function sData = som_read_data(filename, varargin)%SOM_READ_DATA Read data from an ascii file in SOM_PAK format.%% sD = som_read_data(filename, dim, [missing])% sD = som_read_data(filename, [missing])%%  sD = som_read_data('system.data');%  sD = som_read_data('system.data',10);%  sD = som_read_data('system.data','*');%  sD = som_read_data('system.data',10,'*');%%  Input and output arguments ([]'s are optional): %   filename    (string) input file name%   dim         (scalar) input space dimension%   [missing]   (string) string which indicates a missing component%                        value, 'NaN' by default%%   sD          (struct) data struct%% Reads data from an ascii file. The file must be in SOM_PAK format, % except that it may lack the input space dimension from the first% line. %% For more help, try 'type som_read_data' or check out online documentation.% See also  SOM_WRITE_DATA, SOM_READ_COD, SOM_WRITE_COD, SOM_DATA_STRUCT.%%%%%%%%%%%%% DETAILED DESCRIPTION %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% som_read_data%% PURPOSE%% Reads data from an ascii file in SOM_PAK format.%% SYNTAX%%  sD = som_read_data(filename)%  sD = som_read_data(..., dim)%  sD = som_read_data(..., 'missing')%  sD = som_read_data(..., dim, 'missing')%% DESCRIPTION%% This function is offered for compatibility with SOM_PAK, a SOM software% package in C. It reads data from a file in SOM_PAK format.%% The SOM_PAK data file format is as follows. The first line must% contain the input space dimension and nothing else. The following% lines are comment lines, empty lines or data lines. Unlike programs% in SOM_PAK, this function can also determine the input dimension% from the first data lines, if the input space dimension line is% missing.  Note that the SOM_PAK format is not fully supported: data% vector 'weight' and 'fixed' properties are ignored (they are treated% as labels).%% Each data line contains one data vector and its labels. From the beginning% of the line, first are values of the vector components separated by% whitespaces, then labels also separated by whitespaces. If there are% missing values in the vector, the missing value marker needs to be% specified as the last input argument ('NaN' by default). The missing% values are stored as NaNs in the data struct. % % Comment lines start with '#'. Comment lines as well as empty lines are% ignored, except if the comment lines that start with '#n' or '#l'. In that% case the line should contain names of the vector components or label names% separated by whitespaces.%% NOTE: The minimum value Matlab is able to deal with (realmax)% should not appear in the input file. This is because function sscanf is% not able to read NaNs: the NaNs are in the read phase converted to value% realmax.%% REQUIRED INPUT ARGUMENTS%%  filename    (string) input filename%% OPTIONAL INPUT ARGUMENTS%%  dim         (scalar) input space dimension%  missing     (string) string used to denote missing components (NaNs); %                       default is 'NaN'%% OUTPUT ARGUMENTS%%  sD   (struct) the resulting data struct%% EXAMPLES%% The basic usage is:%  sD = som_read_data('system.data');%% If you know the input space dimension beforehand, and the file does% not contain it on the first line, it helps if you specify it as the% second argument: %  sD = som_read_data('system.data',9);%% If the missing components in the data are marked with some other% characters than with 'NaN', you can specify it with the last argument: %  sD = som_read_data('system.data',9,'*')%  sD = som_read_data('system.data','NaN')%% Here's an example data file:%% 5% #n one two three four five% #l ID% 10 2 3 4 5 1stline label% 0.4 0.3 0.2 0.5 0.1 2ndline label1 label2% # comment line: missing components are indicated by 'x':s% 1 x 1 x 1 3rdline missing_components% x 1 2 2 2 % x x x x x 5thline emptyline%% SEE ALSO%%  som_write_data   Writes data structs/matrices to a file in SOM_PAK format.%  som_read_cod     Read a map from a file in SOM_PAK format.%  som_write_cod    Writes data struct into a file in SOM_PAK format.%  som_data_struct  Creates data 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 ecco 060899, juuso 151199%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% check argumentserror(nargchk(1, 3, nargin))  % check no. of input args is correctdont_care       = 'NaN';  % default don't care stringcomment_start   = '#';    % the char a SOM_PAK command line starts withcomp_name_line  = '#n';   % string denoting a special command line,                          % which contains names of each componentlabel_name_line = '#l';   % string denoting a special command line,                          % which contains names of each labelblock_size      = 1000;   % block size used in file readkludge          = num2str(realmax, 100); % used in sscanf                  % open input filefid = fopen(filename);if fid < 0  error(['Cannot open ' filename]); end% process input argumentsif nargin == 2   if isstr(varargin{1})    dont_care = varargin{1};  else    dim      = varargin{1};  endelseif nargin == 3  dim       = varargin{1};  dont_care = varargin{2};end% if the data dimension is not specified, find out what it isif nargin == 1 | (nargin == 2 & isstr(varargin{1}))  fpos1 = ftell(fid); c1 = 0;      % read first non-comment line  while c1 == 0,    line1 = strrep(fgetl(fid), dont_care, kludge);    [l1, c1] = sscanf(line1, '%f ');  end  fpos2 = ftell(fid); c2 = 0;      % read second non-comment line  while c2 == 0,    line2 = strrep(fgetl(fid), dont_care, kludge);    [l2, c2] = sscanf(line2, '%f ');  end  if (c1 == 1 & c2 ~= 1) | (c1 == c2 & c1 == 1 & l1 == 1)    dim = l1;    fseek(fid, fpos2, -1);  elseif (c1 == c2)    dim = c1;    fseek(fid, fpos1, -1);    warning on    warning(['Automatically determined data dimension is ' ...	     num2str(dim) '. Is it correct?']);   else    error(['Invalid header line: ' line1]);  endend % check the dimension is validif dim < 1 | dim ~= round(dim)   error(['Illegal data dimension: ' num2str(dim)]);end%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% read datasData       = som_data_struct(zeros(1, dim), 'name', filename); lnum        = 0;                                    % data vector counterdata_temp   = zeros(block_size, dim);labs_temp   = cell(block_size, 1);comp_names  = sData.comp_names;label_names = sData.label_names;form        = [repmat('%g',[1 dim-1]) '%g%[^ \t]'];limit       = block_size;while 1,  li = fgetl(fid);                         % read next line  if ~isstr(li), break, end;               % is this the end of file?   % all missing vectors are replaced by value realmax because  % sscanf is not able to read NaNs    li = strrep(li, dont_care, kludge);       [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 = strrep(li(3:end), kludge, dont_care); 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, label_name_line, 2) % label name line?	li = strrep(li(3:end), kludge, dont_care); i = 0; c = 1;	while c	  [s, c, e, n] = sscanf(li, '%s%[^ \t]');	  if ~isempty(s), i = i + 1; label_names{i} = s; li = li(n:end); end	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 data line ' ...		 num2str(lnum+1) ': [' deblank(li) ']']),	end      end    else      error(['Only ' num2str(c) ' vector components on input file data line ' ...	     num2str(lnum+1) ' (dimension is ' num2str(dim) ')']);    end  else    lnum = lnum + 1;                % this was a line containing data vector    data_temp(lnum, 1:dim) = data'; % add data to struct    if lnum == limit       % reserve more memory if necessary      data_temp(lnum+1:lnum+block_size, 1:dim) = zeros(block_size, dim);      [dummy nl] = size(labs_temp);      labs_temp(lnum+1:lnum+block_size,1:nl) = cell(block_size, nl);      limit = limit + block_size;    end        % read labels        if n < length(li)      li = strrep(li(n:end), kludge, dont_care); i = 0; n = 1; c = 1;      while c	[s, c, e, n_new] = sscanf(li(n:end), '%s%[^ \t]');	if c, i = i + 1; labs_temp{lnum, i} = s; n = n + n_new - 1; end      end    end  endend% close input fileif fclose(fid) < 0, error(['Cannot close file ' filename]);else fprintf(2, '\rdata read ok         \n'); end% set valuesdata_temp(data_temp == realmax) = NaN;sData.data        = data_temp(1:lnum,:);sData.labels      = labs_temp(1:lnum,:);sData.comp_names  = comp_names;sData.label_names = label_names;return;%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%