| 1 |
jmc |
1.25 |
function [AA,itrs,MM] = rdmds(fnamearg,varargin) |
| 2 |
adcroft |
1.4 |
% RDMDS Read MITgcmUV meta/data files |
| 3 |
adcroft |
1.1 |
% |
| 4 |
adcroft |
1.3 |
% A = RDMDS(FNAME) |
| 5 |
|
|
% A = RDMDS(FNAME,ITER) |
| 6 |
|
|
% A = RDMDS(FNAME,[ITER1 ITER2 ...]) |
| 7 |
adcroft |
1.14 |
% A = RDMDS(FNAME,NaN) |
| 8 |
|
|
% A = RDMDS(FNAME,Inf) |
| 9 |
jmc |
1.18 |
% [A,ITS,M] = RDMDS(FNAME,[...]) |
| 10 |
adcroft |
1.15 |
% A = RDMDS(FNAME,[...],'rec',RECNUM) |
| 11 |
adcroft |
1.1 |
% |
| 12 |
adcroft |
1.4 |
% A = RDMDS(FNAME) reads data described by meta/data file format. |
| 13 |
|
|
% FNAME is a string containing the "head" of the file names. |
| 14 |
jmc |
1.18 |
% |
| 15 |
adcroft |
1.4 |
% eg. To load the meta-data files |
| 16 |
|
|
% T.0000002880.000.000.meta, T.0000002880.000.000.data |
| 17 |
|
|
% T.0000002880.001.000.meta, T.0000002880.001.000.data |
| 18 |
|
|
% T.0000002880.002.000.meta, T.0000002880.002.000.data |
| 19 |
|
|
% T.0000002880.003.000.meta, T.0000002880.003.000.data |
| 20 |
|
|
% use |
| 21 |
|
|
% >> A=rdmds('T.0000002880'); |
| 22 |
|
|
% >> size(A) |
| 23 |
|
|
% ans = |
| 24 |
|
|
% 64 32 5 |
| 25 |
|
|
% eg. To load a multiple record file |
| 26 |
|
|
% >> A=rdmds('pickup.0000002880'); |
| 27 |
|
|
% >> size(A) |
| 28 |
|
|
% ans = |
| 29 |
|
|
% 64 32 5 61 |
| 30 |
jmc |
1.18 |
% |
| 31 |
|
|
% |
| 32 |
adcroft |
1.4 |
% A = RDMDS(FNAME,ITER) reads data described by meta/data file format. |
| 33 |
|
|
% FNAME is a string containing the "head" of the file name excluding the |
| 34 |
|
|
% 10-digit iterartion number. |
| 35 |
|
|
% ITER is a vector of positive integers that will expand to the 10-digit |
| 36 |
|
|
% number in the file name. |
| 37 |
adcroft |
1.14 |
% If ITER=NaN, all iterations will be read. |
| 38 |
|
|
% If ITER=Inf, the last (highest) iteration will be read. |
| 39 |
adcroft |
1.15 |
% |
| 40 |
adcroft |
1.4 |
% eg. To repeat above operation |
| 41 |
|
|
% >> A=rdmds('T',2880); |
| 42 |
|
|
% eg. To read multiple time steps |
| 43 |
|
|
% >> A=rdmds('T',[0 1440 2880]); |
| 44 |
adcroft |
1.14 |
% 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 |
adcroft |
1.4 |
% Note: this form can not read files with no iteration count in file name. |
| 49 |
adcroft |
1.15 |
% |
| 50 |
|
|
% |
| 51 |
|
|
% A = RDMDS(FNAME,[...],'rec',RECNUM) reads individual records from |
| 52 |
|
|
% multiple record files. |
| 53 |
jmc |
1.18 |
% |
| 54 |
adcroft |
1.15 |
% 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 |
jmc |
1.18 |
% |
| 60 |
adcroft |
1.15 |
% A = RDMDS(FNAME,ITER,MACHINEFORMAT) allows the machine format to be |
| 61 |
adcroft |
1.4 |
% A = RDMDS(FNAME,MACHINEFORMAT) |
| 62 |
|
|
% specified which MACHINEFORMAT is on of the following strings: |
| 63 |
|
|
% 'n' 'l' 'b' 'd' 'g' 'c' 'a' 's' - see FOPEN for more details |
| 64 |
adcroft |
1.15 |
% |
| 65 |
jmc |
1.18 |
|
| 66 |
jmc |
1.26 |
% $Header: /u/gcmpack/MITgcm/utils/matlab/rdmds.m,v 1.25 2010/01/07 23:20:33 jmc Exp $ |
| 67 |
jmc |
1.21 |
% $Name: $ |
| 68 |
adcroft |
1.14 |
|
| 69 |
|
|
AA=[]; |
| 70 |
jmc |
1.25 |
itrs=[]; |
| 71 |
jmc |
1.18 |
MM=[]; |
| 72 |
adcroft |
1.1 |
|
| 73 |
|
|
% Default options |
| 74 |
|
|
ieee='b'; |
| 75 |
adcroft |
1.3 |
fname=fnamearg; |
| 76 |
adcroft |
1.15 |
userecords=0; |
| 77 |
|
|
recnum=[]; |
| 78 |
adcroft |
1.1 |
|
| 79 |
|
|
% Check optional arguments |
| 80 |
adcroft |
1.3 |
for ind=1:size(varargin,2); |
| 81 |
|
|
arg=varargin{ind}; |
| 82 |
|
|
if ischar(arg) |
| 83 |
|
|
if strcmp(arg,'n') | strcmp(arg,'native') |
| 84 |
|
|
ieee='n'; |
| 85 |
|
|
elseif strcmp(arg,'l') | strcmp(arg,'ieee-le') |
| 86 |
|
|
ieee='l'; |
| 87 |
|
|
elseif strcmp(arg,'b') | strcmp(arg,'ieee-be') |
| 88 |
|
|
ieee='b'; |
| 89 |
|
|
elseif strcmp(arg,'c') | strcmp(arg,'cray') |
| 90 |
|
|
ieee='c'; |
| 91 |
|
|
elseif strcmp(arg,'a') | strcmp(arg,'ieee-le.l64') |
| 92 |
|
|
ieee='a'; |
| 93 |
|
|
elseif strcmp(arg,'s') | strcmp(arg,'ieee-be.l64') |
| 94 |
|
|
ieee='s'; |
| 95 |
adcroft |
1.15 |
elseif strcmp(arg,'rec') |
| 96 |
|
|
userecords=1; |
| 97 |
adcroft |
1.3 |
else |
| 98 |
|
|
error(['Optional argument ' arg ' is unknown']) |
| 99 |
|
|
end |
| 100 |
adcroft |
1.1 |
else |
| 101 |
adcroft |
1.15 |
if userecords==1 |
| 102 |
|
|
recnum=arg; |
| 103 |
jmc |
1.25 |
elseif isempty(itrs) |
| 104 |
adcroft |
1.9 |
if isnan(arg) |
| 105 |
jmc |
1.25 |
itrs=scanforfiles(fname); |
| 106 |
|
|
disp([ sprintf('Reading %i time levels:',size(itrs,2)) sprintf(' %i',itrs) ]); |
| 107 |
adcroft |
1.10 |
elseif isinf(arg) |
| 108 |
jmc |
1.25 |
itrs=scanforfiles(fname); |
| 109 |
|
|
if isempty(itrs) |
| 110 |
|
|
AA=[];itrs=[];return; |
| 111 |
adcroft |
1.13 |
end |
| 112 |
jmc |
1.25 |
disp([ sprintf('Found %i time levels, reading %i',size(itrs,2),itrs(end)) ]); |
| 113 |
|
|
itrs=itrs(end); |
| 114 |
adcroft |
1.17 |
% elseif prod(double(arg>=0)) & prod(double(round(arg)==arg)) |
| 115 |
jmc |
1.16 |
% elseif prod(arg>=0) & prod(round(arg)==arg) |
| 116 |
|
|
elseif min(arg)>=0 & isempty(find(round(arg)~=arg)) |
| 117 |
adcroft |
1.10 |
if arg>=9999999999 |
| 118 |
|
|
error(sprintf('Argument %i > 9999999999',arg)) |
| 119 |
|
|
end |
| 120 |
jmc |
1.25 |
itrs=arg; |
| 121 |
adcroft |
1.3 |
else |
| 122 |
|
|
error(sprintf('Argument %i must be a positive integer',arg)) |
| 123 |
|
|
end |
| 124 |
adcroft |
1.15 |
else |
| 125 |
|
|
error('Multiple iterations should be specified as a vector') |
| 126 |
|
|
end |
| 127 |
adcroft |
1.1 |
end |
| 128 |
adcroft |
1.3 |
end |
| 129 |
|
|
|
| 130 |
jmc |
1.25 |
if isempty(itrs) |
| 131 |
|
|
itrs=-1; |
| 132 |
adcroft |
1.15 |
end |
| 133 |
|
|
|
| 134 |
adcroft |
1.3 |
% Loop over each iteration |
| 135 |
jmc |
1.25 |
for iter=1:size(itrs,2); |
| 136 |
|
|
if itrs(iter)>=0 |
| 137 |
|
|
fname=sprintf('%s.%10.10i',fnamearg,itrs(iter)); |
| 138 |
|
|
end |
| 139 |
adcroft |
1.1 |
|
| 140 |
adcroft |
1.7 |
% Figure out if there is a path in the filename |
| 141 |
jmc |
1.25 |
NS=findstr('/',fname); |
| 142 |
|
|
if size(NS)>0 |
| 143 |
|
|
Dir=fname(1:NS(end)); |
| 144 |
|
|
else |
| 145 |
|
|
Dir='./'; |
| 146 |
|
|
end |
| 147 |
adcroft |
1.7 |
|
| 148 |
adcroft |
1.1 |
% Match name of all meta-files |
| 149 |
jmc |
1.25 |
allfiles=dir( sprintf('%s*.meta',fname) ); |
| 150 |
adcroft |
1.1 |
|
| 151 |
jmc |
1.25 |
if size(allfiles,1)==0 |
| 152 |
|
|
disp(sprintf('No files match the search: %s*.meta',fname)); |
| 153 |
|
|
%allow partial reads% error('No files found.') |
| 154 |
|
|
end |
| 155 |
adcroft |
1.1 |
|
| 156 |
|
|
% Loop through allfiles |
| 157 |
jmc |
1.25 |
for j=1:size(allfiles,1); |
| 158 |
adcroft |
1.1 |
|
| 159 |
|
|
% Read meta- and data-file |
| 160 |
jmc |
1.25 |
[A,N,M,mG] = localrdmds([Dir allfiles(j).name],ieee,recnum); |
| 161 |
jmc |
1.18 |
|
| 162 |
|
|
%- Merge local Meta file content (M) to MM string: |
| 163 |
jmc |
1.25 |
if j > 0, %- to comment out this block: "if j < 0" (since j is always > 0) |
| 164 |
|
|
ii=findstr(M,' timeStepNumber'); |
| 165 |
|
|
if isempty(ii), ii1=0; ii2=0; |
| 166 |
|
|
else ii1=ii; ii2=ii+min(findstr(M(1+ii:end),'];')); end |
| 167 |
|
|
ii=findstr(M,' timeInterval'); |
| 168 |
|
|
if isempty(ii), jj1=0; jj2=0; |
| 169 |
|
|
else jj1=ii; jj2=ii+min(findstr(M(1+ii:end),'];')); end |
| 170 |
|
|
if iter==1 & j==1, |
| 171 |
jmc |
1.26 |
MM=M; ind1=0; ind2=0; is1=ii1; js1=jj1; M3=''; |
| 172 |
jmc |
1.25 |
if ii1*jj1 > 0, |
| 173 |
|
|
%ind1=min(ii1,jj1); ind2=max(ii2,jj2); |
| 174 |
|
|
%if ii1 < jj1, ii3=ii2+1; jj3=jj1-1; |
| 175 |
|
|
%else ii3=jj2+1; jj3=ii1-1; end |
| 176 |
|
|
order=sort([ii1 ii2 jj1 jj2]); |
| 177 |
|
|
ind1=order(1); ii3=order(2)+1; jj3=order(3)-1; ind2=order(4); |
| 178 |
|
|
M2=M(ii1:ii2); M4=M(jj1:jj2); M3=M(ii3:jj3); |
| 179 |
|
|
elseif ii1 > 0, |
| 180 |
|
|
ind1=ii1; ind2=ii2; |
| 181 |
|
|
M2=M(ii1:ii2); M4=''; |
| 182 |
|
|
elseif jj1 > 0, |
| 183 |
|
|
ind1=jj1; ind2=jj2; |
| 184 |
|
|
M4=M(jj1:jj2); M2=''; |
| 185 |
|
|
end |
| 186 |
|
|
M5=M(1+ind2:end); |
| 187 |
|
|
%fprintf(' ii1,ii2 = %i %i ; jj1,jj2= %i %i ;', ii1,ii2, jj1,jj2); |
| 188 |
|
|
%fprintf(' ii3,jj3= %i %i ; ind1,ind2= %i %i\n',ii3,jj3,ind1,ind2); |
| 189 |
|
|
%fprintf('M(1:ind1)=%s<\n',M(1:ind1)); |
| 190 |
|
|
%fprintf(' M2=%s<\n',M2); |
| 191 |
|
|
%fprintf(' M3=%s<\n',M3); |
| 192 |
|
|
%fprintf(' M4=%s<\n',M4); |
| 193 |
|
|
%fprintf(' M5=%s<\n',M5); |
| 194 |
|
|
else |
| 195 |
|
|
if ii1*jj1 > 0, |
| 196 |
|
|
order=sort([ii1 ii2 jj1 jj2]); |
| 197 |
|
|
ind=order(1); ii3=order(2)+1; jj3=order(3)-1; ind2=order(4); |
| 198 |
|
|
else ind=max(ii1,jj1); ind2=ii2+jj2; end |
| 199 |
|
|
compar=(ind == ind1); ii=0; |
| 200 |
|
|
if compar & ind1 == 0, ii=1; compar=strcmp (MM,M); end |
| 201 |
|
|
if compar & ind1 > 0, ii=2; compar=strncmp(MM,M,ind1) ; end |
| 202 |
|
|
if compar & ind1 > 0, ii=3; compar=strcmp(M5,M(1+ind2:end)); end |
| 203 |
|
|
if compar & ii1*jj1 > 0, ii=4; compar=strcmp(M3,M(ii3:jj3)); end |
| 204 |
|
|
if ~compar, |
| 205 |
|
|
fprintf('WARNING: Meta file (%s) is different (%i) from 1rst one:\n', ... |
| 206 |
|
|
allfiles(j).name,ii); |
| 207 |
|
|
fprintf(' it=%i :MM:%s\n',itrs(1),MM); |
| 208 |
|
|
fprintf(' it=%i :M :%s\n\n',itrs(iter),M); |
| 209 |
|
|
elseif ind1 > 0, |
| 210 |
|
|
if ii1 > 0, |
| 211 |
|
|
Mj=M(ii1:ii2); ii=findstr(Mj,'['); Mj=Mj(1+ii:end); |
| 212 |
jmc |
1.18 |
% add it-number from Mj to M2 (if different): |
| 213 |
jmc |
1.25 |
if isempty(findstr(M2,Mj)), M2=[deblank(M2(1:end-1)),Mj]; end |
| 214 |
|
|
end |
| 215 |
|
|
if jj1 > 0, |
| 216 |
|
|
Mj=M(jj1:jj2); ii=findstr(Mj,'['); Mj=Mj(1+ii:end); |
| 217 |
|
|
% add time interval from Mj to M4 (if different): |
| 218 |
|
|
if isempty(findstr(M4,Mj)), M4=[deblank(M4(1:end-1)),' ;',Mj]; end |
| 219 |
|
|
end |
| 220 |
|
|
end |
| 221 |
|
|
end |
| 222 |
|
|
% save modifications: |
| 223 |
|
|
if ind1>0 & j==size(allfiles,1) & iter==size(itrs,2), |
| 224 |
|
|
if ii1 < jj1, MM=[MM(1:ind1-1),M2,M3,M4,M5]; |
| 225 |
|
|
else MM=[MM(1:ind1-1),M4,M3,M2,M5]; end |
| 226 |
|
|
end |
| 227 |
jmc |
1.18 |
end |
| 228 |
adcroft |
1.1 |
|
| 229 |
jmc |
1.18 |
%- put local data file content in global array AA: |
| 230 |
jmc |
1.25 |
bdims=N(1,:); |
| 231 |
|
|
r0=N(2,:); |
| 232 |
|
|
rN=N(3,:); |
| 233 |
|
|
ndims=prod(size(bdims)); |
| 234 |
|
|
if j==1 & iter==1, AA=zeros([bdims size(itrs,2)]); end |
| 235 |
|
|
if mG(1)==0 & mG(2)==1, |
| 236 |
|
|
if (ndims == 1) |
| 237 |
|
|
AA(r0(1):rN(1),iter)=A; |
| 238 |
|
|
elseif (ndims == 2) |
| 239 |
|
|
AA(r0(1):rN(1),r0(2):rN(2),iter)=A; |
| 240 |
|
|
elseif (ndims == 3) |
| 241 |
|
|
AA(r0(1):rN(1),r0(2):rN(2),r0(3):rN(3),iter)=A; |
| 242 |
|
|
elseif (ndims == 4) |
| 243 |
|
|
AA(r0(1):rN(1),r0(2):rN(2),r0(3):rN(3),r0(4):rN(4),iter)=A; |
| 244 |
|
|
elseif (ndims == 5) |
| 245 |
|
|
AA(r0(1):rN(1),r0(2):rN(2),r0(3):rN(3),r0(4):rN(4),r0(5):rN(5),iter)=A; |
| 246 |
|
|
else |
| 247 |
|
|
error('Dimension of data set is larger than currently coded. Sorry!') |
| 248 |
|
|
end |
| 249 |
|
|
elseif (ndims == 1) |
| 250 |
|
|
AA(r0(1):rN(1),iter)=A; |
| 251 |
jmc |
1.22 |
else |
| 252 |
|
|
%- to debug: do simple stransfert (with a loop on 2nd index); |
| 253 |
|
|
% will need to change this later, to improve efficiency: |
| 254 |
jmc |
1.25 |
for i=0:rN(2)-r0(2), |
| 255 |
|
|
if (ndims == 2) |
| 256 |
|
|
AA(r0(1)+i*mG(1):rN(1)+i*mG(1),r0(2)+i*mG(2),iter)=A(:,1+i); |
| 257 |
|
|
elseif (ndims == 3) |
| 258 |
|
|
AA(r0(1)+i*mG(1):rN(1)+i*mG(1),r0(2)+i*mG(2), ... |
| 259 |
jmc |
1.22 |
r0(3):rN(3),iter)=A(:,1+i,:); |
| 260 |
jmc |
1.25 |
elseif (ndims == 4) |
| 261 |
|
|
AA(r0(1)+i*mG(1):rN(1)+i*mG(1),r0(2)+i*mG(2), ... |
| 262 |
jmc |
1.22 |
r0(3):rN(3),r0(4):rN(4),iter)=A(:,1+i,:,:); |
| 263 |
jmc |
1.25 |
elseif (ndims == 5) |
| 264 |
|
|
AA(r0(1)+i*mG(1):rN(1)+i*mG(1),r0(2)+i*mG(2), ... |
| 265 |
jmc |
1.22 |
r0(3):rN(3),r0(4):rN(4),r0(5):rN(5),iter)=A(:,1+i,:,:,:); |
| 266 |
jmc |
1.25 |
else |
| 267 |
|
|
error('Dimension of data set is larger than currently coded. Sorry!') |
| 268 |
|
|
end |
| 269 |
|
|
end |
| 270 |
jmc |
1.22 |
end |
| 271 |
adcroft |
1.1 |
|
| 272 |
jmc |
1.25 |
end % files |
| 273 |
adcroft |
1.3 |
end % iterations |
| 274 |
adcroft |
1.1 |
|
| 275 |
|
|
%------------------------------------------------------------------------------- |
| 276 |
|
|
|
| 277 |
jmc |
1.22 |
function [A,N,M,map2glob] = localrdmds(fname,ieee,recnum) |
| 278 |
adcroft |
1.1 |
|
| 279 |
|
|
mname=strrep(fname,' ',''); |
| 280 |
|
|
dname=strrep(mname,'.meta','.data'); |
| 281 |
|
|
|
| 282 |
jmc |
1.22 |
%- set default mapping from tile to global file: |
| 283 |
|
|
map2glob=[0 1]; |
| 284 |
|
|
|
| 285 |
adcroft |
1.1 |
% Read and interpret Meta file |
| 286 |
|
|
fid = fopen(mname,'r'); |
| 287 |
|
|
if (fid == -1) |
| 288 |
|
|
error(['File' mname ' could not be opened']) |
| 289 |
|
|
end |
| 290 |
|
|
|
| 291 |
|
|
% Scan each line of the Meta file |
| 292 |
|
|
allstr=' '; |
| 293 |
|
|
keepgoing = 1; |
| 294 |
|
|
while keepgoing > 0, |
| 295 |
|
|
line = fgetl(fid); |
| 296 |
|
|
if (line == -1) |
| 297 |
|
|
keepgoing=-1; |
| 298 |
|
|
else |
| 299 |
|
|
% Strip out "(PID.TID *.*)" by finding first ")" |
| 300 |
|
|
%old ind=findstr([line ')'],')'); line=line(ind(1)+1:end); |
| 301 |
|
|
ind=findstr(line,')'); |
| 302 |
|
|
if size(ind) ~= 0 |
| 303 |
|
|
line=line(ind(1)+1:end); |
| 304 |
|
|
end |
| 305 |
|
|
% Remove comments of form // |
| 306 |
jmc |
1.20 |
line=[line,' //']; ind=findstr(line,'//'); line=line(1:ind(1)-1); |
| 307 |
|
|
% Add to total string (without starting & ending blanks) |
| 308 |
|
|
while line(1:1) == ' ', line=line(2:end); end |
| 309 |
jmc |
1.22 |
if strncmp(line,'map2glob',8), eval(line); |
| 310 |
|
|
else allstr=[allstr,deblank(line),' ']; |
| 311 |
|
|
end |
| 312 |
adcroft |
1.1 |
end |
| 313 |
|
|
end |
| 314 |
|
|
|
| 315 |
|
|
% Close meta file |
| 316 |
|
|
fclose(fid); |
| 317 |
|
|
|
| 318 |
|
|
% Strip out comments of form /* ... */ |
| 319 |
|
|
ind1=findstr(allstr,'/*'); ind2=findstr(allstr,'*/'); |
| 320 |
|
|
if size(ind1) ~= size(ind2) |
| 321 |
|
|
error('The /* ... */ comments are not properly paired') |
| 322 |
|
|
end |
| 323 |
|
|
while size(ind1,2) > 0 |
| 324 |
jmc |
1.20 |
allstr=[deblank(allstr(1:ind1(1)-1)) allstr(ind2(1)+2:end)]; |
| 325 |
|
|
%allstr=[allstr(1:ind1(1)-1) allstr(ind2(1)+3:end)]; |
| 326 |
adcroft |
1.1 |
ind1=findstr(allstr,'/*'); ind2=findstr(allstr,'*/'); |
| 327 |
|
|
end |
| 328 |
|
|
|
| 329 |
|
|
% This is a kludge to catch whether the meta-file is of the |
| 330 |
|
|
% old or new type. nrecords does not exist in the old type. |
| 331 |
adcroft |
1.14 |
nrecords = NaN; |
| 332 |
adcroft |
1.1 |
|
| 333 |
jmc |
1.18 |
%- store the full string for output: |
| 334 |
|
|
M=strrep(allstr,'format','dataprec'); |
| 335 |
|
|
|
| 336 |
adcroft |
1.1 |
% Everything in lower case |
| 337 |
|
|
allstr=lower(allstr); |
| 338 |
|
|
|
| 339 |
|
|
% Fix the unfortunate choice of 'format' |
| 340 |
|
|
allstr=strrep(allstr,'format','dataprec'); |
| 341 |
|
|
|
| 342 |
|
|
% Evaluate meta information |
| 343 |
|
|
eval(allstr); |
| 344 |
|
|
|
| 345 |
|
|
N=reshape( dimlist , 3 , prod(size(dimlist))/3 ); |
| 346 |
jmc |
1.18 |
rep=[' dimList = [ ',sprintf('%i ',N(1,:)),']']; |
| 347 |
adcroft |
1.15 |
if ~isnan(nrecords) & nrecords > 1 & isempty(recnum) |
| 348 |
adcroft |
1.4 |
N=[N,[nrecords 1 nrecords]']; |
| 349 |
adcroft |
1.15 |
elseif ~isempty(recnum) & recnum>nrecords |
| 350 |
|
|
error('Requested record number is higher than the number of available records') |
| 351 |
|
|
end |
| 352 |
|
|
|
| 353 |
jmc |
1.18 |
%- make "dimList" shorter (& fit output array size) in output "M": |
| 354 |
|
|
pat=' dimList = \[(\s*\d+\,?)*\s*\]'; |
| 355 |
|
|
M=regexprep(M,pat,rep); |
| 356 |
|
|
% and remove double space within sq.brakets: |
| 357 |
|
|
ind1=findstr(M,'['); ind2=findstr(M,']'); |
| 358 |
|
|
if length(ind1) == length(ind2), |
| 359 |
|
|
for i=length(ind1):-1:1, if ind1(i) < ind2(i), |
| 360 |
|
|
M=[M(1:ind1(i)),regexprep(M(ind1(i)+1:ind2(i)-1),'(\s+)',' '),M(ind2(i):end)]; |
| 361 |
|
|
end; end |
| 362 |
|
|
else error('The [ ... ] brakets are not properly paired') |
| 363 |
|
|
end |
| 364 |
|
|
|
| 365 |
adcroft |
1.15 |
if isempty(recnum) |
| 366 |
|
|
recnum=1; |
| 367 |
adcroft |
1.4 |
end |
| 368 |
adcroft |
1.1 |
|
| 369 |
adcroft |
1.14 |
if isnan(nrecords) |
| 370 |
adcroft |
1.1 |
% This is the old 'meta' method that used sequential access |
| 371 |
|
|
|
| 372 |
|
|
A=allstr; |
| 373 |
|
|
% Open data file |
| 374 |
|
|
fid=fopen(dname,'r',ieee); |
| 375 |
|
|
|
| 376 |
|
|
% Read record size in bytes |
| 377 |
|
|
recsz=fread(fid,1,'uint32'); |
| 378 |
|
|
ldims=N(3,:)-N(2,:)+1; |
| 379 |
|
|
numels=prod(ldims); |
| 380 |
|
|
|
| 381 |
|
|
rat=recsz/numels; |
| 382 |
|
|
if rat == 4 |
| 383 |
|
|
A=fread(fid,numels,'real*4'); |
| 384 |
|
|
elseif rat == 8 |
| 385 |
|
|
A=fread(fid,numels,'real*8'); |
| 386 |
|
|
else |
| 387 |
|
|
sprintf(' Implied size in meta-file = %d', numels ) |
| 388 |
|
|
sprintf(' Record size in data-file = %d', recsz ) |
| 389 |
|
|
error('Ratio between record size and size in meta-file inconsistent') |
| 390 |
|
|
end |
| 391 |
|
|
|
| 392 |
|
|
erecsz=fread(fid,1,'uint32'); |
| 393 |
|
|
if erecsz ~= recsz |
| 394 |
|
|
sprintf('WARNING: Record sizes at beginning and end of file are inconsistent') |
| 395 |
|
|
end |
| 396 |
|
|
|
| 397 |
|
|
fclose(fid); |
| 398 |
|
|
|
| 399 |
|
|
A=reshape(A,ldims); |
| 400 |
|
|
|
| 401 |
|
|
else |
| 402 |
|
|
% This is the new MDS format that uses direct access |
| 403 |
|
|
|
| 404 |
|
|
ldims=N(3,:)-N(2,:)+1; |
| 405 |
adcroft |
1.15 |
for r=1:size(recnum(:),1); |
| 406 |
adcroft |
1.1 |
if dataprec == 'float32' |
| 407 |
adcroft |
1.15 |
A(:,r)=myrdda(dname,ldims,recnum(r),'real*4',ieee); |
| 408 |
adcroft |
1.1 |
elseif dataprec == 'float64' |
| 409 |
adcroft |
1.15 |
A(:,r)=myrdda(dname,ldims,recnum(r),'real*8',ieee); |
| 410 |
adcroft |
1.1 |
else |
| 411 |
|
|
error(['Unrecognized format in meta-file = ' format]); |
| 412 |
|
|
end |
| 413 |
adcroft |
1.15 |
end |
| 414 |
|
|
|
| 415 |
|
|
A=reshape(A,[ldims size(recnum(:),1)]); |
| 416 |
|
|
if size(recnum(:),1)>1 |
| 417 |
|
|
N(1,end+1)=size(recnum(:),1); |
| 418 |
|
|
N(2,end)=1; |
| 419 |
|
|
N(3,end)=size(recnum(:),1); |
| 420 |
|
|
end |
| 421 |
adcroft |
1.1 |
|
| 422 |
|
|
end |
| 423 |
|
|
|
| 424 |
|
|
%------------------------------------------------------------------------------- |
| 425 |
|
|
|
| 426 |
|
|
% result = RDDA( file, dim, irec [options] ) |
| 427 |
|
|
% |
| 428 |
|
|
% This routine reads the irec'th record of shape 'dim' from the |
| 429 |
|
|
% direct-access binary file (float or double precision) 'file'. |
| 430 |
|
|
% |
| 431 |
|
|
% Required arguments: |
| 432 |
|
|
% |
| 433 |
|
|
% file - string - name of file to read from |
| 434 |
|
|
% dim - vector - dimensions of the file records and the resulting array |
| 435 |
|
|
% irec - integer - record number in file in which to write data |
| 436 |
|
|
% |
| 437 |
|
|
% Optional arguments (must appear after the required arguments): |
| 438 |
|
|
% prec - string - precision of storage in file. Default = 'real*8'. |
| 439 |
|
|
% ieee - string - IEEE bit-wise representation in file. Default = 'b'. |
| 440 |
|
|
% |
| 441 |
|
|
% 'prec' may take the values: |
| 442 |
|
|
% 'real*4' - floating point, 32 bits. |
| 443 |
|
|
% 'real*8' - floating point, 64 bits - the efault. |
| 444 |
|
|
% |
| 445 |
|
|
% 'ieee' may take values: |
| 446 |
|
|
% 'ieee-be' or 'b' - IEEE floating point with big-endian |
| 447 |
|
|
% byte ordering - the default |
| 448 |
|
|
% 'ieee-le' or 'l' - IEEE floating point with little-endian |
| 449 |
|
|
% byte ordering |
| 450 |
|
|
% 'native' or 'n' - local machine format |
| 451 |
|
|
% 'cray' or 'c' - Cray floating point with big-endian |
| 452 |
|
|
% byte ordering |
| 453 |
|
|
% 'ieee-le.l64' or 'a' - IEEE floating point with little-endian |
| 454 |
|
|
% byte ordering and 64 bit long data type |
| 455 |
|
|
% 'ieee-be.l64' or 's' - IEEE floating point with big-endian byte |
| 456 |
|
|
% ordering and 64 bit long data type. |
| 457 |
|
|
% |
| 458 |
|
|
% eg. T=rdda('t.data',[64 64 32],1); |
| 459 |
|
|
% T=rdda('t.data',[256],4,'real*4'); |
| 460 |
|
|
% T=rdda('t.data',[128 64],2,'real*4','b'); |
| 461 |
|
|
function [arr] = myrdda(file,N,k,varargin) |
| 462 |
|
|
|
| 463 |
|
|
% Defaults |
| 464 |
|
|
WORDLENGTH=8; |
| 465 |
|
|
rtype='real*8'; |
| 466 |
|
|
ieee='b'; |
| 467 |
|
|
|
| 468 |
|
|
% Check optional arguments |
| 469 |
|
|
args=char(varargin); |
| 470 |
|
|
while (size(args,1) > 0) |
| 471 |
|
|
if deblank(args(1,:)) == 'real*4' |
| 472 |
|
|
WORDLENGTH=4; |
| 473 |
|
|
rtype='real*4'; |
| 474 |
|
|
elseif deblank(args(1,:)) == 'real*8' |
| 475 |
|
|
WORDLENGTH=8; |
| 476 |
|
|
rtype='real*8'; |
| 477 |
|
|
elseif deblank(args(1,:)) == 'n' | deblank(args(1,:)) == 'native' |
| 478 |
|
|
ieee='n'; |
| 479 |
|
|
elseif deblank(args(1,:)) == 'l' | deblank(args(1,:)) == 'ieee-le' |
| 480 |
|
|
ieee='l'; |
| 481 |
|
|
elseif deblank(args(1,:)) == 'b' | deblank(args(1,:)) == 'ieee-be' |
| 482 |
|
|
ieee='b'; |
| 483 |
|
|
elseif deblank(args(1,:)) == 'c' | deblank(args(1,:)) == 'cray' |
| 484 |
|
|
ieee='c'; |
| 485 |
|
|
elseif deblank(args(1,:)) == 'a' | deblank(args(1,:)) == 'ieee-le.l64' |
| 486 |
|
|
ieee='a'; |
| 487 |
|
|
elseif deblank(args(1,:)) == 's' | deblank(args(1,:)) == 'ieee-be.l64' |
| 488 |
|
|
ieee='s'; |
| 489 |
|
|
else |
| 490 |
|
|
error(['Optional argument ' args(1,:) ' is unknown']) |
| 491 |
|
|
end |
| 492 |
|
|
args=args(2:end,:); |
| 493 |
|
|
end |
| 494 |
|
|
|
| 495 |
|
|
nnn=prod(N); |
| 496 |
|
|
|
| 497 |
|
|
[fid mess]=fopen(file,'r',ieee); |
| 498 |
|
|
if fid == -1 |
| 499 |
|
|
error('Error while opening file:\n%s',mess) |
| 500 |
|
|
end |
| 501 |
|
|
st=fseek(fid,nnn*(k-1)*WORDLENGTH,'bof'); |
| 502 |
|
|
if st ~= 0 |
| 503 |
|
|
mess=ferror(fid); |
| 504 |
|
|
error('There was an error while positioning the file pointer:\n%s',mess) |
| 505 |
|
|
end |
| 506 |
|
|
[arr count]=fread(fid,nnn,rtype); |
| 507 |
|
|
if count ~= nnn |
| 508 |
|
|
error('Not enough data was available to be read: off EOF?') |
| 509 |
|
|
end |
| 510 |
|
|
st=fclose(fid); |
| 511 |
adcroft |
1.15 |
%arr=reshape(arr,N); |
| 512 |
adcroft |
1.9 |
|
| 513 |
|
|
% |
| 514 |
jmc |
1.25 |
function [itrs] = scanforfiles(fname) |
| 515 |
adcroft |
1.9 |
|
| 516 |
jmc |
1.25 |
itrs=[]; |
| 517 |
adcroft |
1.12 |
allfiles=dir([fname '.*.001.001.meta']); |
| 518 |
adcroft |
1.10 |
if isempty(allfiles) |
| 519 |
adcroft |
1.12 |
allfiles=dir([fname '.*.meta']); |
| 520 |
adcroft |
1.11 |
ioff=0; |
| 521 |
|
|
else |
| 522 |
adcroft |
1.10 |
ioff=8; |
| 523 |
|
|
end |
| 524 |
adcroft |
1.9 |
for k=1:size(allfiles,1); |
| 525 |
|
|
hh=allfiles(k).name; |
| 526 |
jmc |
1.25 |
itrs(k)=str2num( hh(end-14-ioff:end-5-ioff) ); |
| 527 |
adcroft |
1.9 |
end |
| 528 |
jmc |
1.25 |
itrs=sort(itrs); |
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