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 argumentserror(nargchk(1, 1, nargin))  % check no. of input args is correct%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% initialize variableslnum           = 0;    % codebook vector countercomment_start  = '#';  % the char a SOM_PAK command line starts withcomp_name_line = '#n'; % string used to start a special command line,                       % which contains names of each component% open input filefid = fopen(filename);if fid < 0, error(['Cannot open ' filename]); end % read header lineok_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 linemunits = 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 filecodebook   = 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  endend% close the input fileif fclose(fid) < 0  error(['Cannot close file ' filename]); else  fprintf(2, '\rmap read ok         \n');end% check that the number of lines read was correctif 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;%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%