Passing .txt and .xsl files to som_read_data.m

Hello, I'm quite new to matlab....I am using the som toolbox and by default only .dat datasets are read by the toolbox.....there have been certain tweaks to the code that allow the passage of both .dat files and .txt and .xsl....I do not know how to effectively implement those tweaks for this som_read_data.....I have tried to make some changes but i always get errors at certain lines like error using ftell and some other  errors..... I have attached the som_read_data file and also the sample dataset(.txt) i intend to pass through it.....I would really appreciate any help on this issue

% if the data dimension is not specified, find out what it is

if 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
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 arguments

error(nargchk(1, 3, nargin))  % check no. of input args is correct

dont_care       = 'NaN';  % default don't care string
comment_start   = '#';    % the char a SOM_PAK command line starts with
comp_name_line  = '#n';   % string denoting a special command line,
                          % which contains names of each component
label_name_line = '#l';   % string denoting a special command line,
                          % which contains names of each label
block_size      = 1000;   % block size used in file read

kludge          = num2str(realmax, 100); % used in sscanf                
  

% open input file

fid = fopen(filename);
if fid < 0
  error(['Cannot open ' filename]); 
end

% process input arguments

if nargin == 2 
  if isstr(varargin{1})
    dont_care = varargin{1};
  else
    dim      = varargin{1};
  end
elseif nargin == 3
  dim       = varargin{1};
  dont_care = varargin{2};
end

% if the data dimension is not specified, find out what it is

if 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]);
  end
end 

% check the dimension is valid

if dim < 1 | dim ~= round(dim) 
  error(['Illegal data dimension: ' num2str(dim)]);
end

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% read data

sData       = som_data_struct(zeros(1, dim), 'name', filename); 
lnum        = 0;                                    % data vector counter
data_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
  end
end

% close input file
if fclose(fid) < 0, error(['Cannot close file ' filename]);
else fprintf(2, '\rdata read ok         \n'); end

% set values
data_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;

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

Open in new window

tests.txt
som-read-data.txt
TJ11Asked:
Who is Participating?
 
yuk99Commented:
The input file has to be in SOM_PAK format. The formati is described in details in the comment in som_read_data.m file.

The first line (without comments) should be a single number - number of data columns without last row labels column if it exist. In your tests.txt the number should be 4.
Try to put this line and everything should work.

Read the SOM_PAK description for further information and options.
0
 
yuk99Commented:
The data file may have any extension: dat, txt, xls are ok. But it has to be tab-delimited text file. You cannot pass binary Excel file, you have to save it first as text file.
0
Question has a verified solution.

Are you are experiencing a similar issue? Get a personalized answer when you ask a related question.

Have a better answer? Share it in a comment.

All Courses

From novice to tech pro — start learning today.