/[MITgcm]/MITgcm/utils/matlab/rdmds.m
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revision 1.8.4.1 by heimbach, Wed Feb 6 15:48:10 2002 UTC revision 1.8.4.2 by heimbach, Fri Mar 7 05:24:37 2003 UTC
# Line 1  Line 1 
1  function [AA] = rdmds(fnamearg,varargin)  function [AA,iters] = rdmds(fnamearg,varargin)
2  % RDMDS  Read MITgcmUV meta/data files  % RDMDS  Read MITgcmUV meta/data files
3  %  %
4  % A = RDMDS(FNAME)  % A = RDMDS(FNAME)
5  % A = RDMDS(FNAME,ITER)  % A = RDMDS(FNAME,ITER)
6  % A = RDMDS(FNAME,[ITER1 ITER2 ...])  % 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.  %   A = RDMDS(FNAME) reads data described by meta/data file format.
13  %   FNAME is a string containing the "head" of the file names.  %   FNAME is a string containing the "head" of the file names.
# Line 30  function [AA] = rdmds(fnamearg,varargin) Line 34  function [AA] = rdmds(fnamearg,varargin)
34  %   10-digit iterartion number.  %   10-digit iterartion number.
35  %   ITER is a vector of positive integers that will expand to the 10-digit  %   ITER is a vector of positive integers that will expand to the 10-digit
36  %   number in the file name.  %   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  %   eg. To repeat above operation
41  %      >> A=rdmds('T',2880);  %      >> A=rdmds('T',2880);
42  %   eg. To read multiple time steps  %   eg. To read multiple time steps
43  %      >> A=rdmds('T',[0 1440 2880]);  %      >> 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.  %   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  %    %  
 %   A = RDMDS(FNAME,MACHINEFORMAT)  
60  %   A = RDMDS(FNAME,ITER,MACHINEFORMAT) allows the machine format to be  %   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:  %   specified which MACHINEFORMAT is on of the following strings:
63  %     'n' 'l' 'b' 'd' 'g' 'c' 'a' 's'  - see FOPEN for more details  %     'n' 'l' 'b' 'd' 'g' 'c' 'a' 's'  - see FOPEN for more details
64  %    %
65  %    %  
66  % $Header$  % $Header$
67    
68    AA=[];
69    iters=[];
70    
71  % Default options  % Default options
72  ieee='b';  ieee='b';
73  fname=fnamearg;  fname=fnamearg;
74  iters=-1;  userecords=0;
75    recnum=[];
76    
77  % Check optional arguments  % Check optional arguments
78  for ind=1:size(varargin,2);  for ind=1:size(varargin,2);
# Line 66  for ind=1:size(varargin,2); Line 90  for ind=1:size(varargin,2);
90     ieee='a';     ieee='a';
91    elseif strcmp(arg,'s') | strcmp(arg,'ieee-be.l64')    elseif strcmp(arg,'s') | strcmp(arg,'ieee-be.l64')
92     ieee='s';     ieee='s';
93      elseif strcmp(arg,'rec')
94       userecords=1;
95    else    else
96     error(['Optional argument ' arg ' is unknown'])     error(['Optional argument ' arg ' is unknown'])
97    end    end
98   else   else
99      if userecords==1
100       recnum=arg;
101      elseif isempty(iters)
102    if isnan(arg)    if isnan(arg)
103     iters=scanforfiles(fname);     iters=scanforfiles(fname);
104     disp([ sprintf('Reading %i time levels:',size(iters,2)) sprintf(' %i',iters) ]);     disp([ sprintf('Reading %i time levels:',size(iters,2)) sprintf(' %i',iters) ]);
105    elseif isinf(arg)    elseif isinf(arg)
106     iters=scanforfiles(fname);     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)) ]);     disp([ sprintf('Found %i time levels, reading %i',size(iters,2),iters(end)) ]);
111     iters=iters(end);     iters=iters(end);
112    elseif prod(arg>=0) & prod(round(arg)==arg)    elseif prod(arg>=0) & prod(round(arg)==arg)
# Line 85  for ind=1:size(varargin,2); Line 117  for ind=1:size(varargin,2);
117    else    else
118     error(sprintf('Argument %i must be a positive integer',arg))     error(sprintf('Argument %i must be a positive integer',arg))
119    end    end
120      else
121       error('Multiple iterations should be specified as a vector')
122      end
123   end   end
124  end  end
125    
126    if isempty(iters)
127     iters=-1;
128    end
129    
130  % Loop over each iteration  % Loop over each iteration
131  for iter=1:size(iters,2);  for iter=1:size(iters,2);
132  if iters(iter)>=0  if iters(iter)>=0
# Line 106  end Line 145  end
145  allfiles=dir( sprintf('%s*.meta',fname) );  allfiles=dir( sprintf('%s*.meta',fname) );
146    
147  if size(allfiles,1)==0  if size(allfiles,1)==0
148   disp(sprintf('No files match the search: %s.*.meta',fname));   disp(sprintf('No files match the search: %s*.meta',fname));
149  %allow partial reads%  error('No files found.')  %allow partial reads%  error('No files found.')
150  end  end
151    
# Line 114  end Line 153  end
153  for j=1:size(allfiles,1);  for j=1:size(allfiles,1);
154    
155  % Read meta- and data-file  % Read meta- and data-file
156  [A,N] = localrdmds([Dir allfiles(j).name],ieee);  [A,N] = localrdmds([Dir allfiles(j).name],ieee,recnum);
157    
158  bdims=N(1,:);  bdims=N(1,:);
159  r0=N(2,:);  r0=N(2,:);
# Line 139  end % iterations Line 178  end % iterations
178    
179  %-------------------------------------------------------------------------------  %-------------------------------------------------------------------------------
180    
181  function [A,N] = localrdmds(fname,ieee)  function [A,N] = localrdmds(fname,ieee,recnum)
182    
183  mname=strrep(fname,' ','');  mname=strrep(fname,' ','');
184  dname=strrep(mname,'.meta','.data');  dname=strrep(mname,'.meta','.data');
# Line 186  end Line 225  end
225    
226  % This is a kludge to catch whether the meta-file is of the  % 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.  % old or new type. nrecords does not exist in the old type.
228  nrecords = -987;  nrecords = NaN;
229    
230  % Everything in lower case  % Everything in lower case
231  allstr=lower(allstr);  allstr=lower(allstr);
# Line 198  allstr=strrep(allstr,'format','dataprec' Line 237  allstr=strrep(allstr,'format','dataprec'
237  eval(allstr);  eval(allstr);
238    
239  N=reshape( dimlist , 3 , prod(size(dimlist))/3 );  N=reshape( dimlist , 3 , prod(size(dimlist))/3 );
240  if nrecords ~= -987 & nrecords > 1  if ~isnan(nrecords) & nrecords > 1 & isempty(recnum)
241   N=[N,[nrecords 1 nrecords]'];   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  end
245    
246  if nrecords == -987  if isempty(recnum)
247     recnum=1;
248    end
249    
250    if isnan(nrecords)
251  % This is the old 'meta' method that used sequential access  % This is the old 'meta' method that used sequential access
252    
253  A=allstr;  A=allstr;
# Line 238  else Line 283  else
283  % This is the new MDS format that uses direct access  % This is the new MDS format that uses direct access
284    
285   ldims=N(3,:)-N(2,:)+1;   ldims=N(3,:)-N(2,:)+1;
286     for r=1:size(recnum(:),1);
287   if dataprec == 'float32'   if dataprec == 'float32'
288    A=myrdda(dname,ldims,1,'real*4',ieee);    A(:,r)=myrdda(dname,ldims,recnum(r),'real*4',ieee);
289   elseif dataprec == 'float64'   elseif dataprec == 'float64'
290    A=myrdda(dname,ldims,1,'real*8',ieee);    A(:,r)=myrdda(dname,ldims,recnum(r),'real*8',ieee);
291   else   else
292    error(['Unrecognized format in meta-file = ' format]);    error(['Unrecognized format in meta-file = ' format]);
293   end   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  end
304    
# Line 335  if count ~= nnn Line 389  if count ~= nnn
389   error('Not enough data was available to be read: off EOF?')   error('Not enough data was available to be read: off EOF?')
390  end  end
391  st=fclose(fid);  st=fclose(fid);
392  arr=reshape(arr,N);  %arr=reshape(arr,N);
393    
394  %  %
395  function [iters] = scanforfiles(fname)  function [iters] = scanforfiles(fname)
396    
397    iters=[];
398  allfiles=dir([fname '.*.001.001.meta']);  allfiles=dir([fname '.*.001.001.meta']);
399  if isempty(allfiles)  if isempty(allfiles)
400   allfiles=dir([fname '.*.meta']);   allfiles=dir([fname '.*.meta']);
# Line 351  for k=1:size(allfiles,1); Line 406  for k=1:size(allfiles,1);
406   hh=allfiles(k).name;   hh=allfiles(k).name;
407   iters(k)=str2num( hh(end-14-ioff:end-5-ioff) );   iters(k)=str2num( hh(end-14-ioff:end-5-ioff) );
408  end  end
409    iters=sort(iters);
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