comparison toolboxes/MIRtoolbox1.3.2/somtoolbox/som_read_data.m @ 0:e9a9cd732c1e tip

first hg version after svn

+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;
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%