diff toolboxes/MIRtoolbox1.3.2/somtoolbox/som_topol_struct.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_topol_struct.m	Tue Feb 10 15:05:51 2015 +0000
@@ -0,0 +1,272 @@
+function sTopol = som_topol_struct(varargin)
+
+%SOM_TOPOL_STRUCT Default values for SOM topology.
+%
+% sT = som_topol_struct([[argID,] value, ...])
+%
+%  sTopol = som_topol_struct('data',D); 
+%  sTopol = som_topol_struct('data',D,'munits',200); 
+%  sTopol = som_topol_struct(sTopol); 
+%  sTopol = som_topol_struct; 
+% 
+%  Input and output arguments ([]'s are optional): 
+%    [argID,  (string) Default map topology depends on a number of 
+%     value]  (varies) factors (see below). These are given as a 
+%                      argument ID - argument value pairs, listed below.
+%
+%    sT       (struct) The ready topology struct.
+%
+% Topology struct contains values for map size, lattice (default is 'hexa')
+% and shape (default is 'sheet'). Map size depends on training data and the
+% number of map units. The number of map units depends on number of training
+% samples.
+%
+% Here are the valid argument IDs and corresponding values. The values which
+% are unambiguous (marked with '*') can be given without the preceeding argID.
+%  'dlen'         (scalar) length of the training data
+%  'data'         (matrix) the training data
+%                *(struct) the training data
+%  'munits'       (scalar) number of map units
+%  'msize'        (vector) map size
+%  'lattice'     *(string) map lattice: 'hexa' or 'rect'
+%  'shape'       *(string) map shape: 'sheet', 'cyl' or 'toroid'
+%  'topol'       *(struct) incomplete topology struct: its empty fields 
+%                          will be given values
+%  'som_topol','sTopol'    = 'topol'
+%
+% For more help, try 'type som_topol_struct' or check out online documentation.
+% See also SOM_SET, SOM_TRAIN_STRUCT, SOM_MAKE.
+
+%%%%%%%%%%%%% DETAILED DESCRIPTION %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% som_topol_struct
+%
+% PURPOSE
+%
+% Default values for map topology and training parameters.
+%
+% SYNTAX
+%
+%  sT = som_topol_struct('argID',value,...);
+%  sT = som_topol_struct(value,...);
+%
+% DESCRIPTION
+%
+% This function is used to give sensible values for map topology (ie. map
+% size). The topology struct is returned. 
+%
+% The topology struct has three fields: '.msize', '.lattice' and
+% '.shape'. Of these, default value for '.lattice' is 'hexa' and for
+% '.shape' 'sheet'. Only the '.msize' field depends on the optional
+% arguments: 'dlen', 'munits' and 'data'.  The value for '.msize' field is
+% determined as follows.
+%
+% First, the number of map units is determined (unless it is given). A
+% heuristic formula of 'munits = 5*sqrt(dlen)' is used to calculate
+% it. After this, the map size is determined. Basically, the two biggest
+% eigenvalues of the training data are calculated and the ratio between
+% sidelengths of the map grid is set to the square root of this ratio. The
+% actual sidelengths are then set so that their product is as close to the
+% desired number of map units as possible. If the lattice of the grid is
+% 'hexa', the ratio is modified a bit to take it into account. If the
+% lattice is 'hexa' and shape is 'toroid', the map size along the first axis
+% must be even.
+%  
+% OPTIONAL INPUT ARGUMENTS 
+%
+%  argID (string) Argument identifier string (see below).
+%  value (varies) Value for the argument (see below).
+%
+%  The optional arguments can be given as 'argID',value -pairs. If an
+%  argument is given value multiple times, the last one is
+%  used. The valid IDs and corresponding values are listed below. The values 
+%  which are unambiguous (marked with '*') can be given without the 
+%  preceeding argID.
+%
+%  'dlen'         (scalar) length of the training data
+%  'data'         (matrix) the training data
+%                *(struct) the training data
+%  'munits'       (scalar) number of map units
+%  'msize'        (vector) map size
+%  'lattice'     *(string) map lattice: 'hexa' or 'rect'
+%  'shape'       *(string) map shape: 'sheet', 'cyl' or 'toroid'
+%  'topol'       *(struct) incomplete topology struct: its empty fields 
+%                          will be given values
+%  'som_topol','sTopol'    = 'topol'
+%
+% OUTPUT ARGUMENTS
+% 
+%  sT     (struct) The topology struct.
+%
+% EXAMPLES
+%
+%  The most important optional argument for the default topology is 'data'.
+%  To get a default topology (given data) use:
+%
+%    sTopol = som_topol_struct('data',D); 
+%
+%  This sets lattice to its default value 'hexa'. If you want to have a
+%  'rect' lattice instead: 
+%
+%    sTopol = som_topol_struct('data',D,'lattice','rect');
+%     or 
+%    sTopol = som_topol_struct('data',D,'rect');
+%
+%  If you want to have (close to) a specific number of map units, e.g. 100: 
+%
+%    sTopol = som_topol_struct('data',D,'munits',100);
+%
+% SEE ALSO
+%
+%  som_make         Initialize and train a map using default parameters.
+%  som_train_struct Default training parameters.
+%  som_randinint    Random initialization algorithm.
+%  som_lininit      Linear initialization algorithm.
+%  som_seqtrain     Sequential training algorithm.
+%  som_batchtrain   Batch training algorithm.
+
+% Copyright (c) 1999-2000 by the SOM toolbox programming team.
+% http://www.cis.hut.fi/projects/somtoolbox/
+
+% Version 2.0alpha juuso 060898 250399 070499 050899 240801
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%% check arguments
+
+% initialize
+sTopol = som_set('som_topol','lattice','hexa','shape','sheet'); 
+D = [];
+dlen = NaN;
+dim = 2; 
+munits = NaN;
+
+% varargin
+i=1; 
+while i<=length(varargin), 
+  argok = 1; 
+  if ischar(varargin{i}), 
+    switch varargin{i}, 
+     case 'dlen',       i=i+1; dlen = varargin{i}; 
+     case 'munits',     i=i+1; munits = varargin{i}; sTopol.msize = 0;
+     case 'msize',      i=i+1; sTopol.msize = varargin{i}; 
+     case 'lattice',    i=i+1; sTopol.lattice = varargin{i}; 
+     case 'shape',      i=i+1; sTopol.shape = varargin{i}; 
+     case 'data',       
+      i=i+1; 
+      if isstruct(varargin{i}), D = varargin{i}.data; 
+      else D = varargin{i}; 
+      end
+      [dlen dim] = size(D); 
+     case {'hexa','rect'}, sTopol.lattice = varargin{i}; 
+     case {'sheet','cyl','toroid'}, sTopol.shape = varargin{i};
+     case {'som_topol','sTopol','topol'}, 
+      i=i+1;
+      if ~isempty(varargin{i}.msize) & prod(varargin{i}.msize), 
+	sTopol.msize = varargin{i}.msize; 
+      end
+      if ~isempty(varargin{i}.lattice), sTopol.lattice = varargin{i}.lattice; end   
+      if ~isempty(varargin{i}.shape), sTopol.shape = varargin{i}.shape; end
+     otherwise argok=0; 
+    end
+  elseif isstruct(varargin{i}) & isfield(varargin{i},'type'), 
+    switch varargin{i}.type, 
+     case 'som_topol',
+      if ~isempty(varargin{i}.msize) & prod(varargin{i}.msize), 
+	sTopol.msize = varargin{i}.msize; 
+      end
+      if ~isempty(varargin{i}.lattice), sTopol.lattice = varargin{i}.lattice; end   
+      if ~isempty(varargin{i}.shape), sTopol.shape = varargin{i}.shape; end
+     case 'som_data', 
+      D = varargin{i}.data; 
+      [dlen dim] = size(D);       
+     otherwise argok=0; 
+    end
+  else
+    argok = 0; 
+  end
+  if ~argok, 
+    disp(['(som_topol_struct) Ignoring invalid argument #' num2str(i)]); 
+  end
+  i = i+1; 
+end
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%% action - topology struct
+
+% lattice and shape set already, so if msize is also set, there's
+% nothing else to do
+if prod(sTopol.msize) & ~isempty(sTopol.msize), return; end
+
+% otherwise, decide msize 
+% first (if necessary) determine the number of map units (munits)
+if isnan(munits), 
+  if ~isnan(dlen), 
+    munits = ceil(5 * dlen^0.5); % this is just one way to make a guess...
+  else
+    munits = 100; % just a convenient value
+  end
+end
+
+% then determine the map size (msize)
+if dim == 1, % 1-D data
+
+  sTopol.msize = [1 ceil(munits)]; 
+
+elseif size(D,1)<2, % eigenvalues cannot be determined since there's no data
+
+  sTopol.msize = round(sqrt(munits)); 
+  sTopol.msize(2) = round(munits/sTopol.msize(1));
+
+else % determine map size based on eigenvalues
+  
+  % initialize xdim/ydim ratio using principal components of the input
+  % space; the ratio is the square root of ratio of two largest eigenvalues	
+  
+  % autocorrelation matrix
+  A = zeros(dim)+Inf;
+  for i=1:dim, D(:,i) = D(:,i) - mean(D(isfinite(D(:,i)),i)); end  
+  for i=1:dim, 
+    for j=i:dim, 
+      c = D(:,i).*D(:,j); c = c(isfinite(c));
+      A(i,j) = sum(c)/length(c); A(j,i) = A(i,j); 
+    end
+  end  
+  % take mdim first eigenvectors with the greatest eigenvalues
+  [V,S]   = eig(A);
+  eigval  = diag(S);
+  [y,ind] = sort(eigval); 
+  eigval  = eigval(ind);
+  
+  %me     = mean(D);
+  %D      = D - me(ones(length(ind),1),:); % remove mean from data
+  %eigval = sort(eig((D'*D)./size(D,1))); 
+  if eigval(end)==0 | eigval(end-1)*munits<eigval(end), 
+    ratio = 1; 
+  else
+    ratio  = sqrt(eigval(end)/eigval(end-1)); % ratio between map sidelengths
+  end
+  
+  % in hexagonal lattice, the sidelengths are not directly 
+  % proportional to the number of units since the units on the 
+  % y-axis are squeezed together by a factor of sqrt(0.75)
+  if strcmp(sTopol.lattice,'hexa'), 
+    sTopol.msize(2)  = min(munits, round(sqrt(munits / ratio * sqrt(0.75))));
+  else
+    sTopol.msize(2)  = min(munits, round(sqrt(munits / ratio)));
+  end
+  sTopol.msize(1)  = round(munits / sTopol.msize(2));
+  
+  % if actual dimension of the data is 1, make the map 1-D    
+  if min(sTopol.msize) == 1, sTopol.msize = [1 max(sTopol.msize)]; end;
+  
+  % a special case: if the map is toroid with hexa lattice, 
+  % size along first axis must be even
+  if strcmp(sTopol.lattice,'hexa') & strcmp(sTopol.shape,'toroid'), 
+    if mod(sTopol.msize(1),2), sTopol.msize(1) = sTopol.msize(1) + 1; end
+  end
+
+end
+  
+return;
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%