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function sMap = som_read_cod(filename)
%SOM_READ_COD Reads a SOM_PAK format codebook file.
%
% sMap = som_read_cod(filename);
%
% sMap = som_read_cod('map1.cod');
%
% Input and output arguments:
% filename (string) name of input file
% sMap (struct) self-organizing map structure
%
% The file must be in SOM_PAK format. Empty lines and lines starting
% with a '#' are ignored, except the ones starting with '#n'. The strings
% after '#n' are read to field 'comp_names' of the map structure.
%
% For more help, try 'type som_read_cod' or check out online documentation.
% See also SOM_WRITE_COD, SOM_READ_DATA, SOM_WRITE_DATA, SOM_MAP_STRUCT.
%%%%%%%%%%%%% DETAILED DESCRIPTION %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% som_read_cod
%
% PURPOSE
%
% Reads a Self-Organizing Map from an ascii file in SOM_PAK format.
%
% SYNTAX
%
% sMap = som_read_cod(filename);
%
% DESCRIPTION
%
% This function is offered for compatibility with SOM_PAK, a SOM
% software package in C. It reads map files written in SOM_PAK format.
%
% The SOM_PAK map file format is as follows. The first line must contain
% the input space dimension, lattice type ('rect' or 'hexa'), map grid
% size in x-direction, map grid size in y-direction, and neighborhood
% function ('bubble' or 'gaussian'), in that order. The following lines
% are comment lines, empty lines or data lines.
%
% Each data line contains the weight vector of one map unit and its
% labels. From the beginning of the line, first are values of the vector
% components separated by whitespaces, then labels, again separated by
% whitespaces. The order of map units in the file are one row at a time
% from right to left, from the top to the bottom of the map (x-direction
% first, then y-direction).
%
% Comment lines start with '#'. Comment lines as well as empty lines are
% ignored, except if the comment line starts with '#n'. In that case the
% line should contain names of the vector components separated by
% whitespaces.
%
% In the returned map struct, several fields has to be set to default
% values, since the SOM_PAK file does not contain information on
% them. These include map shape ('sheet'), mask ([1 ... 1]),
% normalizations (none), trainhist (two entries, first with algorithm
% 'init' and the second with 'seq', both with data name 'unknown'),
% possibly also component names ('Var1',...).
%
% REQUIRED INPUT PARAMETERS
%
% filename (string) the name of the input file
%
% OUTPUT ARGUMENTS
%
% sMap (struct) the resulting SOM struct
%
% EXAMPLES
%
% sMap = som_read_cod('map1.cod');
%
% SEE ALSO
%
% som_write_cod Writes a map struct into a file in SOM_PAK format.
% som_read_data Reads data from an ascii file.
% som_write_data Writes data struct into a file in SOM_PAK format.
% som_map_struct Creates map structs.
% Copyright (c) 1997-2000 by the SOM toolbox programming team.
% http://www.cis.hut.fi/projects/somtoolbox/
% Version 1.0beta ecco 221097
% Version 2.0beta juuso 151199 250400
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% check arguments
error(nargchk(1, 1, nargin)) % check no. of input args is correct
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% initialize variables
lnum = 0; % codebook vector counter
comment_start = '#'; % the char a SOM_PAK command line starts with
comp_name_line = '#n'; % string used to start a special command line,
% which contains names of each component
% open input file
fid = fopen(filename);
if fid < 0, error(['Cannot open ' filename]); end
% read header line
ok_cnt = 0;
lin = fgetl(fid); li = lin;
[dim c err n] = sscanf(li, '%d%[^ \t]'); ok_cnt=ok_cnt+c; li = li(n:end);
[lattice c err n] = sscanf(li,'%s%[^ \t]'); ok_cnt=ok_cnt+c; li = li(n:end);
[msize(2) c err n] = sscanf(li, '%d%[^ \t]'); ok_cnt=ok_cnt+c; li = li(n:end);
[msize(1) c err n] = sscanf(li, '%d%[^ \t]'); ok_cnt=ok_cnt+c; li = li(n:end);
[neigh c err n] = sscanf(li, '%s%[^ \t\n]'); ok_cnt=ok_cnt+c;
if ok_cnt ~= 5
error([ 'Invalid header line: ' lin ]);
end
% create map struct and set its fields according to header line
munits = prod(msize);
sMap = som_map_struct(dim, 'msize', msize, ...
lattice, 'sheet', 'neigh', neigh);
[sT0, ok] = som_set('som_train','algorithm','init','data_name','unknown');
sT1 = som_set('som_train','algorithm','seq','data_name','unknown',...
'neigh',neigh,'mask',ones(dim,1));
[sMap, ok, msgs] = som_set(sMap,'name',filename,'trainhist',{sT0,sT1});
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% read codebook from the file
codebook = zeros(munits,dim);
labels = cell(munits,1);
comp_names = sMap.comp_names;
form = [repmat('%f',[1 dim-1]) '%f%[^ \t]'];
while 1,
li = fgetl(fid); % read next line
if ~isstr(li), break, end; % is this the end of file?
[data, c, err, n] = sscanf(li, form);
if c < dim % if there were less numbers than dim on the input file line
if c == 0
if strncmp(li, comp_name_line, 2) % component name line?
li = li(3:end); i = 0; c = 1;
while c
[s, c, e, n] = sscanf(li, '%s%[^ \t]');
if ~isempty(s), i = i + 1; comp_names{i} = s; li = li(n:end); end
end
if i ~= dim
error(['Illegal number of component names: ' num2str(i) ...
' (dimension is ' num2str(dim) ')']);
end
elseif ~strncmp(li, comment_start, 1) % not a comment, is it error?
[s, c, e, n] = sscanf(li, '%s%[^ \t]');
if c
error(['Invalid vector on input file line ' ...
num2str(lnum+1) ': [' deblank(li) ']']),
end
end
else
error(['Only ' num2str(c) ' vector components on input file line ' ...
num2str(lnum+1) ' (dimension is ' num2str(dim) ')']);
end
else
lnum = lnum + 1; % this was a line containing data vector
codebook(lnum, 1:dim) = data'; % add data to struct
% read labels
if n < length(li)
li = li(n:end);
i = 0; n = 1; c = 1;
while c
[s, c, e, n_new] = sscanf(li(n:end), '%s%[^ \t]');
if c, i = i + 1; labels{lnum, i} = s; n = n + n_new - 1; end
end
end
end
end
% close the input file
if fclose(fid) < 0
error(['Cannot close file ' filename]);
else
fprintf(2, '\rmap read ok \n');
end
% check that the number of lines read was correct
if lnum ~= munits
error(['Illegal number of map units: ' num2str(lnum) ' (should be ' num2str(munits) ').']);
end
% set values
% in SOM_PAK the xy-indexing is used, while in Matlab ij-indexing
% therefore, the codebook vectors have to be reorganized
order = reshape([1:munits],msize);
order = reshape(order',[munits 1]);
codebook(order,:) = codebook;
labels(order,:) = labels;
sMap.codebook = codebook;
sMap.labels = labels;
sMap.comp_names = comp_names;
return;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%