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

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Revision 1.15 - (show annotations) (download)
Fri Oct 11 14:29:45 2002 UTC (18 years, 9 months ago) by adcroft
Branch: MAIN
CVS Tags: checkpoint46n_post, checkpoint47e_post, checkpoint46l_post, checkpoint47c_post, checkpoint48e_post, checkpoint48i_post, checkpoint46l_pre, checkpoint50, checkpoint48b_post, checkpoint48c_pre, checkpoint47d_pre, checkpoint47a_post, checkpoint48d_pre, checkpoint47i_post, checkpoint47d_post, checkpoint48d_post, checkpoint48f_post, checkpoint48h_post, checkpoint47g_post, checkpoint46k_post, checkpoint48a_post, checkpoint50a_post, checkpoint47j_post, branch-exfmods-tag, checkpoint48c_post, checkpoint47b_post, checkpoint46m_post, checkpoint47f_post, checkpoint47, checkpoint48, checkpoint49, checkpoint48g_post, checkpoint47h_post
Branch point for: branch-exfmods-curt
Changes since 1.14: +50 -11 lines
Updated record reading ability.
 o multi-record used to be read in their entirety
 o now individual or groups of records can be specified
See "help rdmds" in Matlab for more info.

1 function [AA,iters] = 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] = 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/models/MITgcmUV/utils/matlab/rdmds.m,v 1.14 2002/10/11 13:45:36 adcroft Exp $
67
68 AA=[];
69 iters=[];
70
71 % Default options
72 ieee='b';
73 fname=fnamearg;
74 userecords=0;
75 recnum=[];
76
77 % Check optional arguments
78 for ind=1:size(varargin,2);
79 arg=varargin{ind};
80 if ischar(arg)
81 if strcmp(arg,'n') | strcmp(arg,'native')
82 ieee='n';
83 elseif strcmp(arg,'l') | strcmp(arg,'ieee-le')
84 ieee='l';
85 elseif strcmp(arg,'b') | strcmp(arg,'ieee-be')
86 ieee='b';
87 elseif strcmp(arg,'c') | strcmp(arg,'cray')
88 ieee='c';
89 elseif strcmp(arg,'a') | strcmp(arg,'ieee-le.l64')
90 ieee='a';
91 elseif strcmp(arg,'s') | strcmp(arg,'ieee-be.l64')
92 ieee='s';
93 elseif strcmp(arg,'rec')
94 userecords=1;
95 else
96 error(['Optional argument ' arg ' is unknown'])
97 end
98 else
99 if userecords==1
100 recnum=arg;
101 elseif isempty(iters)
102 if isnan(arg)
103 iters=scanforfiles(fname);
104 disp([ sprintf('Reading %i time levels:',size(iters,2)) sprintf(' %i',iters) ]);
105 elseif isinf(arg)
106 iters=scanforfiles(fname);
107 if isempty(iters)
108 AA=[];iters=[];return;
109 end
110 disp([ sprintf('Found %i time levels, reading %i',size(iters,2),iters(end)) ]);
111 iters=iters(end);
112 elseif prod(arg>=0) & prod(round(arg)==arg)
113 if arg>=9999999999
114 error(sprintf('Argument %i > 9999999999',arg))
115 end
116 iters=arg;
117 else
118 error(sprintf('Argument %i must be a positive integer',arg))
119 end
120 else
121 error('Multiple iterations should be specified as a vector')
122 end
123 end
124 end
125
126 if isempty(iters)
127 iters=-1;
128 end
129
130 % Loop over each iteration
131 for iter=1:size(iters,2);
132 if iters(iter)>=0
133 fname=sprintf('%s.%10.10i',fnamearg,iters(iter));
134 end
135
136 % Figure out if there is a path in the filename
137 NS=findstr('/',fname);
138 if size(NS)>0
139 Dir=fname(1:NS(end));
140 else
141 Dir='./';
142 end
143
144 % Match name of all meta-files
145 allfiles=dir( sprintf('%s*.meta',fname) );
146
147 if size(allfiles,1)==0
148 disp(sprintf('No files match the search: %s*.meta',fname));
149 %allow partial reads% error('No files found.')
150 end
151
152 % Loop through allfiles
153 for j=1:size(allfiles,1);
154
155 % Read meta- and data-file
156 [A,N] = localrdmds([Dir allfiles(j).name],ieee,recnum);
157
158 bdims=N(1,:);
159 r0=N(2,:);
160 rN=N(3,:);
161 ndims=prod(size(bdims));
162 if (ndims == 1)
163 AA(r0(1):rN(1),iter)=A;
164 elseif (ndims == 2)
165 AA(r0(1):rN(1),r0(2):rN(2),iter)=A;
166 elseif (ndims == 3)
167 AA(r0(1):rN(1),r0(2):rN(2),r0(3):rN(3),iter)=A;
168 elseif (ndims == 4)
169 AA(r0(1):rN(1),r0(2):rN(2),r0(3):rN(3),r0(4):rN(4),iter)=A;
170 elseif (ndims == 5)
171 AA(r0(1):rN(1),r0(2):rN(2),r0(3):rN(3),r0(4):rN(4),r0(5):rN(5),iter)=A;
172 else
173 error('Dimension of data set is larger than currently coded. Sorry!')
174 end
175
176 end % files
177 end % iterations
178
179 %-------------------------------------------------------------------------------
180
181 function [A,N] = localrdmds(fname,ieee,recnum)
182
183 mname=strrep(fname,' ','');
184 dname=strrep(mname,'.meta','.data');
185
186 % Read and interpret Meta file
187 fid = fopen(mname,'r');
188 if (fid == -1)
189 error(['File' mname ' could not be opened'])
190 end
191
192 % Scan each line of the Meta file
193 allstr=' ';
194 keepgoing = 1;
195 while keepgoing > 0,
196 line = fgetl(fid);
197 if (line == -1)
198 keepgoing=-1;
199 else
200 % Strip out "(PID.TID *.*)" by finding first ")"
201 %old ind=findstr([line ')'],')'); line=line(ind(1)+1:end);
202 ind=findstr(line,')');
203 if size(ind) ~= 0
204 line=line(ind(1)+1:end);
205 end
206 % Remove comments of form //
207 line=[line ' //']; ind=findstr(line,'//'); line=line(1:ind(1)-1);
208 % Add to total string
209 allstr=[allstr line];
210 end
211 end
212
213 % Close meta file
214 fclose(fid);
215
216 % Strip out comments of form /* ... */
217 ind1=findstr(allstr,'/*'); ind2=findstr(allstr,'*/');
218 if size(ind1) ~= size(ind2)
219 error('The /* ... */ comments are not properly paired')
220 end
221 while size(ind1,2) > 0
222 allstr=[allstr(1:ind1(1)-1) allstr(ind2(1)+3:end)];
223 ind1=findstr(allstr,'/*'); ind2=findstr(allstr,'*/');
224 end
225
226 % This is a kludge to catch whether the meta-file is of the
227 % old or new type. nrecords does not exist in the old type.
228 nrecords = NaN;
229
230 % Everything in lower case
231 allstr=lower(allstr);
232
233 % Fix the unfortunate choice of 'format'
234 allstr=strrep(allstr,'format','dataprec');
235
236 % Evaluate meta information
237 eval(allstr);
238
239 N=reshape( dimlist , 3 , prod(size(dimlist))/3 );
240 if ~isnan(nrecords) & nrecords > 1 & isempty(recnum)
241 N=[N,[nrecords 1 nrecords]'];
242 elseif ~isempty(recnum) & recnum>nrecords
243 error('Requested record number is higher than the number of available records')
244 end
245
246 if isempty(recnum)
247 recnum=1;
248 end
249
250 if isnan(nrecords)
251 % This is the old 'meta' method that used sequential access
252
253 A=allstr;
254 % Open data file
255 fid=fopen(dname,'r',ieee);
256
257 % Read record size in bytes
258 recsz=fread(fid,1,'uint32');
259 ldims=N(3,:)-N(2,:)+1;
260 numels=prod(ldims);
261
262 rat=recsz/numels;
263 if rat == 4
264 A=fread(fid,numels,'real*4');
265 elseif rat == 8
266 A=fread(fid,numels,'real*8');
267 else
268 sprintf(' Implied size in meta-file = %d', numels )
269 sprintf(' Record size in data-file = %d', recsz )
270 error('Ratio between record size and size in meta-file inconsistent')
271 end
272
273 erecsz=fread(fid,1,'uint32');
274 if erecsz ~= recsz
275 sprintf('WARNING: Record sizes at beginning and end of file are inconsistent')
276 end
277
278 fclose(fid);
279
280 A=reshape(A,ldims);
281
282 else
283 % This is the new MDS format that uses direct access
284
285 ldims=N(3,:)-N(2,:)+1;
286 for r=1:size(recnum(:),1);
287 if dataprec == 'float32'
288 A(:,r)=myrdda(dname,ldims,recnum(r),'real*4',ieee);
289 elseif dataprec == 'float64'
290 A(:,r)=myrdda(dname,ldims,recnum(r),'real*8',ieee);
291 else
292 error(['Unrecognized format in meta-file = ' format]);
293 end
294 end
295
296 A=reshape(A,[ldims size(recnum(:),1)]);
297 if size(recnum(:),1)>1
298 N(1,end+1)=size(recnum(:),1);
299 N(2,end)=1;
300 N(3,end)=size(recnum(:),1);
301 end
302
303 end
304
305 %-------------------------------------------------------------------------------
306
307 % result = RDDA( file, dim, irec [options] )
308 %
309 % This routine reads the irec'th record of shape 'dim' from the
310 % direct-access binary file (float or double precision) 'file'.
311 %
312 % Required arguments:
313 %
314 % file - string - name of file to read from
315 % dim - vector - dimensions of the file records and the resulting array
316 % irec - integer - record number in file in which to write data
317 %
318 % Optional arguments (must appear after the required arguments):
319 % prec - string - precision of storage in file. Default = 'real*8'.
320 % ieee - string - IEEE bit-wise representation in file. Default = 'b'.
321 %
322 % 'prec' may take the values:
323 % 'real*4' - floating point, 32 bits.
324 % 'real*8' - floating point, 64 bits - the efault.
325 %
326 % 'ieee' may take values:
327 % 'ieee-be' or 'b' - IEEE floating point with big-endian
328 % byte ordering - the default
329 % 'ieee-le' or 'l' - IEEE floating point with little-endian
330 % byte ordering
331 % 'native' or 'n' - local machine format
332 % 'cray' or 'c' - Cray floating point with big-endian
333 % byte ordering
334 % 'ieee-le.l64' or 'a' - IEEE floating point with little-endian
335 % byte ordering and 64 bit long data type
336 % 'ieee-be.l64' or 's' - IEEE floating point with big-endian byte
337 % ordering and 64 bit long data type.
338 %
339 % eg. T=rdda('t.data',[64 64 32],1);
340 % T=rdda('t.data',[256],4,'real*4');
341 % T=rdda('t.data',[128 64],2,'real*4','b');
342 function [arr] = myrdda(file,N,k,varargin)
343
344 % Defaults
345 WORDLENGTH=8;
346 rtype='real*8';
347 ieee='b';
348
349 % Check optional arguments
350 args=char(varargin);
351 while (size(args,1) > 0)
352 if deblank(args(1,:)) == 'real*4'
353 WORDLENGTH=4;
354 rtype='real*4';
355 elseif deblank(args(1,:)) == 'real*8'
356 WORDLENGTH=8;
357 rtype='real*8';
358 elseif deblank(args(1,:)) == 'n' | deblank(args(1,:)) == 'native'
359 ieee='n';
360 elseif deblank(args(1,:)) == 'l' | deblank(args(1,:)) == 'ieee-le'
361 ieee='l';
362 elseif deblank(args(1,:)) == 'b' | deblank(args(1,:)) == 'ieee-be'
363 ieee='b';
364 elseif deblank(args(1,:)) == 'c' | deblank(args(1,:)) == 'cray'
365 ieee='c';
366 elseif deblank(args(1,:)) == 'a' | deblank(args(1,:)) == 'ieee-le.l64'
367 ieee='a';
368 elseif deblank(args(1,:)) == 's' | deblank(args(1,:)) == 'ieee-be.l64'
369 ieee='s';
370 else
371 error(['Optional argument ' args(1,:) ' is unknown'])
372 end
373 args=args(2:end,:);
374 end
375
376 nnn=prod(N);
377
378 [fid mess]=fopen(file,'r',ieee);
379 if fid == -1
380 error('Error while opening file:\n%s',mess)
381 end
382 st=fseek(fid,nnn*(k-1)*WORDLENGTH,'bof');
383 if st ~= 0
384 mess=ferror(fid);
385 error('There was an error while positioning the file pointer:\n%s',mess)
386 end
387 [arr count]=fread(fid,nnn,rtype);
388 if count ~= nnn
389 error('Not enough data was available to be read: off EOF?')
390 end
391 st=fclose(fid);
392 %arr=reshape(arr,N);
393
394 %
395 function [iters] = scanforfiles(fname)
396
397 iters=[];
398 allfiles=dir([fname '.*.001.001.meta']);
399 if isempty(allfiles)
400 allfiles=dir([fname '.*.meta']);
401 ioff=0;
402 else
403 ioff=8;
404 end
405 for k=1:size(allfiles,1);
406 hh=allfiles(k).name;
407 iters(k)=str2num( hh(end-14-ioff:end-5-ioff) );
408 end
409 iters=sort(iters);

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