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gyacomo/matlab/load/read_namelist.m
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read_namelist.m
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function S = read_namelist(filename)
% S = READ_NAMELIST(FILENAME) returns the struct S containg namelists and
% variables in the file FILENAME organised in hierachical way:
%
% |--VAR1
% |--VAR2
% |-- NMLST_A--|...
% | |--VARNa
% |
% | |--VAR1
% |-- NMLST_B--|--VAR2
% | |...
% S --| ... |--VARNb
% |
% | |--VAR1
% |-- NMLST_M--|--VAR2
% |...
% |--VARNm
%
% Note: The function can read multidimensioal variables as well. The
% function assumes that there is no more than one namelist section per
% line. At this time there is no syntax checking functionality so the
% function will crash in case of errors.
%
% Example:
% NMLST = read_namelist('OPTIONS.nam');
% NMLST.NAM_FRAC.XUNIF_NATURE = 0.1;
% write_namelist(NMlST, 'MOD_OPTIONS.nam');
%
% Written by: Darien Pardinas Diaz (darien.pardinas-diaz@monash.edu)
% Version: 1.0
% Date: 16 Dec 2011
S = struct();
% Open and read the text file containing the namelists
fid = fopen(filename,'r');
c = 0;
lines = cell(1);
% Read all the text lines in namelist file
while ~feof(fid)
line = fgetl(fid);
% Remove comments if any on the line
idx = find(line == '!');
if ~isempty(idx),
line = line(1:idx(1)-1);
end
if ~isempty(line),
c = c + 1;
lines{c} = line;
end
end
fclose(fid);
i = 0;
while i < c;
% Find a record
i = i + 1;
line = lines{i};
idx = find(line == '&');
if ~isempty(idx), % i.e. a namelist start
line = line(idx(1) + 1:end);
% find next space
idx = find(line == ' ');
if ~isempty(idx),
namelst = line(1:idx(1) - 1);
line = line(idx(1) + 1:end);
else
namelst = line;
line = [];
end
nmlst_bdy = [];
idx = strfind(line,'/');
% Get the variable specification section
while isempty(idx) && i < c,
nmlst_bdy = [nmlst_bdy ' ' line];
i = i + 1;
line = lines{i};
idx = strfind(line,'/');
end
if ~isempty(idx) && idx(1) > 1,
nmlst_bdy = [nmlst_bdy ' ' line];
end
% Parse current namelist (set of variables)
switch namelst
case 'info'
otherwise
S.(namelst) = parse_namelist(nmlst_bdy);
end
end
end
function S = parse_namelist(strng)
% Internal function to parse the body text of a namelist section.
% Limitations: the following patterns are prohibited inside the literal
% strings: '.t.' '.f.' '.true.' '.false.' '(:)'
% Get all .true., .t. and .false., .f. to T and F
strng = regexprep(strng,'\.true\.' ,'T','ignorecase');
strng = regexprep(strng,'\.false\.','F','ignorecase');
strng = regexprep(strng,'\.t\.','T','ignorecase');
strng = regexprep(strng,'\.f\.','F','ignorecase');
% Make evaluable the (:) expression in MATLAB if any
strng = regexprep(strng, '\(:\)', '(1,:)');
[strng, islit] = parse_literal_strings([strng ' ']);
% Find the position of all the '='
eq_idx = find(strng == '=');
nvars = length(eq_idx);
arg_start = eq_idx + 1;
arg_end = zeros(size(eq_idx));
vars = cell(nvars,1);
S = struct;
% Loop through every variable
for k = 1:nvars,
i = eq_idx(k) - 1;
% Move to the left and discard blank spaces
while strng(i) == ' ', i = i - 1; end
% Now we are over the variable name or closing parentesis
j = i;
if strng(i) == ')',
while strng(i) ~= '(', i = i - 1; end
i = i - 1;
% Move to the left and discard any possible blank spaces
while strng(i) == ' ', i = i - 1; end
end
% Now we are over the last character of the variable name
while strng(i) ~= ' ', i = i - 1; end
if k > 1, arg_end(k - 1) = i; end
vars{k} = ['S.' strng(i + 1: j)];
end
if numel(arg_end) > 0
arg_end(end) = length(strng);
end
% This variables are used in the eval function to evaluate True/False,
% so don't remove it!
T = '.true.';
F = '.false.';
% Loop through every variable guess varible type
for k = 1:nvars,
arg = strng(arg_start(k):arg_end(k));
arglit = islit(arg_start(k):arg_end(k))';
% Remove commas in non literal string...
commas = ~arglit & arg == ',';
if any(commas)
arg(commas) = ' ';
end
if any(arglit),
% We are parsing a variable that is literal string
arg = ['{' arg '};'];
elseif ~isempty(find( arg == 'T' | arg == 'F', 1)),
% We are parsing a boolean variable
arg = ['{' arg '};'];
else
% We are parsing a numerical array
arg = ['[' arg '];'];
end
% Eval the modified syntax in Matlab
eval([vars{k} ' = ' arg]);
end
function [strng, is_lit] = parse_literal_strings(strng)
% Parse the literal declarations of strings and change to Matlab syntax
len = length(strng);
add_squote = []; % Positions to add a scape single quote on syntax
rem_dquote = []; % Positions to remove a double quote scape on syntax
i = 1;
while i < len,
if strng(i) == '''', % Opening string with single quote...
i = i + 1;
while i < len && strng(i) ~= '''' || strcmp(strng(i:i+1),'''''') ,
i = i + 1;
if strcmp(strng(i-1:i),''''''),
i = i + 1;
end
end
end
if strng(i) == '"', % Opening string with double quote...
strng(i) = ''''; % Change to single quote
i = i + 1;
while strng(i) ~= '"' || strcmp(strng(i:i+1),'""') && i < len,
% Check for a possible sigle quote here
if strng(i) == '''',
add_squote = [add_squote i];
end
i = i + 1;
if strcmp(strng(i-1:i),'""'),
rem_dquote = [rem_dquote i-1];
i = i + 1;
end
end
strng(i) = ''''; % Change to single quote
end
i = i + 1;
end
for i = 1:length(add_squote);
strng = [strng(1:add_squote(i)) strng(add_squote(i):end)];
end
for i = 1:length(rem_dquote);
strng = [strng(1:rem_dquote(i)-1) strng(rem_squote(i)+1:end)];
end
% Now everything should be in Matlab string syntax
% Classify syntax as literal or regular expression
i = 1;
len = length(strng);
is_lit = zeros(len,1);
while i < len,
if strng(i) == '''', % Opening string with single quote...
is_lit(i) = 1;
i = i + 1;
while i < len && strng(i) ~= '''' || strcmp(strng(i:i+1),''''''),
is_lit(i) = 1;
i = i + 1;
if strcmp(strng(i-1:i),''''''),
is_lit(i) = 1;
i = i + 1;
end
end
is_lit(i) = 1;
end
i = i + 1;
end
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