utils/matlab/rdmeta.m

function [AA] = rdmds(fname,varargin)
%
% Read MITgcmUV Meta/Data files
%
% A = RDMDS(FNAME) reads data described by meta/data file format.
% FNAME is a string containing the "head" of the file names.
%
% eg. To load the meta-data files
%     T.0000002880.000.000.meta, T.0000002880.000.000.data
%     T.0000002880.001.000.meta, T.0000002880.001.000.data
%     T.0000002880.002.000.meta, T.0000002880.002.000.data
%     T.0000002880.003.000.meta, T.0000002880.003.000.data
% use
%    >> A=rdmds('T.0000002880');
%
% A = RDMDS(FNAME,MACHINEFORMAT) allows the machine format to be specified
% which MACHINEFORMAT is on of the following strings:
%
%   'native'      or 'n' - local machine format - the default
%   'ieee-le'     or 'l' - IEEE floating point with little-endian
%                          byte ordering
%   'ieee-be'     or 'b' - IEEE floating point with big-endian
%                          byte ordering
%   'vaxd'        or 'd' - VAX D floating point and VAX ordering
%   'vaxg'        or 'g' - VAX G floating point and VAX ordering
%   'cray'        or 'c' - Cray floating point with big-endian
%                          byte ordering
%   'ieee-le.l64' or 'a' - IEEE floating point with little-endian
%                          byte ordering and 64 bit long data type
%   'ieee-be.l64' or 's' - IEEE floating point with big-endian byte
%                          ordering and 64 bit long data type.
%
% $Header: /u/gcmpack/models/MITgcmUV/utils/matlab/rdmeta.m,v 1.1.4.1 2001/04/13 18:28:23 adcroft Exp $

% Default options
ieee='b';

% Check optional arguments
args=char(varargin);
while (size(args,1) > 0)
 if deblank(args(1,:)) == 'n' | deblank(args(1,:)) == 'native'
  ieee='n';
 elseif deblank(args(1,:)) == 'l' | deblank(args(1,:)) == 'ieee-le'
  ieee='l';
 elseif deblank(args(1,:)) == 'b' | deblank(args(1,:)) == 'ieee-be'
  ieee='b';
 elseif deblank(args(1,:)) == 'c' | deblank(args(1,:)) == 'cray'
  ieee='c';
 elseif deblank(args(1,:)) == 'a' | deblank(args(1,:)) == 'ieee-le.l64'
  ieee='a';
 elseif deblank(args(1,:)) == 's' | deblank(args(1,:)) == 'ieee-be.l64'
  ieee='s';
 else
  error(['Optional argument ' args(1,:) ' is unknown'])
 end
 args=args(2:end,:);
end

% Match name of all meta-files
eval(['ls ' fname '*.meta;']);
allfiles=ans;

% Beginning and end of strings
Iend=findstr(allfiles,'.meta')+4;
Ibeg=[1 Iend(1:end-1)+2];

% Loop through allfiles
for j=1:prod(size(Ibeg)),

% Read meta- and data-file
[A,N] = localrdmds(allfiles(Ibeg(j):Iend(j)),ieee);

bdims=N(1,:);
r0=N(2,:);
rN=N(3,:);
ndims=prod(size(bdims));
if     (ndims == 1)
 AA(r0(1):rN(1))=A;
elseif (ndims == 2)
 AA(r0(1):rN(1),r0(2):rN(2))=A;
elseif (ndims == 3)
 AA(r0(1):rN(1),r0(2):rN(2),r0(3):rN(3))=A;
elseif (ndims == 4)
 AA(r0(1):rN(1),r0(2):rN(2),r0(3):rN(3),r0(4):rN(4))=A;
else
 error('Dimension of data set is larger than currently coded. Sorry!')
end

end

%-------------------------------------------------------------------------------

function [A,N] = localrdmds(fname,ieee)

mname=strrep(fname,' ','');
dname=strrep(mname,'.meta','.data');

% Read and interpret Meta file
fid = fopen(mname,'r');
if (fid == -1)
 error(['File' mname ' could not be opened'])
end

% Scan each line of the Meta file
allstr=' ';
keepgoing = 1;
while keepgoing > 0,
 line = fgetl(fid);
 if (line == -1)
  keepgoing=-1;
 else
% Strip out "(PID.TID *.*)" by finding first ")"
%old  ind=findstr([line ')'],')'); line=line(ind(1)+1:end);
  ind=findstr(line,')');
  if size(ind) ~= 0
    line=line(ind(1)+1:end);
  end
% Remove comments of form //
  line=[line ' //']; ind=findstr(line,'//'); line=line(1:ind(1)-1);
% Add to total string
  allstr=[allstr line];
 end
end

% Close meta file
fclose(fid);

% Strip out comments of form /* ... */
ind1=findstr(allstr,'/*'); ind2=findstr(allstr,'*/');
if size(ind1) ~= size(ind2)
 error('The /* ... */ comments are not properly paired')
end
while size(ind1,2) > 0
 allstr=[allstr(1:ind1(1)-1) allstr(ind2(1)+3:end)];
 ind1=findstr(allstr,'/*'); ind2=findstr(allstr,'*/');
end

% This is a kludge to catch whether the meta-file is of the
% old or new type. nrecords does not exist in the old type.
nrecords = -987;

% Everything in lower case
allstr=lower(allstr);

% Fix the unfortunate choice of 'format'
allstr=strrep(allstr,'format','dataprec');

% Evaluate meta information
eval(allstr);

N=reshape( dimlist , 3 , prod(size(dimlist))/3 );

if nrecords == -987
% This is the old 'meta' method that used sequential access

A=allstr;
% Open data file
fid=fopen(dname,'r',ieee);

% Read record size in bytes
recsz=fread(fid,1,'uint32');
ldims=N(3,:)-N(2,:)+1;
numels=prod(ldims);

rat=recsz/numels;
if rat == 4
 A=fread(fid,numels,'real*4');
elseif rat == 8
 A=fread(fid,numels,'real*8');
else
 sprintf(' Implied size in meta-file = %d', numels )
 sprintf(' Record size in data-file = %d', recsz )
 error('Ratio between record size and size in meta-file inconsistent')
end

erecsz=fread(fid,1,'uint32');
if erecsz ~= recsz
 sprintf('WARNING: Record sizes at beginning and end of file are inconsistent')
end

fclose(fid);

A=reshape(A,ldims);

else
% This is the new MDS format that uses direct access

 ldims=N(3,:)-N(2,:)+1;
 if dataprec == 'float32'
  A=myrdda(dname,ldims,1,'real*4',ieee);
 elseif dataprec == 'float64'
  A=myrdda(dname,ldims,1,'real*8',ieee);
 else
  error(['Unrecognized format in meta-file = ' format]);
 end

end

%-------------------------------------------------------------------------------

% result = RDDA( file, dim, irec [options] )
%
% This routine reads the irec'th record of shape 'dim' from the
% direct-access binary file (float or double precision) 'file'.
%
% Required arguments:
%
%   file  - string  - name of file to read from
%   dim   - vector  - dimensions of the file records and the resulting array
%   irec  - integer - record number in file in which to write data
%
% Optional arguments (must appear after the required arguments):
%   prec  - string  - precision of storage in file. Default = 'real*8'.
%   ieee  - string  - IEEE bit-wise representation in file. Default = 'b'.
%
% 'prec' may take the values:
%       'real*4' - floating point, 32 bits.
%       'real*8' - floating point, 64 bits - the efault.
%
% 'ieee' may take values:
%    'ieee-be'     or 'b' - IEEE floating point with big-endian
%                           byte ordering - the default
%    'ieee-le'     or 'l' - IEEE floating point with little-endian
%                           byte ordering
%    'native'      or 'n' - local machine format
%    'cray'        or 'c' - Cray floating point with big-endian
%                           byte ordering
%    'ieee-le.l64' or 'a' - IEEE floating point with little-endian
%                           byte ordering and 64 bit long data type
%    'ieee-be.l64' or 's' - IEEE floating point with big-endian byte
%                           ordering and 64 bit long data type.
%
% eg.   T=rdda('t.data',[64 64 32],1);
%       T=rdda('t.data',[256],4,'real*4');
%       T=rdda('t.data',[128 64],2,'real*4','b');
function [arr] = myrdda(file,N,k,varargin)

% Defaults
WORDLENGTH=8;
rtype='real*8';
ieee='b';

% Check optional arguments
args=char(varargin);
while (size(args,1) > 0)
 if deblank(args(1,:)) == 'real*4'
  WORDLENGTH=4;
  rtype='real*4';
 elseif deblank(args(1,:)) == 'real*8'
  WORDLENGTH=8;
  rtype='real*8';
 elseif deblank(args(1,:)) == 'n' | deblank(args(1,:)) == 'native'
  ieee='n';
 elseif deblank(args(1,:)) == 'l' | deblank(args(1,:)) == 'ieee-le'
  ieee='l';
 elseif deblank(args(1,:)) == 'b' | deblank(args(1,:)) == 'ieee-be'
  ieee='b';
 elseif deblank(args(1,:)) == 'c' | deblank(args(1,:)) == 'cray'
  ieee='c';
 elseif deblank(args(1,:)) == 'a' | deblank(args(1,:)) == 'ieee-le.l64'
  ieee='a';
 elseif deblank(args(1,:)) == 's' | deblank(args(1,:)) == 'ieee-be.l64'
  ieee='s';
 else
  error(['Optional argument ' args(1,:) ' is unknown'])
 end
 args=args(2:end,:);
end

nnn=prod(N);

[fid mess]=fopen(file,'r',ieee);
if fid == -1
 error('Error while opening file:\n%s',mess)
end
st=fseek(fid,nnn*(k-1)*WORDLENGTH,'bof');
if st ~= 0
 mess=ferror(fid);
 error('There was an error while positioning the file pointer:\n%s',mess)
end
[arr count]=fread(fid,nnn,rtype);
if count ~= nnn
 error('Not enough data was available to be read: off EOF?')
end
st=fclose(fid);
arr=reshape(arr,N);
1	adcroft	1.1	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	adcroft	1.2	% $Header: /u/gcmpack/models/MITgcmUV/utils/matlab/rdmeta.m,v 1.1.4.1 2001/04/13 18:28:23 adcroft Exp $
34	adcroft	1.1
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);