,1,'uint32');
382 ldims=N(3,:)-N(2,:)+1;
383 numels=prod(ldims);
384
385 rat=recsz/numels;
386 if rat == 4
387 A=fread(fid,numels,'real*4');
388 elseif rat == 8
389 A=fread(fid,numels,'real*8');
390 else
391 sprintf(' Implied size in meta-file = %d', numels )
392 sprintf(' Record size in data-file = %d', recsz )
393 error('Ratio between record size and size in meta-file inconsistent')
394 end
395
396 erecsz=fread(fid,1,'uint32');
397 if erecsz ~= recsz
398 sprintf('WARNING: Record sizes at beginning and end of file are inconsistent')
399 end
400
401 fclose(fid);
402
403 A=reshape(A,ldims);
404
405 else
406 % This is the new MDS format that uses direct access
407
408 ldims=N(3,:)-N(2,:)+1;
409 for r=1:size(recnum(:),1);
410 if dataprec == 'float32'
411 A(:,r)=myrdda(dname,ldims,recnum(r),'real*4',ieee);
412 elseif dataprec == 'float64'
413 A(:,r)=myrdda(dname,ldims,recnum(r),'real*8',ieee);
414 else
415 error(['Unrecognized format in meta-file = ' format]);
416 end
417 end
418
419 A=reshape(A,[ldims size(recnum(:),1)]);
420 if size(recnum(:),1)>1
421 N(1,end+1)=size(recnum(:),1);
422 N(2,end)=1;
423 N(3,end)=size(recnum(:),1);
424 end
425
426 end
427
428 %-------------------------------------------------------------------------------
429
430 % result = RDDA( file, dim, irec [options] )
431 %
432 % This routine reads the irec'th record of shape 'dim' from the
433 % direct-access binary file (float or double precision) 'file'.
434 %
435 % Required arguments:
436 %
437 % file - string - name of file to read from
438 % dim - vector - dimensions of the file records and the resulting array
439 % irec - integer - record number in file in which to write data
440 %
441 % Optional arguments (must appear after the required arguments):
442 % prec - string - precision of storage in file. Default = 'real*8'.
443 % ieee - string - IEEE bit-wise representation in file. Default = 'b'.
444 %
445 % 'prec' may take the values:
446 % 'real*4' - floating point, 32 bits.
447 % 'real*8' - floating point, 64 bits - the efault.
448 %
449 % 'ieee' may take values:
450 % 'ieee-be' or 'b' - IEEE floating point with big-endian
451 % byte ordering - the default
452 % 'ieee-le' or 'l' - IEEE floating point with little-endian
453 % byte ordering
454 % 'native' or 'n' - local machine format
455 % 'cray' or 'c' - Cray floating point with big-endian
456 % byte ordering
457 % 'ieee-le.l64' or 'a' - IEEE floating point with little-endian
458 % byte ordering and 64 bit long data type
459 % 'ieee-be.l64' or 's' - IEEE floating point with big-endian byte
460 % ordering and 64 bit long data type.
461 %
462 % eg. T=rdda('t.data',[64 64 32],1);
463 % T=rdda('t.data',[256],4,'real*4');
464 % T=rdda('t.data',[128 64],2,'real*4','b');
465 function [arr] = myrdda(file,N,k,varargin)
466
467 % Defaults
468 WORDLENGTH=8;
469 rtype='real*8';
470 ieee='b';
471
472 % Check optional arguments
473 args=char(varargin);
474 while (size(args,1) > 0)
475 if deblank(args(1,:)) == 'real*4'
476 WORDLENGTH=4;
477 rtype='real*4';
478 elseif deblank(args(1,:)) == 'real*8'
479 WORDLENGTH=8;
480 rtype='real*8';
481 elseif deblank(args(1,:)) == 'n' | deblank(args(1,:)) == 'native'
482 ieee='n';
483 elseif deblank(args(1,:)) == 'l' | deblank(args(1,:)) == 'ieee-le'
484 ieee='l';
485 elseif deblank(args(1,:)) == 'b' | deblank(args(1,:)) == 'ieee-be'
486 ieee='b';
487 elseif deblank(args(1,:)) == 'c' | deblank(args(1,:)) == 'cray'
488 ieee='c';
489 elseif deblank(args(1,:)) == 'a' | deblank(args(1,:)) == 'ieee-le.l64'
490 ieee='a';
491 elseif deblank(args(1,:)) == 's' | deblank(args(1,:)) == 'ieee-be.l64'
492 ieee='s';
493 else
494 error(['Optional argument ' args(1,:) ' is unknown'])
495 end
496 args=args(2:end,:);
497 end
498
499 nnn=prod(N);
500
501 [fid mess]=fopen(file,'r',ieee);
502 if fid == -1
503 error('Error while opening file:\n%s',mess)
504 end
505 st=fseek(fid,nnn*(k-1)*WORDLENGTH,'bof');
506 if st ~= 0
507 mess=ferror(fid);
508 error('There was an error while positioning the file pointer:\n%s',mess)
509 end
510 [arr count]=fread(fid,nnn,rtype);
511 if count ~= nnn
512 error('Not enough data was available to be read: off EOF?')
513 end
514 st=fclose(fid);
515 %arr=reshape(arr,N);
516
517 %
518 function [itrs] = scanforfiles(fname)
519
520 itrs=[];
521 allfiles=dir([fname '.*.001.001.meta']);
522 if isempty(allfiles)
523 allfiles=dir([fname '.*.meta']);
524 ioff=0;
525 else
526 ioff=8;
527 end
528 for k=1:size(allfiles,1);
529 hh=allfiles(k).name;
530 itrs(k)=str2num( hh(end-14-ioff:end-5-ioff) );
531 end
532 itrs=sort(itrs);

  ViewVC Help
Powered by ViewVC 1.1.22