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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;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%