| 1 |
mmazloff |
1.1 |
function [AA,iters] = rdmds(fnamearg,varargin) |
| 2 |
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% RDMDS Read MITgcmUV meta/data files |
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% |
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% A = RDMDS(FNAME) |
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% A = RDMDS(FNAME,ITER) |
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% A = RDMDS(FNAME,[ITER1 ITER2 ...]) |
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% A = RDMDS(FNAME,NaN) |
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% A = RDMDS(FNAME,Inf) |
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% [A,ITS] = RDMDS(FNAME,[...]) |
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% A = RDMDS(FNAME,[...],'rec',RECNUM) |
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% |
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% A = RDMDS(FNAME) reads data described by meta/data file format. |
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% FNAME is a string containing the "head" of the file names. |
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% |
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% eg. To load the meta-data files |
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% T.0000002880.000.000.meta, T.0000002880.000.000.data |
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% T.0000002880.001.000.meta, T.0000002880.001.000.data |
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% T.0000002880.002.000.meta, T.0000002880.002.000.data |
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% T.0000002880.003.000.meta, T.0000002880.003.000.data |
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% use |
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% >> A=rdmds('T.0000002880'); |
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% >> size(A) |
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% ans = |
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% 64 32 5 |
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% eg. To load a multiple record file |
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% >> A=rdmds('pickup.0000002880'); |
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% >> size(A) |
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% ans = |
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% 64 32 5 61 |
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% |
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% |
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% A = RDMDS(FNAME,ITER) reads data described by meta/data file format. |
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% FNAME is a string containing the "head" of the file name excluding the |
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% 10-digit iterartion number. |
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% ITER is a vector of positive integers that will expand to the 10-digit |
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% number in the file name. |
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% If ITER=NaN, all iterations will be read. |
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% If ITER=Inf, the last (highest) iteration will be read. |
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% |
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% eg. To repeat above operation |
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% >> A=rdmds('T',2880); |
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% eg. To read multiple time steps |
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% >> A=rdmds('T',[0 1440 2880]); |
| 44 |
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% eg. To read all time steps |
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% >> [A,ITS]=rdmds('T',NaN); |
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% eg. To read the last time step |
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% >> [A,IT]=rdmds('T',Inf); |
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% Note: this form can not read files with no iteration count in file name. |
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% |
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% |
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% A = RDMDS(FNAME,[...],'rec',RECNUM) reads individual records from |
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% multiple record files. |
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% |
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% eg. To read a single record from a multi-record file |
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% >> [A,IT]=rdmds('pickup.ckptA',11); |
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% eg. To read several records from a multi-record file |
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% >> [A,IT]=rdmds('pickup',Inf,'rec',[1:5 8 12]); |
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% |
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% |
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% A = RDMDS(FNAME,ITER,MACHINEFORMAT) allows the machine format to be |
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% A = RDMDS(FNAME,MACHINEFORMAT) |
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% specified which MACHINEFORMAT is on of the following strings: |
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% 'n' 'l' 'b' 'd' 'g' 'c' 'a' 's' - see FOPEN for more details |
| 64 |
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% |
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% |
| 66 |
mmazloff |
1.2 |
% $Header: /u/gcmpack/MITgcm_contrib/SOSE/BoxAdj/input/rdmds.m,v 1.1 2011/01/18 19:34:25 mmazloff Exp $ |
| 67 |
mmazloff |
1.1 |
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| 68 |
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AA=[]; |
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iters=[]; |
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| 71 |
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% Default options |
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ieee='b'; |
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fname=fnamearg; |
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userecords=0; |
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recnum=[]; |
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% Check optional arguments |
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for ind=1:size(varargin,2); |
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arg=varargin{ind}; |
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if ischar(arg) |
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if strcmp(arg,'n') | strcmp(arg,'native') |
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ieee='n'; |
| 83 |
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elseif strcmp(arg,'l') | strcmp(arg,'ieee-le') |
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ieee='l'; |
| 85 |
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elseif strcmp(arg,'b') | strcmp(arg,'ieee-be') |
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ieee='b'; |
| 87 |
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elseif strcmp(arg,'c') | strcmp(arg,'cray') |
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ieee='c'; |
| 89 |
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elseif strcmp(arg,'a') | strcmp(arg,'ieee-le.l64') |
| 90 |
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ieee='a'; |
| 91 |
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elseif strcmp(arg,'s') | strcmp(arg,'ieee-be.l64') |
| 92 |
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ieee='s'; |
| 93 |
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elseif strcmp(arg,'rec') |
| 94 |
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userecords=1; |
| 95 |
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else |
| 96 |
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error(['Optional argument ' arg ' is unknown']) |
| 97 |
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end |
| 98 |
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else |
| 99 |
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if userecords==1 |
| 100 |
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recnum=arg; |
| 101 |
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elseif isempty(iters) |
| 102 |
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if isnan(arg) |
| 103 |
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iters=scanforfiles(fname); |
| 104 |
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disp([ sprintf('Reading %i time levels:',size(iters,2)) sprintf(' %i',iters) ]); |
| 105 |
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elseif isinf(arg) |
| 106 |
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iters=scanforfiles(fname); |
| 107 |
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if isempty(iters) |
| 108 |
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AA=[];iters=[];return; |
| 109 |
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end |
| 110 |
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disp([ sprintf('Found %i time levels, reading %i',size(iters,2),iters(end)) ]); |
| 111 |
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iters=iters(end); |
| 112 |
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% elseif prod(arg>=0) & prod(round(arg)==arg) |
| 113 |
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elseif min(arg)>=0 & isempty(find(round(arg)~=arg)) |
| 114 |
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if arg>=9999999999 |
| 115 |
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error(sprintf('Argument %i > 9999999999',arg)) |
| 116 |
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end |
| 117 |
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iters=arg; |
| 118 |
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else |
| 119 |
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error(sprintf('Argument %i must be a positive integer',arg)) |
| 120 |
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end |
| 121 |
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else |
| 122 |
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error('Multiple iterations should be specified as a vector') |
| 123 |
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end |
| 124 |
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end |
| 125 |
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end |
| 126 |
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| 127 |
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if isempty(iters) |
| 128 |
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iters=-1; |
| 129 |
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end |
| 130 |
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| 131 |
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% Loop over each iteration |
| 132 |
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for iter=1:size(iters,2); |
| 133 |
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if iters(iter)>=0 |
| 134 |
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fname=sprintf('%s.%10.10i',fnamearg,iters(iter)); |
| 135 |
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end |
| 136 |
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| 137 |
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% Figure out if there is a path in the filename |
| 138 |
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NS=findstr('/',fname); |
| 139 |
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if size(NS)>0 |
| 140 |
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Dir=fname(1:NS(end)); |
| 141 |
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else |
| 142 |
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Dir='./'; |
| 143 |
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end |
| 144 |
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| 145 |
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% Match name of all meta-files |
| 146 |
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allfiles=dir( sprintf('%s*.meta',fname) ); |
| 147 |
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| 148 |
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if size(allfiles,1)==0 |
| 149 |
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disp(sprintf('No files match the search: %s*.meta',fname)); |
| 150 |
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%allow partial reads% error('No files found.') |
| 151 |
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end |
| 152 |
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| 153 |
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% Loop through allfiles |
| 154 |
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for j=1:size(allfiles,1); |
| 155 |
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| 156 |
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% Read meta- and data-file |
| 157 |
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[A,N] = localrdmds([Dir allfiles(j).name],ieee,recnum); |
| 158 |
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| 159 |
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bdims=N(1,:); |
| 160 |
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r0=N(2,:); |
| 161 |
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rN=N(3,:); |
| 162 |
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ndims=prod(size(bdims)); |
| 163 |
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if (ndims == 1) |
| 164 |
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AA(r0(1):rN(1),iter)=A; |
| 165 |
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elseif (ndims == 2) |
| 166 |
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AA(r0(1):rN(1),r0(2):rN(2),iter)=A; |
| 167 |
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elseif (ndims == 3) |
| 168 |
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AA(r0(1):rN(1),r0(2):rN(2),r0(3):rN(3),iter)=A; |
| 169 |
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elseif (ndims == 4) |
| 170 |
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AA(r0(1):rN(1),r0(2):rN(2),r0(3):rN(3),r0(4):rN(4),iter)=A; |
| 171 |
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elseif (ndims == 5) |
| 172 |
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AA(r0(1):rN(1),r0(2):rN(2),r0(3):rN(3),r0(4):rN(4),r0(5):rN(5),iter)=A; |
| 173 |
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else |
| 174 |
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error('Dimension of data set is larger than currently coded. Sorry!') |
| 175 |
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end |
| 176 |
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| 177 |
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end % files |
| 178 |
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end % iterations |
| 179 |
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| 180 |
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%------------------------------------------------------------------------------- |
| 181 |
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| 182 |
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function [A,N] = localrdmds(fname,ieee,recnum) |
| 183 |
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| 184 |
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mname=strrep(fname,' ',''); |
| 185 |
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dname=strrep(mname,'.meta','.data'); |
| 186 |
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| 187 |
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% Read and interpret Meta file |
| 188 |
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fid = fopen(mname,'r'); |
| 189 |
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if (fid == -1) |
| 190 |
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error(['File' mname ' could not be opened']) |
| 191 |
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end |
| 192 |
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| 193 |
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% Scan each line of the Meta file |
| 194 |
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allstr=' '; |
| 195 |
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keepgoing = 1; |
| 196 |
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while keepgoing > 0, |
| 197 |
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line = fgetl(fid); |
| 198 |
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if (line == -1) |
| 199 |
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keepgoing=-1; |
| 200 |
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else |
| 201 |
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% Strip out "(PID.TID *.*)" by finding first ")" |
| 202 |
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%old ind=findstr([line ')'],')'); line=line(ind(1)+1:end); |
| 203 |
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ind=findstr(line,')'); |
| 204 |
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if size(ind) ~= 0 |
| 205 |
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line=line(ind(1)+1:end); |
| 206 |
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end |
| 207 |
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% Remove comments of form // |
| 208 |
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line=[line ' //']; ind=findstr(line,'//'); line=line(1:ind(1)-1); |
| 209 |
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% Add to total string |
| 210 |
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allstr=[allstr line]; |
| 211 |
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end |
| 212 |
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end |
| 213 |
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| 214 |
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% Close meta file |
| 215 |
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fclose(fid); |
| 216 |
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| 217 |
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% Strip out comments of form /* ... */ |
| 218 |
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ind1=findstr(allstr,'/*'); ind2=findstr(allstr,'*/'); |
| 219 |
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if size(ind1) ~= size(ind2) |
| 220 |
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error('The /* ... */ comments are not properly paired') |
| 221 |
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end |
| 222 |
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while size(ind1,2) > 0 |
| 223 |
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allstr=[allstr(1:ind1(1)-1) allstr(ind2(1)+3:end)]; |
| 224 |
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ind1=findstr(allstr,'/*'); ind2=findstr(allstr,'*/'); |
| 225 |
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end |
| 226 |
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| 227 |
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% This is a kludge to catch whether the meta-file is of the |
| 228 |
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% old or new type. nrecords does not exist in the old type. |
| 229 |
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nrecords = NaN; |
| 230 |
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| 231 |
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% Everything in lower case |
| 232 |
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allstr=lower(allstr); |
| 233 |
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| 234 |
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% Fix the unfortunate choice of 'format' |
| 235 |
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allstr=strrep(allstr,'format','dataprec'); |
| 236 |
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| 237 |
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% Evaluate meta information |
| 238 |
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eval(allstr); |
| 239 |
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| 240 |
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N=reshape( dimlist , 3 , prod(size(dimlist))/3 ); |
| 241 |
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if ~isnan(nrecords) & nrecords > 1 & isempty(recnum) |
| 242 |
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N=[N,[nrecords 1 nrecords]']; |
| 243 |
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elseif ~isempty(recnum) & recnum>nrecords |
| 244 |
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%CMM error('Requested record number is higher than the number of available records') |
| 245 |
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nrecords = recnum; |
| 246 |
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end |
| 247 |
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| 248 |
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if isempty(recnum) |
| 249 |
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recnum=1; |
| 250 |
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end |
| 251 |
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| 252 |
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if isnan(nrecords) |
| 253 |
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% This is the old 'meta' method that used sequential access |
| 254 |
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| 255 |
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A=allstr; |
| 256 |
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% Open data file |
| 257 |
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fid=fopen(dname,'r',ieee); |
| 258 |
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| 259 |
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% Read record size in bytes |
| 260 |
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recsz=fread(fid,1,'uint32'); |
| 261 |
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ldims=N(3,:)-N(2,:)+1; |
| 262 |
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numels=prod(ldims); |
| 263 |
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| 264 |
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rat=recsz/numels; |
| 265 |
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if rat == 4 |
| 266 |
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A=fread(fid,numels,'real*4'); |
| 267 |
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elseif rat == 8 |
| 268 |
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A=fread(fid,numels,'real*8'); |
| 269 |
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else |
| 270 |
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sprintf(' Implied size in meta-file = %d', numels ) |
| 271 |
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sprintf(' Record size in data-file = %d', recsz ) |
| 272 |
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error('Ratio between record size and size in meta-file inconsistent') |
| 273 |
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end |
| 274 |
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| 275 |
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erecsz=fread(fid,1,'uint32'); |
| 276 |
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if erecsz ~= recsz |
| 277 |
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sprintf('WARNING: Record sizes at beginning and end of file are inconsistent') |
| 278 |
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end |
| 279 |
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| 280 |
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fclose(fid); |
| 281 |
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| 282 |
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A=reshape(A,ldims); |
| 283 |
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| 284 |
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else |
| 285 |
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% This is the new MDS format that uses direct access |
| 286 |
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| 287 |
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ldims=N(3,:)-N(2,:)+1; |
| 288 |
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for r=1:size(recnum(:),1); |
| 289 |
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if dataprec == 'float32' |
| 290 |
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A(:,r)=myrdda(dname,ldims,recnum(r),'real*4',ieee); |
| 291 |
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elseif dataprec == 'float64' |
| 292 |
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A(:,r)=myrdda(dname,ldims,recnum(r),'real*8',ieee); |
| 293 |
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else |
| 294 |
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error(['Unrecognized format in meta-file = ' format]); |
| 295 |
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end |
| 296 |
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end |
| 297 |
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| 298 |
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A=reshape(A,[ldims size(recnum(:),1)]); |
| 299 |
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if size(recnum(:),1)>1 |
| 300 |
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N(1,end+1)=size(recnum(:),1); |
| 301 |
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N(2,end)=1; |
| 302 |
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N(3,end)=size(recnum(:),1); |
| 303 |
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end |
| 304 |
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| 305 |
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end |
| 306 |
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| 307 |
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%------------------------------------------------------------------------------- |
| 308 |
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| 309 |
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% result = RDDA( file, dim, irec [options] ) |
| 310 |
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% |
| 311 |
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% This routine reads the irec'th record of shape 'dim' from the |
| 312 |
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% direct-access binary file (float or double precision) 'file'. |
| 313 |
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% |
| 314 |
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% Required arguments: |
| 315 |
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% |
| 316 |
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% file - string - name of file to read from |
| 317 |
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% dim - vector - dimensions of the file records and the resulting array |
| 318 |
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% irec - integer - record number in file in which to write data |
| 319 |
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% |
| 320 |
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% Optional arguments (must appear after the required arguments): |
| 321 |
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% prec - string - precision of storage in file. Default = 'real*8'. |
| 322 |
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% ieee - string - IEEE bit-wise representation in file. Default = 'b'. |
| 323 |
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% |
| 324 |
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% 'prec' may take the values: |
| 325 |
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% 'real*4' - floating point, 32 bits. |
| 326 |
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% 'real*8' - floating point, 64 bits - the efault. |
| 327 |
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% |
| 328 |
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% 'ieee' may take values: |
| 329 |
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% 'ieee-be' or 'b' - IEEE floating point with big-endian |
| 330 |
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% byte ordering - the default |
| 331 |
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% 'ieee-le' or 'l' - IEEE floating point with little-endian |
| 332 |
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% byte ordering |
| 333 |
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% 'native' or 'n' - local machine format |
| 334 |
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% 'cray' or 'c' - Cray floating point with big-endian |
| 335 |
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% byte ordering |
| 336 |
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% 'ieee-le.l64' or 'a' - IEEE floating point with little-endian |
| 337 |
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% byte ordering and 64 bit long data type |
| 338 |
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% 'ieee-be.l64' or 's' - IEEE floating point with big-endian byte |
| 339 |
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% ordering and 64 bit long data type. |
| 340 |
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% |
| 341 |
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% eg. T=rdda('t.data',[64 64 32],1); |
| 342 |
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% T=rdda('t.data',[256],4,'real*4'); |
| 343 |
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% T=rdda('t.data',[128 64],2,'real*4','b'); |
| 344 |
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function [arr] = myrdda(file,N,k,varargin) |
| 345 |
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| 346 |
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% Defaults |
| 347 |
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WORDLENGTH=8; |
| 348 |
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rtype='real*8'; |
| 349 |
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ieee='b'; |
| 350 |
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| 351 |
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% Check optional arguments |
| 352 |
|
|
args=char(varargin); |
| 353 |
|
|
while (size(args,1) > 0) |
| 354 |
|
|
if deblank(args(1,:)) == 'real*4' |
| 355 |
|
|
WORDLENGTH=4; |
| 356 |
|
|
rtype='real*4'; |
| 357 |
|
|
elseif deblank(args(1,:)) == 'real*8' |
| 358 |
|
|
WORDLENGTH=8; |
| 359 |
|
|
rtype='real*8'; |
| 360 |
|
|
elseif deblank(args(1,:)) == 'n' | deblank(args(1,:)) == 'native' |
| 361 |
|
|
ieee='n'; |
| 362 |
|
|
elseif deblank(args(1,:)) == 'l' | deblank(args(1,:)) == 'ieee-le' |
| 363 |
|
|
ieee='l'; |
| 364 |
|
|
elseif deblank(args(1,:)) == 'b' | deblank(args(1,:)) == 'ieee-be' |
| 365 |
|
|
ieee='b'; |
| 366 |
|
|
elseif deblank(args(1,:)) == 'c' | deblank(args(1,:)) == 'cray' |
| 367 |
|
|
ieee='c'; |
| 368 |
|
|
elseif deblank(args(1,:)) == 'a' | deblank(args(1,:)) == 'ieee-le.l64' |
| 369 |
|
|
ieee='a'; |
| 370 |
|
|
elseif deblank(args(1,:)) == 's' | deblank(args(1,:)) == 'ieee-be.l64' |
| 371 |
|
|
ieee='s'; |
| 372 |
|
|
else |
| 373 |
|
|
error(['Optional argument ' args(1,:) ' is unknown']) |
| 374 |
|
|
end |
| 375 |
|
|
args=args(2:end,:); |
| 376 |
|
|
end |
| 377 |
|
|
|
| 378 |
|
|
nnn=prod(N); |
| 379 |
|
|
|
| 380 |
|
|
[fid mess]=fopen(file,'r',ieee); |
| 381 |
|
|
if fid == -1 |
| 382 |
|
|
error('Error while opening file:\n%s',mess) |
| 383 |
|
|
end |
| 384 |
|
|
st=fseek(fid,nnn*(k-1)*WORDLENGTH,'bof'); |
| 385 |
|
|
if st ~= 0 |
| 386 |
|
|
mess=ferror(fid); |
| 387 |
|
|
error('There was an error while positioning the file pointer:\n%s',mess) |
| 388 |
|
|
end |
| 389 |
|
|
[arr count]=fread(fid,nnn,rtype); |
| 390 |
|
|
if count ~= nnn |
| 391 |
|
|
error('Not enough data was available to be read: off EOF?') |
| 392 |
|
|
end |
| 393 |
|
|
st=fclose(fid); |
| 394 |
|
|
%arr=reshape(arr,N); |
| 395 |
|
|
|
| 396 |
|
|
% |
| 397 |
|
|
function [iters] = scanforfiles(fname) |
| 398 |
|
|
|
| 399 |
|
|
iters=[]; |
| 400 |
|
|
allfiles=dir([fname '.*.001.001.meta']); |
| 401 |
|
|
if isempty(allfiles) |
| 402 |
|
|
allfiles=dir([fname '.*.meta']); |
| 403 |
|
|
ioff=0; |
| 404 |
|
|
else |
| 405 |
|
|
ioff=8; |
| 406 |
|
|
end |
| 407 |
|
|
for k=1:size(allfiles,1); |
| 408 |
|
|
hh=allfiles(k).name; |
| 409 |
|
|
iters(k)=str2num( hh(end-14-ioff:end-5-ioff) ); |
| 410 |
|
|
end |
| 411 |
|
|
iters=sort(iters); |
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