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 |
% |
8 |
% A = RDMDS(FNAME) reads data described by meta/data file format. |
9 |
% FNAME is a string containing the "head" of the file names. |
10 |
% |
11 |
% eg. To load the meta-data files |
12 |
% T.0000002880.000.000.meta, T.0000002880.000.000.data |
13 |
% T.0000002880.001.000.meta, T.0000002880.001.000.data |
14 |
% T.0000002880.002.000.meta, T.0000002880.002.000.data |
15 |
% T.0000002880.003.000.meta, T.0000002880.003.000.data |
16 |
% use |
17 |
% >> A=rdmds('T.0000002880'); |
18 |
% >> size(A) |
19 |
% ans = |
20 |
% 64 32 5 |
21 |
% eg. To load a multiple record file |
22 |
% >> A=rdmds('pickup.0000002880'); |
23 |
% >> size(A) |
24 |
% ans = |
25 |
% 64 32 5 61 |
26 |
% |
27 |
% |
28 |
% A = RDMDS(FNAME,ITER) reads data described by meta/data file format. |
29 |
% FNAME is a string containing the "head" of the file name excluding the |
30 |
% 10-digit iterartion number. |
31 |
% ITER is a vector of positive integers that will expand to the 10-digit |
32 |
% number in the file name. |
33 |
% |
34 |
% eg. To repeat above operation |
35 |
% >> A=rdmds('T',2880); |
36 |
% eg. To read multiple time steps |
37 |
% >> A=rdmds('T',[0 1440 2880]); |
38 |
% Note: this form can not read files with no iteration count in file name. |
39 |
% |
40 |
% A = RDMDS(FNAME,MACHINEFORMAT) |
41 |
% A = RDMDS(FNAME,ITER,MACHINEFORMAT) allows the machine format to be |
42 |
% specified which MACHINEFORMAT is on of the following strings: |
43 |
% 'n' 'l' 'b' 'd' 'g' 'c' 'a' 's' - see FOPEN for more details |
44 |
% |
45 |
% |
46 |
% $Header: /u/u0/gcmpack/MITgcm/utils/matlab/rdmds.m,v 1.13 2002/06/12 14:57:29 adcroft Exp $ |
47 |
|
48 |
% Default options |
49 |
ieee='b'; |
50 |
fname=fnamearg; |
51 |
iters=-1; |
52 |
|
53 |
% Check optional arguments |
54 |
for ind=1:size(varargin,2); |
55 |
arg=varargin{ind}; |
56 |
if ischar(arg) |
57 |
if strcmp(arg,'n') | strcmp(arg,'native') |
58 |
ieee='n'; |
59 |
elseif strcmp(arg,'l') | strcmp(arg,'ieee-le') |
60 |
ieee='l'; |
61 |
elseif strcmp(arg,'b') | strcmp(arg,'ieee-be') |
62 |
ieee='b'; |
63 |
elseif strcmp(arg,'c') | strcmp(arg,'cray') |
64 |
ieee='c'; |
65 |
elseif strcmp(arg,'a') | strcmp(arg,'ieee-le.l64') |
66 |
ieee='a'; |
67 |
elseif strcmp(arg,'s') | strcmp(arg,'ieee-be.l64') |
68 |
ieee='s'; |
69 |
else |
70 |
error(['Optional argument ' arg ' is unknown']) |
71 |
end |
72 |
else |
73 |
if isnan(arg) |
74 |
iters=scanforfiles(fname); |
75 |
disp([ sprintf('Reading %i time levels:',size(iters,2)) sprintf(' %i',iters) ]); |
76 |
elseif isinf(arg) |
77 |
iters=scanforfiles(fname); |
78 |
if isempty(iters) |
79 |
AA=[];iters=[];return; |
80 |
end |
81 |
disp([ sprintf('Found %i time levels, reading %i',size(iters,2),iters(end)) ]); |
82 |
iters=iters(end); |
83 |
elseif prod(arg>=0) & prod(round(arg)==arg) |
84 |
if arg>=9999999999 |
85 |
error(sprintf('Argument %i > 9999999999',arg)) |
86 |
end |
87 |
iters=arg; |
88 |
else |
89 |
error(sprintf('Argument %i must be a positive integer',arg)) |
90 |
end |
91 |
end |
92 |
end |
93 |
|
94 |
% Loop over each iteration |
95 |
for iter=1:size(iters,2); |
96 |
if iters(iter)>=0 |
97 |
fname=sprintf('%s.%10.10i',fnamearg,iters(iter)); |
98 |
end |
99 |
|
100 |
% Figure out if there is a path in the filename |
101 |
NS=findstr('/',fname); |
102 |
if size(NS)>0 |
103 |
Dir=fname(1:NS(end)); |
104 |
else |
105 |
Dir='./'; |
106 |
end |
107 |
|
108 |
% Match name of all meta-files |
109 |
allfiles=dir( sprintf('%s*.meta',fname) ); |
110 |
|
111 |
if size(allfiles,1)==0 |
112 |
disp(sprintf('No files match the search: %s.*.meta',fname)); |
113 |
%allow partial reads% error('No files found.') |
114 |
end |
115 |
|
116 |
% Loop through allfiles |
117 |
for j=1:size(allfiles,1); |
118 |
|
119 |
% Read meta- and data-file |
120 |
[A,N] = localrdmds([Dir allfiles(j).name],ieee); |
121 |
|
122 |
bdims=N(1,:); |
123 |
r0=N(2,:); |
124 |
rN=N(3,:); |
125 |
ndims=prod(size(bdims)); |
126 |
if (ndims == 1) |
127 |
AA(r0(1):rN(1),iter)=A; |
128 |
elseif (ndims == 2) |
129 |
AA(r0(1):rN(1),r0(2):rN(2),iter)=A; |
130 |
elseif (ndims == 3) |
131 |
AA(r0(1):rN(1),r0(2):rN(2),r0(3):rN(3),iter)=A; |
132 |
elseif (ndims == 4) |
133 |
AA(r0(1):rN(1),r0(2):rN(2),r0(3):rN(3),r0(4):rN(4),iter)=A; |
134 |
elseif (ndims == 5) |
135 |
AA(r0(1):rN(1),r0(2):rN(2),r0(3):rN(3),r0(4):rN(4),r0(5):rN(5),iter)=A; |
136 |
else |
137 |
error('Dimension of data set is larger than currently coded. Sorry!') |
138 |
end |
139 |
|
140 |
end % files |
141 |
end % iterations |
142 |
|
143 |
%------------------------------------------------------------------------------- |
144 |
|
145 |
function [A,N] = localrdmds(fname,ieee) |
146 |
|
147 |
mname=strrep(fname,' ',''); |
148 |
dname=strrep(mname,'.meta','.data'); |
149 |
|
150 |
% Read and interpret Meta file |
151 |
fid = fopen(mname,'r'); |
152 |
if (fid == -1) |
153 |
error(['File' mname ' could not be opened']) |
154 |
end |
155 |
|
156 |
% Scan each line of the Meta file |
157 |
allstr=' '; |
158 |
keepgoing = 1; |
159 |
while keepgoing > 0, |
160 |
line = fgetl(fid); |
161 |
if (line == -1) |
162 |
keepgoing=-1; |
163 |
else |
164 |
% Strip out "(PID.TID *.*)" by finding first ")" |
165 |
%old ind=findstr([line ')'],')'); line=line(ind(1)+1:end); |
166 |
ind=findstr(line,')'); |
167 |
if size(ind) ~= 0 |
168 |
line=line(ind(1)+1:end); |
169 |
end |
170 |
% Remove comments of form // |
171 |
line=[line ' //']; ind=findstr(line,'//'); line=line(1:ind(1)-1); |
172 |
% Add to total string |
173 |
allstr=[allstr line]; |
174 |
end |
175 |
end |
176 |
|
177 |
% Close meta file |
178 |
fclose(fid); |
179 |
|
180 |
% Strip out comments of form /* ... */ |
181 |
ind1=findstr(allstr,'/*'); ind2=findstr(allstr,'*/'); |
182 |
if size(ind1) ~= size(ind2) |
183 |
error('The /* ... */ comments are not properly paired') |
184 |
end |
185 |
while size(ind1,2) > 0 |
186 |
allstr=[allstr(1:ind1(1)-1) allstr(ind2(1)+3:end)]; |
187 |
ind1=findstr(allstr,'/*'); ind2=findstr(allstr,'*/'); |
188 |
end |
189 |
|
190 |
% This is a kludge to catch whether the meta-file is of the |
191 |
% old or new type. nrecords does not exist in the old type. |
192 |
nrecords = -987; |
193 |
|
194 |
% Everything in lower case |
195 |
allstr=lower(allstr); |
196 |
|
197 |
% Fix the unfortunate choice of 'format' |
198 |
allstr=strrep(allstr,'format','dataprec'); |
199 |
|
200 |
% Evaluate meta information |
201 |
eval(allstr); |
202 |
|
203 |
N=reshape( dimlist , 3 , prod(size(dimlist))/3 ); |
204 |
if nrecords ~= -987 & nrecords > 1 |
205 |
N=[N,[nrecords 1 nrecords]']; |
206 |
end |
207 |
|
208 |
if nrecords == -987 |
209 |
% This is the old 'meta' method that used sequential access |
210 |
|
211 |
A=allstr; |
212 |
% Open data file |
213 |
fid=fopen(dname,'r',ieee); |
214 |
|
215 |
% Read record size in bytes |
216 |
recsz=fread(fid,1,'uint32'); |
217 |
ldims=N(3,:)-N(2,:)+1; |
218 |
numels=prod(ldims); |
219 |
|
220 |
rat=recsz/numels; |
221 |
if rat == 4 |
222 |
A=fread(fid,numels,'real*4'); |
223 |
elseif rat == 8 |
224 |
A=fread(fid,numels,'real*8'); |
225 |
else |
226 |
sprintf(' Implied size in meta-file = %d', numels ) |
227 |
sprintf(' Record size in data-file = %d', recsz ) |
228 |
error('Ratio between record size and size in meta-file inconsistent') |
229 |
end |
230 |
|
231 |
erecsz=fread(fid,1,'uint32'); |
232 |
if erecsz ~= recsz |
233 |
sprintf('WARNING: Record sizes at beginning and end of file are inconsistent') |
234 |
end |
235 |
|
236 |
fclose(fid); |
237 |
|
238 |
A=reshape(A,ldims); |
239 |
|
240 |
else |
241 |
% This is the new MDS format that uses direct access |
242 |
|
243 |
ldims=N(3,:)-N(2,:)+1; |
244 |
if dataprec == 'float32' |
245 |
A=myrdda(dname,ldims,1,'real*4',ieee); |
246 |
elseif dataprec == 'float64' |
247 |
A=myrdda(dname,ldims,1,'real*8',ieee); |
248 |
else |
249 |
error(['Unrecognized format in meta-file = ' format]); |
250 |
end |
251 |
|
252 |
end |
253 |
|
254 |
%------------------------------------------------------------------------------- |
255 |
|
256 |
% result = RDDA( file, dim, irec [options] ) |
257 |
% |
258 |
% This routine reads the irec'th record of shape 'dim' from the |
259 |
% direct-access binary file (float or double precision) 'file'. |
260 |
% |
261 |
% Required arguments: |
262 |
% |
263 |
% file - string - name of file to read from |
264 |
% dim - vector - dimensions of the file records and the resulting array |
265 |
% irec - integer - record number in file in which to write data |
266 |
% |
267 |
% Optional arguments (must appear after the required arguments): |
268 |
% prec - string - precision of storage in file. Default = 'real*8'. |
269 |
% ieee - string - IEEE bit-wise representation in file. Default = 'b'. |
270 |
% |
271 |
% 'prec' may take the values: |
272 |
% 'real*4' - floating point, 32 bits. |
273 |
% 'real*8' - floating point, 64 bits - the efault. |
274 |
% |
275 |
% 'ieee' may take values: |
276 |
% 'ieee-be' or 'b' - IEEE floating point with big-endian |
277 |
% byte ordering - the default |
278 |
% 'ieee-le' or 'l' - IEEE floating point with little-endian |
279 |
% byte ordering |
280 |
% 'native' or 'n' - local machine format |
281 |
% 'cray' or 'c' - Cray floating point with big-endian |
282 |
% byte ordering |
283 |
% 'ieee-le.l64' or 'a' - IEEE floating point with little-endian |
284 |
% byte ordering and 64 bit long data type |
285 |
% 'ieee-be.l64' or 's' - IEEE floating point with big-endian byte |
286 |
% ordering and 64 bit long data type. |
287 |
% |
288 |
% eg. T=rdda('t.data',[64 64 32],1); |
289 |
% T=rdda('t.data',[256],4,'real*4'); |
290 |
% T=rdda('t.data',[128 64],2,'real*4','b'); |
291 |
function [arr] = myrdda(file,N,k,varargin) |
292 |
|
293 |
% Defaults |
294 |
WORDLENGTH=8; |
295 |
rtype='real*8'; |
296 |
ieee='b'; |
297 |
|
298 |
% Check optional arguments |
299 |
args=char(varargin); |
300 |
while (size(args,1) > 0) |
301 |
if deblank(args(1,:)) == 'real*4' |
302 |
WORDLENGTH=4; |
303 |
rtype='real*4'; |
304 |
elseif deblank(args(1,:)) == 'real*8' |
305 |
WORDLENGTH=8; |
306 |
rtype='real*8'; |
307 |
elseif deblank(args(1,:)) == 'n' | deblank(args(1,:)) == 'native' |
308 |
ieee='n'; |
309 |
elseif deblank(args(1,:)) == 'l' | deblank(args(1,:)) == 'ieee-le' |
310 |
ieee='l'; |
311 |
elseif deblank(args(1,:)) == 'b' | deblank(args(1,:)) == 'ieee-be' |
312 |
ieee='b'; |
313 |
elseif deblank(args(1,:)) == 'c' | deblank(args(1,:)) == 'cray' |
314 |
ieee='c'; |
315 |
elseif deblank(args(1,:)) == 'a' | deblank(args(1,:)) == 'ieee-le.l64' |
316 |
ieee='a'; |
317 |
elseif deblank(args(1,:)) == 's' | deblank(args(1,:)) == 'ieee-be.l64' |
318 |
ieee='s'; |
319 |
else |
320 |
error(['Optional argument ' args(1,:) ' is unknown']) |
321 |
end |
322 |
args=args(2:end,:); |
323 |
end |
324 |
|
325 |
nnn=prod(N); |
326 |
|
327 |
[fid mess]=fopen(file,'r',ieee); |
328 |
if fid == -1 |
329 |
error('Error while opening file:\n%s',mess) |
330 |
end |
331 |
st=fseek(fid,nnn*(k-1)*WORDLENGTH,'bof'); |
332 |
if st ~= 0 |
333 |
mess=ferror(fid); |
334 |
error('There was an error while positioning the file pointer:\n%s',mess) |
335 |
end |
336 |
[arr count]=fread(fid,nnn,rtype); |
337 |
if count ~= nnn |
338 |
error('Not enough data was available to be read: off EOF?') |
339 |
end |
340 |
st=fclose(fid); |
341 |
arr=reshape(arr,N); |
342 |
|
343 |
% |
344 |
function [iters] = scanforfiles(fname) |
345 |
|
346 |
iters=[]; |
347 |
allfiles=dir([fname '.*.001.001.meta']); |
348 |
if isempty(allfiles) |
349 |
allfiles=dir([fname '.*.meta']); |
350 |
ioff=0; |
351 |
else |
352 |
ioff=8; |
353 |
end |
354 |
for k=1:size(allfiles,1); |
355 |
hh=allfiles(k).name; |
356 |
iters(k)=str2num( hh(end-14-ioff:end-5-ioff) ); |
357 |
end |
358 |
|