Daniel@0: function sData = som_read_data(filename, varargin)
Daniel@0: 
Daniel@0: %SOM_READ_DATA Read data from an ascii file in SOM_PAK format.
Daniel@0: %
Daniel@0: % sD = som_read_data(filename, dim, [missing])
Daniel@0: % sD = som_read_data(filename, [missing])
Daniel@0: %
Daniel@0: %  sD = som_read_data('system.data');
Daniel@0: %  sD = som_read_data('system.data',10);
Daniel@0: %  sD = som_read_data('system.data','*');
Daniel@0: %  sD = som_read_data('system.data',10,'*');
Daniel@0: %
Daniel@0: %  Input and output arguments ([]'s are optional): 
Daniel@0: %   filename    (string) input file name
Daniel@0: %   dim         (scalar) input space dimension
Daniel@0: %   [missing]   (string) string which indicates a missing component
Daniel@0: %                        value, 'NaN' by default
Daniel@0: %
Daniel@0: %   sD          (struct) data struct
Daniel@0: %
Daniel@0: % Reads data from an ascii file. The file must be in SOM_PAK format, 
Daniel@0: % except that it may lack the input space dimension from the first
Daniel@0: % line. 
Daniel@0: %
Daniel@0: % For more help, try 'type som_read_data' or check out online documentation.
Daniel@0: % See also  SOM_WRITE_DATA, SOM_READ_COD, SOM_WRITE_COD, SOM_DATA_STRUCT.
Daniel@0: 
Daniel@0: %%%%%%%%%%%%% DETAILED DESCRIPTION %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Daniel@0: %
Daniel@0: % som_read_data
Daniel@0: %
Daniel@0: % PURPOSE
Daniel@0: %
Daniel@0: % Reads data from an ascii file in SOM_PAK format.
Daniel@0: %
Daniel@0: % SYNTAX
Daniel@0: %
Daniel@0: %  sD = som_read_data(filename)
Daniel@0: %  sD = som_read_data(..., dim)
Daniel@0: %  sD = som_read_data(..., 'missing')
Daniel@0: %  sD = som_read_data(..., dim, 'missing')
Daniel@0: %
Daniel@0: % DESCRIPTION
Daniel@0: %
Daniel@0: % This function is offered for compatibility with SOM_PAK, a SOM software
Daniel@0: % package in C. It reads data from a file in SOM_PAK format.
Daniel@0: %
Daniel@0: % The SOM_PAK data file format is as follows. The first line must
Daniel@0: % contain the input space dimension and nothing else. The following
Daniel@0: % lines are comment lines, empty lines or data lines. Unlike programs
Daniel@0: % in SOM_PAK, this function can also determine the input dimension
Daniel@0: % from the first data lines, if the input space dimension line is
Daniel@0: % missing.  Note that the SOM_PAK format is not fully supported: data
Daniel@0: % vector 'weight' and 'fixed' properties are ignored (they are treated
Daniel@0: % as labels).
Daniel@0: %
Daniel@0: % Each data line contains one data vector and its labels. From the beginning
Daniel@0: % of the line, first are values of the vector components separated by
Daniel@0: % whitespaces, then labels also separated by whitespaces. If there are
Daniel@0: % missing values in the vector, the missing value marker needs to be
Daniel@0: % specified as the last input argument ('NaN' by default). The missing
Daniel@0: % values are stored as NaNs in the data struct. 
Daniel@0: % 
Daniel@0: % Comment lines start with '#'. Comment lines as well as empty lines are
Daniel@0: % ignored, except if the comment lines that start with '#n' or '#l'. In that
Daniel@0: % case the line should contain names of the vector components or label names
Daniel@0: % separated by whitespaces.
Daniel@0: %
Daniel@0: % NOTE: The minimum value Matlab is able to deal with (realmax)
Daniel@0: % should not appear in the input file. This is because function sscanf is
Daniel@0: % not able to read NaNs: the NaNs are in the read phase converted to value
Daniel@0: % realmax.
Daniel@0: %
Daniel@0: % REQUIRED INPUT ARGUMENTS
Daniel@0: %
Daniel@0: %  filename    (string) input filename
Daniel@0: %
Daniel@0: % OPTIONAL INPUT ARGUMENTS
Daniel@0: %
Daniel@0: %  dim         (scalar) input space dimension
Daniel@0: %  missing     (string) string used to denote missing components (NaNs); 
Daniel@0: %                       default is 'NaN'
Daniel@0: %
Daniel@0: % OUTPUT ARGUMENTS
Daniel@0: %
Daniel@0: %  sD   (struct) the resulting data struct
Daniel@0: %
Daniel@0: % EXAMPLES
Daniel@0: %
Daniel@0: % The basic usage is:
Daniel@0: %  sD = som_read_data('system.data');
Daniel@0: %
Daniel@0: % If you know the input space dimension beforehand, and the file does
Daniel@0: % not contain it on the first line, it helps if you specify it as the
Daniel@0: % second argument: 
Daniel@0: %  sD = som_read_data('system.data',9);
Daniel@0: %
Daniel@0: % If the missing components in the data are marked with some other
Daniel@0: % characters than with 'NaN', you can specify it with the last argument: 
Daniel@0: %  sD = som_read_data('system.data',9,'*')
Daniel@0: %  sD = som_read_data('system.data','NaN')
Daniel@0: %
Daniel@0: % Here's an example data file:
Daniel@0: %
Daniel@0: % 5
Daniel@0: % #n one two three four five
Daniel@0: % #l ID
Daniel@0: % 10 2 3 4 5 1stline label
Daniel@0: % 0.4 0.3 0.2 0.5 0.1 2ndline label1 label2
Daniel@0: % # comment line: missing components are indicated by 'x':s
Daniel@0: % 1 x 1 x 1 3rdline missing_components
Daniel@0: % x 1 2 2 2 
Daniel@0: % x x x x x 5thline emptyline
Daniel@0: %
Daniel@0: % SEE ALSO
Daniel@0: %
Daniel@0: %  som_write_data   Writes data structs/matrices to a file in SOM_PAK format.
Daniel@0: %  som_read_cod     Read a map from a file in SOM_PAK format.
Daniel@0: %  som_write_cod    Writes data struct into a file in SOM_PAK format.
Daniel@0: %  som_data_struct  Creates data structs.
Daniel@0: 
Daniel@0: % Copyright (c) 1997-2000 by the SOM toolbox programming team.
Daniel@0: % http://www.cis.hut.fi/projects/somtoolbox/
Daniel@0: 
Daniel@0: % Version 1.0beta ecco 221097
Daniel@0: % Version 2.0beta ecco 060899, juuso 151199
Daniel@0: 
Daniel@0: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Daniel@0: %% check arguments
Daniel@0: 
Daniel@0: error(nargchk(1, 3, nargin))  % check no. of input args is correct
Daniel@0: 
Daniel@0: dont_care       = 'NaN';  % default don't care string
Daniel@0: comment_start   = '#';    % the char a SOM_PAK command line starts with
Daniel@0: comp_name_line  = '#n';   % string denoting a special command line,
Daniel@0:                           % which contains names of each component
Daniel@0: label_name_line = '#l';   % string denoting a special command line,
Daniel@0:                           % which contains names of each label
Daniel@0: block_size      = 1000;   % block size used in file read
Daniel@0: 
Daniel@0: kludge          = num2str(realmax, 100); % used in sscanf                
Daniel@0:   
Daniel@0: 
Daniel@0: % open input file
Daniel@0: 
Daniel@0: fid = fopen(filename);
Daniel@0: if fid < 0
Daniel@0:   error(['Cannot open ' filename]); 
Daniel@0: end
Daniel@0: 
Daniel@0: % process input arguments
Daniel@0: 
Daniel@0: if nargin == 2 
Daniel@0:   if isstr(varargin{1})
Daniel@0:     dont_care = varargin{1};
Daniel@0:   else
Daniel@0:     dim      = varargin{1};
Daniel@0:   end
Daniel@0: elseif nargin == 3
Daniel@0:   dim       = varargin{1};
Daniel@0:   dont_care = varargin{2};
Daniel@0: end
Daniel@0: 
Daniel@0: % if the data dimension is not specified, find out what it is
Daniel@0: 
Daniel@0: if nargin == 1 | (nargin == 2 & isstr(varargin{1}))
Daniel@0: 
Daniel@0:   fpos1 = ftell(fid); c1 = 0;      % read first non-comment line
Daniel@0:   while c1 == 0,
Daniel@0:     line1 = strrep(fgetl(fid), dont_care, kludge);
Daniel@0:     [l1, c1] = sscanf(line1, '%f ');
Daniel@0:   end
Daniel@0: 
Daniel@0:   fpos2 = ftell(fid); c2 = 0;      % read second non-comment line
Daniel@0:   while c2 == 0,
Daniel@0:     line2 = strrep(fgetl(fid), dont_care, kludge);
Daniel@0:     [l2, c2] = sscanf(line2, '%f ');
Daniel@0:   end
Daniel@0: 
Daniel@0:   if (c1 == 1 & c2 ~= 1) | (c1 == c2 & c1 == 1 & l1 == 1)
Daniel@0:     dim = l1;
Daniel@0:     fseek(fid, fpos2, -1);
Daniel@0:   elseif (c1 == c2)
Daniel@0:     dim = c1;
Daniel@0:     fseek(fid, fpos1, -1);
Daniel@0:     warning on
Daniel@0:     warning(['Automatically determined data dimension is ' ...
Daniel@0: 	     num2str(dim) '. Is it correct?']); 
Daniel@0:   else
Daniel@0:     error(['Invalid header line: ' line1]);
Daniel@0:   end
Daniel@0: end 
Daniel@0: 
Daniel@0: % check the dimension is valid
Daniel@0: 
Daniel@0: if dim < 1 | dim ~= round(dim) 
Daniel@0:   error(['Illegal data dimension: ' num2str(dim)]);
Daniel@0: end
Daniel@0: 
Daniel@0: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Daniel@0: %% read data
Daniel@0: 
Daniel@0: sData       = som_data_struct(zeros(1, dim), 'name', filename); 
Daniel@0: lnum        = 0;                                    % data vector counter
Daniel@0: data_temp   = zeros(block_size, dim);
Daniel@0: labs_temp   = cell(block_size, 1);
Daniel@0: comp_names  = sData.comp_names;
Daniel@0: label_names = sData.label_names;
Daniel@0: form        = [repmat('%g',[1 dim-1]) '%g%[^ \t]'];
Daniel@0: 
Daniel@0: limit       = block_size;
Daniel@0: while 1,
Daniel@0:   li = fgetl(fid);                         % read next line
Daniel@0:   if ~isstr(li), break, end;               % is this the end of file? 
Daniel@0: 
Daniel@0:   % all missing vectors are replaced by value realmax because
Daniel@0:   % sscanf is not able to read NaNs  
Daniel@0:   li = strrep(li, dont_care, kludge);     
Daniel@0:   [data, c, err, n] = sscanf(li, form);
Daniel@0:   if c < dim % if there were less numbers than dim on the input file line
Daniel@0:     if c == 0
Daniel@0:       if strncmp(li, comp_name_line, 2) % component name line?
Daniel@0: 	li = strrep(li(3:end), kludge, dont_care); i = 0; c = 1;
Daniel@0: 	while c
Daniel@0: 	  [s, c, e, n] = sscanf(li, '%s%[^ \t]');
Daniel@0: 	  if ~isempty(s), i = i + 1; comp_names{i} = s; li = li(n:end); end
Daniel@0: 	end
Daniel@0: 
Daniel@0: 	if i ~= dim 
Daniel@0: 	  error(['Illegal number of component names: ' num2str(i) ...
Daniel@0: 		 ' (dimension is ' num2str(dim) ')']); 
Daniel@0: 	end
Daniel@0:       elseif strncmp(li, label_name_line, 2) % label name line?
Daniel@0: 	li = strrep(li(3:end), kludge, dont_care); i = 0; c = 1;
Daniel@0: 	while c
Daniel@0: 	  [s, c, e, n] = sscanf(li, '%s%[^ \t]');
Daniel@0: 	  if ~isempty(s), i = i + 1; label_names{i} = s; li = li(n:end); end
Daniel@0: 	end
Daniel@0:       elseif ~strncmp(li, comment_start, 1) % not a comment, is it error?
Daniel@0: 	[s, c, e, n] = sscanf(li, '%s%[^ \t]');
Daniel@0: 	if c
Daniel@0: 	  error(['Invalid vector on input file data line ' ...
Daniel@0: 		 num2str(lnum+1) ': [' deblank(li) ']']),
Daniel@0: 	end
Daniel@0:       end
Daniel@0:     else
Daniel@0:       error(['Only ' num2str(c) ' vector components on input file data line ' ...
Daniel@0: 	     num2str(lnum+1) ' (dimension is ' num2str(dim) ')']);
Daniel@0:     end
Daniel@0: 
Daniel@0:   else
Daniel@0: 
Daniel@0:     lnum = lnum + 1;                % this was a line containing data vector
Daniel@0:     data_temp(lnum, 1:dim) = data'; % add data to struct
Daniel@0: 
Daniel@0:     if lnum == limit       % reserve more memory if necessary
Daniel@0:       data_temp(lnum+1:lnum+block_size, 1:dim) = zeros(block_size, dim);
Daniel@0:       [dummy nl] = size(labs_temp);
Daniel@0:       labs_temp(lnum+1:lnum+block_size,1:nl) = cell(block_size, nl);
Daniel@0:       limit = limit + block_size;
Daniel@0:     end
Daniel@0:     
Daniel@0:     % read labels
Daniel@0:     
Daniel@0:     if n < length(li)
Daniel@0:       li = strrep(li(n:end), kludge, dont_care); i = 0; n = 1; c = 1;
Daniel@0:       while c
Daniel@0: 	[s, c, e, n_new] = sscanf(li(n:end), '%s%[^ \t]');
Daniel@0: 	if c, i = i + 1; labs_temp{lnum, i} = s; n = n + n_new - 1; end
Daniel@0:       end
Daniel@0:     end
Daniel@0:   end
Daniel@0: end
Daniel@0: 
Daniel@0: % close input file
Daniel@0: if fclose(fid) < 0, error(['Cannot close file ' filename]);
Daniel@0: else fprintf(2, '\rdata read ok         \n'); end
Daniel@0: 
Daniel@0: % set values
Daniel@0: data_temp(data_temp == realmax) = NaN;
Daniel@0: sData.data        = data_temp(1:lnum,:);
Daniel@0: sData.labels      = labs_temp(1:lnum,:);
Daniel@0: sData.comp_names  = comp_names;
Daniel@0: sData.label_names = label_names;
Daniel@0: 
Daniel@0: return;
Daniel@0: 
Daniel@0: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%