1 |
function [AA] = rdmds(fname,varargin) |
2 |
% |
3 |
% Read MITgcmUV Meta/Data files |
4 |
% |
5 |
% A = RDMDS(FNAME) reads data described by meta/data file format. |
6 |
% FNAME is a string containing the "head" of the file names. |
7 |
% |
8 |
% eg. To load the meta-data files |
9 |
% T.0000002880.000.000.meta, T.0000002880.000.000.data |
10 |
% T.0000002880.001.000.meta, T.0000002880.001.000.data |
11 |
% T.0000002880.002.000.meta, T.0000002880.002.000.data |
12 |
% T.0000002880.003.000.meta, T.0000002880.003.000.data |
13 |
% use |
14 |
% >> A=rdmds('T.0000002880'); |
15 |
% |
16 |
% A = RDMDS(FNAME,MACHINEFORMAT) allows the machine format to be specified |
17 |
% which MACHINEFORMAT is on of the following strings: |
18 |
% |
19 |
% 'native' or 'n' - local machine format - the default |
20 |
% 'ieee-le' or 'l' - IEEE floating point with little-endian |
21 |
% byte ordering |
22 |
% 'ieee-be' or 'b' - IEEE floating point with big-endian |
23 |
% byte ordering |
24 |
% 'vaxd' or 'd' - VAX D floating point and VAX ordering |
25 |
% 'vaxg' or 'g' - VAX G floating point and VAX ordering |
26 |
% 'cray' or 'c' - Cray floating point with big-endian |
27 |
% byte ordering |
28 |
% 'ieee-le.l64' or 'a' - IEEE floating point with little-endian |
29 |
% byte ordering and 64 bit long data type |
30 |
% 'ieee-be.l64' or 's' - IEEE floating point with big-endian byte |
31 |
% ordering and 64 bit long data type. |
32 |
|
33 |
% $Header: /u/gcmpack/MITgcm/utils/matlab/rdmeta.m,v 1.4 2009/05/29 13:47:43 jmc Exp $ |
34 |
% $Name: $ |
35 |
|
36 |
% Default options |
37 |
ieee='b'; |
38 |
|
39 |
% Check optional arguments |
40 |
args=char(varargin); |
41 |
while (size(args,1) > 0) |
42 |
if deblank(args(1,:)) == 'n' | deblank(args(1,:)) == 'native' |
43 |
ieee='n'; |
44 |
elseif deblank(args(1,:)) == 'l' | deblank(args(1,:)) == 'ieee-le' |
45 |
ieee='l'; |
46 |
elseif deblank(args(1,:)) == 'b' | deblank(args(1,:)) == 'ieee-be' |
47 |
ieee='b'; |
48 |
elseif deblank(args(1,:)) == 'c' | deblank(args(1,:)) == 'cray' |
49 |
ieee='c'; |
50 |
elseif deblank(args(1,:)) == 'a' | deblank(args(1,:)) == 'ieee-le.l64' |
51 |
ieee='a'; |
52 |
elseif deblank(args(1,:)) == 's' | deblank(args(1,:)) == 'ieee-be.l64' |
53 |
ieee='s'; |
54 |
else |
55 |
error(['Optional argument ' args(1,:) ' is unknown']) |
56 |
end |
57 |
args=args(2:end,:); |
58 |
end |
59 |
|
60 |
% Match name of all meta-files |
61 |
eval(['ls ' fname '*.meta;']); |
62 |
allfiles=ans; |
63 |
|
64 |
% Beginning and end of strings |
65 |
Iend=findstr(allfiles,'.meta')+4; |
66 |
Ibeg=[1 Iend(1:end-1)+2]; |
67 |
|
68 |
% Loop through allfiles |
69 |
for j=1:prod(size(Ibeg)), |
70 |
|
71 |
% Read meta- and data-file |
72 |
[A,N] = localrdmds(allfiles(Ibeg(j):Iend(j)),ieee); |
73 |
|
74 |
bdims=N(1,:); |
75 |
r0=N(2,:); |
76 |
rN=N(3,:); |
77 |
ndims=prod(size(bdims)); |
78 |
if (ndims == 1) |
79 |
AA(r0(1):rN(1))=A; |
80 |
elseif (ndims == 2) |
81 |
AA(r0(1):rN(1),r0(2):rN(2))=A; |
82 |
elseif (ndims == 3) |
83 |
AA(r0(1):rN(1),r0(2):rN(2),r0(3):rN(3))=A; |
84 |
elseif (ndims == 4) |
85 |
AA(r0(1):rN(1),r0(2):rN(2),r0(3):rN(3),r0(4):rN(4))=A; |
86 |
else |
87 |
error('Dimension of data set is larger than currently coded. Sorry!') |
88 |
end |
89 |
|
90 |
end |
91 |
|
92 |
%------------------------------------------------------------------------------- |
93 |
|
94 |
function [A,N] = localrdmds(fname,ieee) |
95 |
|
96 |
mname=strrep(fname,' ',''); |
97 |
dname=strrep(mname,'.meta','.data'); |
98 |
|
99 |
% Read and interpret Meta file |
100 |
fid = fopen(mname,'r'); |
101 |
if (fid == -1) |
102 |
error(['File' mname ' could not be opened']) |
103 |
end |
104 |
|
105 |
% Scan each line of the Meta file |
106 |
allstr=' '; |
107 |
keepgoing = 1; |
108 |
while keepgoing > 0, |
109 |
line = fgetl(fid); |
110 |
if (line == -1) |
111 |
keepgoing=-1; |
112 |
else |
113 |
% Strip out "(PID.TID *.*)" by finding first ")" |
114 |
%old ind=findstr([line ')'],')'); line=line(ind(1)+1:end); |
115 |
ind=findstr(line,')'); |
116 |
if size(ind) ~= 0 |
117 |
line=line(ind(1)+1:end); |
118 |
end |
119 |
% Remove comments of form // |
120 |
line=[line ' //']; ind=findstr(line,'//'); line=line(1:ind(1)-1); |
121 |
% Add to total string |
122 |
allstr=[allstr line]; |
123 |
end |
124 |
end |
125 |
|
126 |
% Close meta file |
127 |
fclose(fid); |
128 |
|
129 |
% Strip out comments of form /* ... */ |
130 |
ind1=findstr(allstr,'/*'); ind2=findstr(allstr,'*/'); |
131 |
if size(ind1) ~= size(ind2) |
132 |
error('The /* ... */ comments are not properly paired') |
133 |
end |
134 |
while size(ind1,2) > 0 |
135 |
allstr=[allstr(1:ind1(1)-1) allstr(ind2(1)+3:end)]; |
136 |
ind1=findstr(allstr,'/*'); ind2=findstr(allstr,'*/'); |
137 |
end |
138 |
|
139 |
% This is a kludge to catch whether the meta-file is of the |
140 |
% old or new type. nrecords does not exist in the old type. |
141 |
nrecords = -987; |
142 |
|
143 |
% Everything in lower case |
144 |
allstr=lower(allstr); |
145 |
|
146 |
% Fix the unfortunate choice of 'format' |
147 |
allstr=strrep(allstr,'format','dataprec'); |
148 |
|
149 |
% Evaluate meta information |
150 |
eval(allstr); |
151 |
|
152 |
N=reshape( dimlist , 3 , prod(size(dimlist))/3 ); |
153 |
|
154 |
if nrecords == -987 |
155 |
% This is the old 'meta' method that used sequential access |
156 |
|
157 |
A=allstr; |
158 |
% Open data file |
159 |
fid=fopen(dname,'r',ieee); |
160 |
|
161 |
% Read record size in bytes |
162 |
recsz=fread(fid,1,'uint32'); |
163 |
ldims=N(3,:)-N(2,:)+1; |
164 |
numels=prod(ldims); |
165 |
|
166 |
rat=recsz/numels; |
167 |
if rat == 4 |
168 |
A=fread(fid,numels,'real*4'); |
169 |
elseif rat == 8 |
170 |
A=fread(fid,numels,'real*8'); |
171 |
else |
172 |
sprintf(' Implied size in meta-file = %d', numels ) |
173 |
sprintf(' Record size in data-file = %d', recsz ) |
174 |
error('Ratio between record size and size in meta-file inconsistent') |
175 |
end |
176 |
|
177 |
erecsz=fread(fid,1,'uint32'); |
178 |
if erecsz ~= recsz |
179 |
sprintf('WARNING: Record sizes at beginning and end of file are inconsistent') |
180 |
end |
181 |
|
182 |
fclose(fid); |
183 |
|
184 |
A=reshape(A,ldims); |
185 |
|
186 |
else |
187 |
% This is the new MDS format that uses direct access |
188 |
|
189 |
ldims=N(3,:)-N(2,:)+1; |
190 |
if dataprec == 'float32' |
191 |
A=myrdda(dname,ldims,1,'real*4',ieee); |
192 |
elseif dataprec == 'float64' |
193 |
A=myrdda(dname,ldims,1,'real*8',ieee); |
194 |
else |
195 |
error(['Unrecognized dataprec in meta-file = ' dataprec]); |
196 |
end |
197 |
|
198 |
end |
199 |
|
200 |
%------------------------------------------------------------------------------- |
201 |
|
202 |
% result = RDDA( file, dim, irec [options] ) |
203 |
% |
204 |
% This routine reads the irec'th record of shape 'dim' from the |
205 |
% direct-access binary file (float or double precision) 'file'. |
206 |
% |
207 |
% Required arguments: |
208 |
% |
209 |
% file - string - name of file to read from |
210 |
% dim - vector - dimensions of the file records and the resulting array |
211 |
% irec - integer - record number in file in which to write data |
212 |
% |
213 |
% Optional arguments (must appear after the required arguments): |
214 |
% prec - string - precision of storage in file. Default = 'real*8'. |
215 |
% ieee - string - IEEE bit-wise representation in file. Default = 'b'. |
216 |
% |
217 |
% 'prec' may take the values: |
218 |
% 'real*4' - floating point, 32 bits. |
219 |
% 'real*8' - floating point, 64 bits - the efault. |
220 |
% |
221 |
% 'ieee' may take values: |
222 |
% 'ieee-be' or 'b' - IEEE floating point with big-endian |
223 |
% byte ordering - the default |
224 |
% 'ieee-le' or 'l' - IEEE floating point with little-endian |
225 |
% byte ordering |
226 |
% 'native' or 'n' - local machine format |
227 |
% 'cray' or 'c' - Cray floating point with big-endian |
228 |
% byte ordering |
229 |
% 'ieee-le.l64' or 'a' - IEEE floating point with little-endian |
230 |
% byte ordering and 64 bit long data type |
231 |
% 'ieee-be.l64' or 's' - IEEE floating point with big-endian byte |
232 |
% ordering and 64 bit long data type. |
233 |
% |
234 |
% eg. T=rdda('t.data',[64 64 32],1); |
235 |
% T=rdda('t.data',[256],4,'real*4'); |
236 |
% T=rdda('t.data',[128 64],2,'real*4','b'); |
237 |
function [arr] = myrdda(file,N,k,varargin) |
238 |
|
239 |
% Defaults |
240 |
WORDLENGTH=8; |
241 |
rtype='real*8'; |
242 |
ieee='b'; |
243 |
|
244 |
% Check optional arguments |
245 |
args=char(varargin); |
246 |
while (size(args,1) > 0) |
247 |
if deblank(args(1,:)) == 'real*4' |
248 |
WORDLENGTH=4; |
249 |
rtype='real*4'; |
250 |
elseif deblank(args(1,:)) == 'real*8' |
251 |
WORDLENGTH=8; |
252 |
rtype='real*8'; |
253 |
elseif deblank(args(1,:)) == 'n' | deblank(args(1,:)) == 'native' |
254 |
ieee='n'; |
255 |
elseif deblank(args(1,:)) == 'l' | deblank(args(1,:)) == 'ieee-le' |
256 |
ieee='l'; |
257 |
elseif deblank(args(1,:)) == 'b' | deblank(args(1,:)) == 'ieee-be' |
258 |
ieee='b'; |
259 |
elseif deblank(args(1,:)) == 'c' | deblank(args(1,:)) == 'cray' |
260 |
ieee='c'; |
261 |
elseif deblank(args(1,:)) == 'a' | deblank(args(1,:)) == 'ieee-le.l64' |
262 |
ieee='a'; |
263 |
elseif deblank(args(1,:)) == 's' | deblank(args(1,:)) == 'ieee-be.l64' |
264 |
ieee='s'; |
265 |
else |
266 |
error(['Optional argument ' args(1,:) ' is unknown']) |
267 |
end |
268 |
args=args(2:end,:); |
269 |
end |
270 |
|
271 |
nnn=prod(N); |
272 |
|
273 |
[fid mess]=fopen(file,'r',ieee); |
274 |
if fid == -1 |
275 |
error('Error while opening file:\n%s',mess) |
276 |
end |
277 |
st=fseek(fid,nnn*(k-1)*WORDLENGTH,'bof'); |
278 |
if st ~= 0 |
279 |
mess=ferror(fid); |
280 |
error('There was an error while positioning the file pointer:\n%s',mess) |
281 |
end |
282 |
[arr count]=fread(fid,nnn,rtype); |
283 |
if count ~= nnn |
284 |
error('Not enough data was available to be read: off EOF?') |
285 |
end |
286 |
st=fclose(fid); |
287 |
arr=reshape(arr,N); |