diff toolboxes/MIRtoolbox1.3.2/somtoolbox/som_read_cod.m @ 0:e9a9cd732c1e tip

first hg version after svn

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/toolboxes/MIRtoolbox1.3.2/somtoolbox/som_read_cod.m	Tue Feb 10 15:05:51 2015 +0000
@@ -0,0 +1,215 @@
+function sMap = som_read_cod(filename)
+
+%SOM_READ_COD Reads a SOM_PAK format codebook file.
+%
+% sMap = som_read_cod(filename);
+%
+%  sMap = som_read_cod('map1.cod');
+%
+%  Input and output arguments: 
+%   filename    (string) name of input file
+%   sMap        (struct) self-organizing map structure
+%
+% The file must be in SOM_PAK format. Empty lines and lines starting 
+% with a '#' are ignored, except the ones starting with '#n'. The strings 
+% after '#n' are read to field 'comp_names' of the map structure.
+%
+% For more help, try 'type som_read_cod' or check out online documentation.
+% See also SOM_WRITE_COD, SOM_READ_DATA, SOM_WRITE_DATA, SOM_MAP_STRUCT.
+
+%%%%%%%%%%%%% DETAILED DESCRIPTION %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% som_read_cod
+%
+% PURPOSE
+%
+% Reads a Self-Organizing Map from an ascii file in SOM_PAK format.
+%
+% SYNTAX
+%
+%  sMap = som_read_cod(filename); 
+%
+% DESCRIPTION
+%
+% This function is offered for compatibility with SOM_PAK, a SOM 
+% software package in C. It reads map files written in SOM_PAK format.
+%
+% The SOM_PAK map file format is as follows. The first line must contain
+% the input space dimension, lattice type ('rect' or 'hexa'), map grid
+% size in x-direction, map grid size in y-direction, and neighborhood
+% function ('bubble' or 'gaussian'), in that order. The following lines
+% are comment lines, empty lines or data lines. 
+%
+% Each data line contains the weight vector of one map unit and its
+% labels. From the beginning of the line, first are values of the vector
+% components separated by whitespaces, then labels, again separated by
+% whitespaces. The order of map units in the file are one row at a time
+% from right to left, from the top to the bottom of the map (x-direction
+% first, then y-direction). 
+% 
+% Comment lines start with '#'. Comment lines as well as empty lines are
+% ignored, except if the comment line starts with '#n'. In that case the
+% line should contain names of the vector components separated by
+% whitespaces.
+%
+% In the returned map struct, several fields has to be set to default
+% values, since the SOM_PAK file does not contain information on
+% them. These include map shape ('sheet'), mask ([1 ... 1]),
+% normalizations (none), trainhist (two entries, first with algorithm
+% 'init' and the second with 'seq', both with data name 'unknown'),
+% possibly also component names ('Var1',...). 
+%
+% REQUIRED INPUT PARAMETERS
+%
+%  filename   (string) the name of the input file
+%
+% OUTPUT ARGUMENTS
+%
+%  sMap       (struct) the resulting SOM struct
+% 
+% EXAMPLES
+%
+%  sMap = som_read_cod('map1.cod');
+%
+% SEE ALSO
+% 
+%  som_write_cod    Writes a map struct into a file in SOM_PAK format.
+%  som_read_data    Reads data from an ascii file.
+%  som_write_data   Writes data struct into a file in SOM_PAK format.
+%  som_map_struct   Creates map 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 juuso 151199 250400
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%% check arguments
+
+error(nargchk(1, 1, nargin))  % check no. of input args is correct
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%% initialize variables
+
+lnum           = 0;    % codebook vector counter
+comment_start  = '#';  % the char a SOM_PAK command line starts with
+comp_name_line = '#n'; % string used to start a special command line,
+                       % which contains names of each component
+
+% open input file
+
+fid = fopen(filename);
+if fid < 0, error(['Cannot open ' filename]); end
+ 
+% read header line
+
+ok_cnt = 0;
+lin = fgetl(fid); li = lin;
+[dim c err n]  = sscanf(li, '%d%[^ \t]'); ok_cnt=ok_cnt+c; li = li(n:end);
+[lattice c err n] = sscanf(li,'%s%[^ \t]'); ok_cnt=ok_cnt+c; li = li(n:end);
+[msize(2) c err n] = sscanf(li, '%d%[^ \t]'); ok_cnt=ok_cnt+c; li = li(n:end);
+[msize(1) c err n] = sscanf(li, '%d%[^ \t]'); ok_cnt=ok_cnt+c; li = li(n:end);
+[neigh c err n] = sscanf(li, '%s%[^ \t\n]'); ok_cnt=ok_cnt+c;
+
+if ok_cnt ~= 5
+  error([ 'Invalid header line: ' lin ]); 
+end                                 
+
+% create map struct and set its fields according to header line
+
+munits = prod(msize);
+sMap   = som_map_struct(dim, 'msize', msize, ...
+			lattice, 'sheet', 'neigh', neigh);
+[sT0, ok] = som_set('som_train','algorithm','init','data_name','unknown');
+sT1       = som_set('som_train','algorithm','seq','data_name','unknown',...
+                    'neigh',neigh,'mask',ones(dim,1));
+[sMap, ok, msgs] = som_set(sMap,'name',filename,'trainhist',{sT0,sT1});
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%% read codebook from the file
+
+codebook   = zeros(munits,dim);
+labels     = cell(munits,1);
+comp_names = sMap.comp_names;
+form       = [repmat('%f',[1 dim-1]) '%f%[^ \t]'];
+
+while 1, 
+  li = fgetl(fid);                         % read next line
+  if ~isstr(li), break, end;               % is this the end of file?
+
+  [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 = li(3:end); 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, 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 line ' ...
+                 num2str(lnum+1) ': [' deblank(li) ']']),
+        end
+      end
+    else
+      error(['Only ' num2str(c) ' vector components on input file line ' ...
+             num2str(lnum+1) ' (dimension is ' num2str(dim) ')']);
+    end
+
+  else
+
+    lnum = lnum + 1;                % this was a line containing data vector
+    codebook(lnum, 1:dim) = data'; % add data to struct
+
+    % read labels
+
+    if n < length(li)
+      li = li(n:end);
+      i = 0; n = 1; c = 1;
+      while c
+        [s, c, e, n_new] = sscanf(li(n:end), '%s%[^ \t]');
+        if c, i = i + 1; labels{lnum, i} = s; n = n + n_new - 1; end
+      end
+    end
+  end
+end
+
+% close the input file
+
+if fclose(fid) < 0
+  error(['Cannot close file ' filename]); 
+else
+  fprintf(2, '\rmap read ok         \n');
+end
+
+% check that the number of lines read was correct
+
+if lnum ~= munits
+  error(['Illegal number of map units: ' num2str(lnum) ' (should be ' num2str(munits) ').']);
+end
+
+% set values
+
+% in SOM_PAK the xy-indexing is used, while in Matlab ij-indexing
+% therefore, the codebook vectors have to be reorganized 
+
+order = reshape([1:munits],msize);
+order = reshape(order',[munits 1]);
+codebook(order,:) = codebook;
+labels(order,:) = labels; 
+
+sMap.codebook   = codebook;
+sMap.labels     = labels;
+sMap.comp_names = comp_names;
+
+return;
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%