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

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Revision 1.2 - (show annotations) (download)
Tue May 29 14:01:41 2001 UTC (22 years, 11 months ago) by adcroft
Branch: MAIN
CVS Tags: checkpoint46n_post, checkpoint51k_post, checkpoint47e_post, checkpoint57m_post, checkpoint52l_pre, checkpoint44e_post, hrcube4, hrcube5, checkpoint46l_post, checkpoint57g_pre, checkpoint46g_pre, checkpoint47c_post, release1_p13_pre, checkpoint50c_post, checkpoint57s_post, checkpoint58b_post, checkpoint57b_post, checkpoint46f_post, checkpoint52d_pre, checkpoint57g_post, checkpoint48e_post, checkpoint56b_post, checkpoint50c_pre, checkpoint57y_post, checkpoint44f_post, checkpoint46b_post, checkpoint52j_pre, checkpoint43a-release1mods, checkpoint51o_pre, checkpoint54d_post, checkpoint54e_post, ecco_c50_e32, ecco_c50_e33, ecco_c50_e30, ecco_c50_e31, release1_p13, checkpoint40pre3, checkpoint40pre1, checkpoint51l_post, checkpoint40pre7, checkpoint40pre6, checkpoint48i_post, checkpoint57r_post, checkpoint40pre9, checkpoint40pre8, checkpoint46l_pre, checkpoint57d_post, checkpoint57i_post, checkpoint52l_post, checkpoint52k_post, chkpt44d_post, checkpoint58, checkpoint55, checkpoint54, checkpoint57, checkpoint56, checkpoint51, checkpoint50, checkpoint53, checkpoint52, release1_p8, release1_p9, checkpoint50d_post, release1_p1, release1_p2, release1_p3, release1_p4, release1_p5, release1_p6, release1_p7, checkpoint58f_post, checkpoint52f_post, checkpoint57n_post, checkpoint58d_post, checkpoint58a_post, checkpoint50b_pre, checkpoint44e_pre, checkpoint57z_post, checkpoint54f_post, checkpoint51f_post, release1_b1, ecco_c51_e34d, ecco_c51_e34e, ecco_c51_e34f, ecco_c51_e34g, ecco_c51_e34a, ecco_c51_e34b, ecco_c51_e34c, checkpoint48b_post, checkpoint43, checkpoint51d_post, checkpoint48c_pre, checkpoint47d_pre, checkpoint51t_post, checkpoint58t_post, checkpoint51n_post, release1_chkpt44d_post, checkpoint55i_post, checkpoint58m_post, checkpoint57l_post, checkpoint52i_pre, hrcube_1, hrcube_2, hrcube_3, checkpoint51s_post, checkpoint47a_post, checkpoint57t_post, checkpoint55c_post, checkpoint48d_pre, checkpoint51j_post, checkpoint47i_post, checkpoint52e_pre, checkpoint57v_post, checkpoint57f_post, checkpoint52e_post, checkpoint51n_pre, checkpoint47d_post, icebear5, icebear4, icebear3, icebear2, checkpoint53d_post, checkpoint46d_pre, checkpoint40pre2, checkpoint57a_post, checkpoint48d_post, release1-branch_tutorials, checkpoint57h_pre, checkpoint48f_post, checkpoint45d_post, checkpoint52b_pre, checkpoint54b_post, checkpoint46j_pre, checkpoint57h_post, checkpoint51l_pre, checkpoint52m_post, checkpoint57y_pre, chkpt44a_post, checkpoint55g_post, checkpoint44h_pre, checkpoint48h_post, checkpoint51q_post, checkpoint40pre4, ecco_c50_e29, checkpoint51b_pre, checkpoint46a_post, checkpoint47g_post, checkpoint52b_post, checkpoint52c_post, checkpoint46j_post, checkpoint51h_pre, checkpoint46k_post, ecco_c50_e28, chkpt44c_pre, checkpoint58o_post, checkpoint48a_post, checkpoint45a_post, checkpoint57c_post, checkpoint50f_post, checkpoint50a_post, checkpoint50f_pre, checkpoint58p_post, checkpoint58q_post, checkpoint52f_pre, checkpoint55d_post, ecco_c44_e19, ecco_c44_e18, ecco_c44_e17, ecco_c44_e16, release1_p12, checkpoint58e_post, release1_p10, release1_p11, release1_p16, release1_p17, release1_p14, release1_p15, checkpoint47j_post, checkpoint54a_pre, ecco_c50_e33a, checkpoint53c_post, checkpoint55d_pre, checkpoint57c_pre, checkpoint58r_post, checkpoint55j_post, branch-exfmods-tag, checkpoint44g_post, branchpoint-genmake2, checkpoint54a_post, checkpoint46e_pre, checkpoint55h_post, checkpoint58n_post, checkpoint51r_post, checkpoint48c_post, checkpoint45b_post, checkpoint46b_pre, checkpoint51i_post, checkpoint57e_post, release1-branch-end, release1_final_v1, checkpoint55b_post, checkpoint51b_post, checkpoint51c_post, checkpoint46c_pre, checkpoint53a_post, checkpoint46, checkpoint47b_post, checkpoint44b_post, checkpoint55f_post, ecco_c51_e34, checkpoint46h_pre, checkpoint52d_post, checkpoint53g_post, checkpoint46m_post, checkpoint57p_post, checkpint57u_post, checkpoint46a_pre, checkpoint50g_post, checkpoint45c_post, checkpoint57q_post, ecco_ice2, ecco_ice1, checkpoint44h_post, eckpoint57e_pre, checkpoint46g_post, release1_p12_pre, checkpoint58k_post, checkpoint52a_pre, ecco_c44_e22, checkpoint58v_post, checkpoint50h_post, checkpoint52i_post, checkpoint50e_pre, checkpoint50i_post, ecco_c44_e25, checkpoint51i_pre, checkpoint52h_pre, checkpoint56a_post, checkpoint58l_post, checkpoint53f_post, checkpoint40pre5, checkpoint57h_done, checkpoint52j_post, checkpoint47f_post, checkpoint50e_post, chkpt44a_pre, checkpoint46i_post, ecco_c44_e23, ecco_c44_e20, ecco_c44_e21, ecco_c44_e26, ecco_c44_e27, ecco_c44_e24, checkpoint57j_post, checkpoint57f_pre, checkpoint46c_post, checkpoint58g_post, ecco-branch-mod1, ecco-branch-mod2, ecco-branch-mod3, ecco-branch-mod4, ecco-branch-mod5, branch-netcdf, checkpoint50d_pre, checkpoint52n_post, checkpoint53b_pre, checkpoint46e_post, release1_beta1, checkpoint58h_post, checkpoint56c_post, checkpoint58j_post, checkpoint51e_post, checkpoint44b_pre, checkpoint42, checkpoint57a_pre, checkpoint40, checkpoint41, checkpoint55a_post, checkpoint47, checkpoint44, checkpoint45, checkpoint48, checkpoint49, checkpoint57o_post, checkpoint46h_post, checkpoint51o_post, checkpoint57k_post, checkpoint51f_pre, chkpt44c_post, checkpoint48g_post, checkpoint53b_post, checkpoint47h_post, checkpoint52a_post, checkpoint57w_post, checkpoint44f_pre, checkpoint58i_post, checkpoint51g_post, ecco_c52_e35, checkpoint57x_post, checkpoint46d_post, checkpoint50b_post, checkpoint58c_post, checkpoint58u_post, release1-branch_branchpoint, checkpoint51m_post, checkpoint53d_pre, checkpoint58s_post, checkpoint55e_post, checkpoint54c_post, checkpoint51a_post, checkpoint51p_post, checkpoint51u_post
Branch point for: c24_e25_ice, branch-exfmods-curt, release1_final, release1-branch, branch-genmake2, release1, branch-nonh, tg2-branch, ecco-branch, release1_50yr, netcdf-sm0, icebear, checkpoint51n_branch, release1_coupled
Changes since 1.1: +1 -0 lines 
Merge from branch pre38:
 o essential mods for cubed sphere
 o debugged atmosphere, dynamcis + physics (aim)
 o new packages (mom_vecinv, mom_fluxform, ...)
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/models/MITgcmUV/utils/matlab/rdmeta.m,v 1.1.4.1 2001/04/13 18:28:23 adcroft Exp $
34
35 % Default options
36 ieee='b';
37
38 % Check optional arguments
39 args=char(varargin);
40 while (size(args,1) > 0)
41 if deblank(args(1,:)) == 'n' | deblank(args(1,:)) == 'native'
42 ieee='n';
43 elseif deblank(args(1,:)) == 'l' | deblank(args(1,:)) == 'ieee-le'
44 ieee='l';
45 elseif deblank(args(1,:)) == 'b' | deblank(args(1,:)) == 'ieee-be'
46 ieee='b';
47 elseif deblank(args(1,:)) == 'c' | deblank(args(1,:)) == 'cray'
48 ieee='c';
49 elseif deblank(args(1,:)) == 'a' | deblank(args(1,:)) == 'ieee-le.l64'
50 ieee='a';
51 elseif deblank(args(1,:)) == 's' | deblank(args(1,:)) == 'ieee-be.l64'
52 ieee='s';
53 else
54 error(['Optional argument ' args(1,:) ' is unknown'])
55 end
56 args=args(2:end,:);
57 end
58
59 % Match name of all meta-files
60 eval(['ls ' fname '*.meta;']);
61 allfiles=ans;
62
63 % Beginning and end of strings
64 Iend=findstr(allfiles,'.meta')+4;
65 Ibeg=[1 Iend(1:end-1)+2];
66
67 % Loop through allfiles
68 for j=1:prod(size(Ibeg)),
69
70 % Read meta- and data-file
71 [A,N] = localrdmds(allfiles(Ibeg(j):Iend(j)),ieee);
72
73 bdims=N(1,:);
74 r0=N(2,:);
75 rN=N(3,:);
76 ndims=prod(size(bdims));
77 if (ndims == 1)
78 AA(r0(1):rN(1))=A;
79 elseif (ndims == 2)
80 AA(r0(1):rN(1),r0(2):rN(2))=A;
81 elseif (ndims == 3)
82 AA(r0(1):rN(1),r0(2):rN(2),r0(3):rN(3))=A;
83 elseif (ndims == 4)
84 AA(r0(1):rN(1),r0(2):rN(2),r0(3):rN(3),r0(4):rN(4))=A;
85 else
86 error('Dimension of data set is larger than currently coded. Sorry!')
87 end
88
89 end
90
91 %-------------------------------------------------------------------------------
92
93 function [A,N] = localrdmds(fname,ieee)
94
95 mname=strrep(fname,' ','');
96 dname=strrep(mname,'.meta','.data');
97
98 % Read and interpret Meta file
99 fid = fopen(mname,'r');
100 if (fid == -1)
101 error(['File' mname ' could not be opened'])
102 end
103
104 % Scan each line of the Meta file
105 allstr=' ';
106 keepgoing = 1;
107 while keepgoing > 0,
108 line = fgetl(fid);
109 if (line == -1)
110 keepgoing=-1;
111 else
112 % Strip out "(PID.TID *.*)" by finding first ")"
113 %old ind=findstr([line ')'],')'); line=line(ind(1)+1:end);
114 ind=findstr(line,')');
115 if size(ind) ~= 0
116 line=line(ind(1)+1:end);
117 end
118 % Remove comments of form //
119 line=[line ' //']; ind=findstr(line,'//'); line=line(1:ind(1)-1);
120 % Add to total string
121 allstr=[allstr line];
122 end
123 end
124
125 % Close meta file
126 fclose(fid);
127
128 % Strip out comments of form /* ... */
129 ind1=findstr(allstr,'/*'); ind2=findstr(allstr,'*/');
130 if size(ind1) ~= size(ind2)
131 error('The /* ... */ comments are not properly paired')
132 end
133 while size(ind1,2) > 0
134 allstr=[allstr(1:ind1(1)-1) allstr(ind2(1)+3:end)];
135 ind1=findstr(allstr,'/*'); ind2=findstr(allstr,'*/');
136 end
137
138 % This is a kludge to catch whether the meta-file is of the
139 % old or new type. nrecords does not exist in the old type.
140 nrecords = -987;
141
142 % Everything in lower case
143 allstr=lower(allstr);
144
145 % Fix the unfortunate choice of 'format'
146 allstr=strrep(allstr,'format','dataprec');
147
148 % Evaluate meta information
149 eval(allstr);
150
151 N=reshape( dimlist , 3 , prod(size(dimlist))/3 );
152
153 if nrecords == -987
154 % This is the old 'meta' method that used sequential access
155
156 A=allstr;
157 % Open data file
158 fid=fopen(dname,'r',ieee);
159
160 % Read record size in bytes
161 recsz=fread(fid,1,'uint32');
162 ldims=N(3,:)-N(2,:)+1;
163 numels=prod(ldims);
164
165 rat=recsz/numels;
166 if rat == 4
167 A=fread(fid,numels,'real*4');
168 elseif rat == 8
169 A=fread(fid,numels,'real*8');
170 else
171 sprintf(' Implied size in meta-file = %d', numels )
172 sprintf(' Record size in data-file = %d', recsz )
173 error('Ratio between record size and size in meta-file inconsistent')
174 end
175
176 erecsz=fread(fid,1,'uint32');
177 if erecsz ~= recsz
178 sprintf('WARNING: Record sizes at beginning and end of file are inconsistent')
179 end
180
181 fclose(fid);
182
183 A=reshape(A,ldims);
184
185 else
186 % This is the new MDS format that uses direct access
187
188 ldims=N(3,:)-N(2,:)+1;
189 if dataprec == 'float32'
190 A=myrdda(dname,ldims,1,'real*4',ieee);
191 elseif dataprec == 'float64'
192 A=myrdda(dname,ldims,1,'real*8',ieee);
193 else
194 error(['Unrecognized format in meta-file = ' format]);
195 end
196
197 end
198
199 %-------------------------------------------------------------------------------
200
201 % result = RDDA( file, dim, irec [options] )
202 %
203 % This routine reads the irec'th record of shape 'dim' from the
204 % direct-access binary file (float or double precision) 'file'.
205 %
206 % Required arguments:
207 %
208 % file - string - name of file to read from
209 % dim - vector - dimensions of the file records and the resulting array
210 % irec - integer - record number in file in which to write data
211 %
212 % Optional arguments (must appear after the required arguments):
213 % prec - string - precision of storage in file. Default = 'real*8'.
214 % ieee - string - IEEE bit-wise representation in file. Default = 'b'.
215 %
216 % 'prec' may take the values:
217 % 'real*4' - floating point, 32 bits.
218 % 'real*8' - floating point, 64 bits - the efault.
219 %
220 % 'ieee' may take values:
221 % 'ieee-be' or 'b' - IEEE floating point with big-endian
222 % byte ordering - the default
223 % 'ieee-le' or 'l' - IEEE floating point with little-endian
224 % byte ordering
225 % 'native' or 'n' - local machine format
226 % 'cray' or 'c' - Cray floating point with big-endian
227 % byte ordering
228 % 'ieee-le.l64' or 'a' - IEEE floating point with little-endian
229 % byte ordering and 64 bit long data type
230 % 'ieee-be.l64' or 's' - IEEE floating point with big-endian byte
231 % ordering and 64 bit long data type.
232 %
233 % eg. T=rdda('t.data',[64 64 32],1);
234 % T=rdda('t.data',[256],4,'real*4');
235 % T=rdda('t.data',[128 64],2,'real*4','b');
236 function [arr] = myrdda(file,N,k,varargin)
237
238 % Defaults
239 WORDLENGTH=8;
240 rtype='real*8';
241 ieee='b';
242
243 % Check optional arguments
244 args=char(varargin);
245 while (size(args,1) > 0)
246 if deblank(args(1,:)) == 'real*4'
247 WORDLENGTH=4;
248 rtype='real*4';
249 elseif deblank(args(1,:)) == 'real*8'
250 WORDLENGTH=8;
251 rtype='real*8';
252 elseif deblank(args(1,:)) == 'n' | deblank(args(1,:)) == 'native'
253 ieee='n';
254 elseif deblank(args(1,:)) == 'l' | deblank(args(1,:)) == 'ieee-le'
255 ieee='l';
256 elseif deblank(args(1,:)) == 'b' | deblank(args(1,:)) == 'ieee-be'
257 ieee='b';
258 elseif deblank(args(1,:)) == 'c' | deblank(args(1,:)) == 'cray'
259 ieee='c';
260 elseif deblank(args(1,:)) == 'a' | deblank(args(1,:)) == 'ieee-le.l64'
261 ieee='a';
262 elseif deblank(args(1,:)) == 's' | deblank(args(1,:)) == 'ieee-be.l64'
263 ieee='s';
264 else
265 error(['Optional argument ' args(1,:) ' is unknown'])
266 end
267 args=args(2:end,:);
268 end
269
270 nnn=prod(N);
271
272 [fid mess]=fopen(file,'r',ieee);
273 if fid == -1
274 error('Error while opening file:\n%s',mess)
275 end
276 st=fseek(fid,nnn*(k-1)*WORDLENGTH,'bof');
277 if st ~= 0
278 mess=ferror(fid);
279 error('There was an error while positioning the file pointer:\n%s',mess)
280 end
281 [arr count]=fread(fid,nnn,rtype);
282 if count ~= nnn
283 error('Not enough data was available to be read: off EOF?')
284 end
285 st=fclose(fid);
286 arr=reshape(arr,N);
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