diff toolboxes/MIRtoolbox1.3.2/somtoolbox/som_umat.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_umat.m	Tue Feb 10 15:05:51 2015 +0000
@@ -0,0 +1,362 @@
+function U = som_umat(sMap, varargin)
+
+%SOM_UMAT Compute unified distance matrix of self-organizing map.
+%
+% U = som_umat(sMap, [argID, value, ...])
+%
+%  U = som_umat(sMap);  
+%  U = som_umat(M,sTopol,'median','mask',[1 1 0 1]);
+%
+%  Input and output arguments ([]'s are optional): 
+%   sMap     (struct) map struct or
+%            (matrix) the codebook matrix of the map
+%   [argID,  (string) See below. The values which are unambiguous can 
+%    value]  (varies) be given without the preceeding argID.
+%
+%   U        (matrix) u-matrix of the self-organizing map 
+%
+% Here are the valid argument IDs and corresponding values. The values which
+% are unambiguous (marked with '*') can be given without the preceeding argID.
+%   'mask'       (vector) size dim x 1, weighting factors for different 
+%                         components (same as BMU search mask)
+%   'msize'      (vector) map grid size
+%   'topol'     *(struct) topology struct
+%   'som_topol','sTopol' = 'topol'
+%   'lattice'   *(string) map lattice, 'hexa' or 'rect'
+%   'mode'      *(string) 'min','mean','median','max', default is 'median'
+%
+% NOTE! the U-matrix is always calculated for 'sheet'-shaped map and
+% the map grid must be at most 2-dimensional.
+% 
+% For more help, try 'type som_umat' or check out online documentation.
+% See also SOM_SHOW, SOM_CPLANE.
+
+%%%%%%%%%%%%% DETAILED DESCRIPTION %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% som_umat
+%
+% PURPOSE
+%
+% Computes the unified distance matrix of a SOM.
+%
+% SYNTAX
+%
+%  U = som_umat(sM)  
+%  U = som_umat(...,'argID',value,...)
+%  U = som_umat(...,value,...)
+%
+% DESCRIPTION
+%
+% Compute and return the unified distance matrix of a SOM. 
+% For example a case of 5x1 -sized map:
+%            m(1) m(2) m(3) m(4) m(5)
+% where m(i) denotes one map unit. The u-matrix is a 9x1 vector:
+%    u(1) u(1,2) u(2) u(2,3) u(3) u(3,4) u(4) u(4,5) u(5) 
+% where u(i,j) is the distance between map units m(i) and m(j)
+% and u(k) is the mean (or minimum, maximum or median) of the 
+% surrounding values, e.g. u(3) = (u(2,3) + u(3,4))/2. 
+%
+% Note that the u-matrix is always calculated for 'sheet'-shaped map and
+% the map grid must be at most 2-dimensional.
+%
+% REFERENCES
+%
+% Ultsch, A., Siemon, H.P., "Kohonen's Self-Organizing Feature Maps
+%   for Exploratory Data Analysis", in Proc. of INNC'90,
+%   International Neural Network Conference, Dordrecht,
+%   Netherlands, 1990, pp. 305-308.
+% Kohonen, T., "Self-Organizing Map", 2nd ed., Springer-Verlag, 
+%    Berlin, 1995, pp. 117-119. 
+% Iivarinen, J., Kohonen, T., Kangas, J., Kaski, S., "Visualizing 
+%   the Clusters on the Self-Organizing Map", in proceedings of
+%   Conference on Artificial Intelligence Research in Finland,
+%   Helsinki, Finland, 1994, pp. 122-126.
+% Kraaijveld, M.A., Mao, J., Jain, A.K., "A Nonlinear Projection
+%   Method Based on Kohonen's Topology Preserving Maps", IEEE
+%   Transactions on Neural Networks, vol. 6, no. 3, 1995, pp. 548-559.
+% 
+% REQUIRED INPUT ARGUMENTS
+%
+%  sM (struct) SOM Toolbox struct or the codebook matrix of the map.
+%     (matrix) The matrix may be 3-dimensional in which case the first 
+%              two dimensions are taken for the map grid dimensions (msize).
+%
+% OPTIONAL INPUT ARGUMENTS
+%
+%  argID (string) Argument identifier string (see below).
+%  value (varies) Value for the argument (see below).
+%
+%  The optional arguments are given as 'argID',value -pairs. If the 
+%  value is unambiguous, it can be given without the preceeding argID.
+%  If an argument is given value multiple times, the last one is used. 
+%
+%  Below is the list of valid arguments: 
+%   'mask'      (vector) mask to be used in calculating
+%                        the interunit distances, size [dim  1]. Default is 
+%                        the one in sM (field sM.mask) or a vector of
+%                        ones if only a codebook matrix was given.
+%   'topol'     (struct) topology of the map. Default is the one
+%                        in sM (field sM.topol).
+%   'sTopol','som_topol' (struct) = 'topol'
+%   'msize'     (vector) map grid dimensions
+%   'lattice'   (string) map lattice 'rect' or 'hexa'
+%   'mode'      (string) 'min', 'mean', 'median' or 'max'
+%                        Map unit value computation method. In fact, 
+%                        eval-function is used to evaluate this, so 
+%                        you can give other computation methods as well.
+%                        Default is 'median'. 
+%
+% OUTPUT ARGUMENTS
+%
+%  U   (matrix) the unified distance matrix of the SOM 
+%               size 2*n1-1 x 2*n2-1, where n1 = msize(1) and n2 = msize(2)
+%
+% EXAMPLES
+%
+%  U = som_umat(sM);  
+%  U = som_umat(sM.codebook,sM.topol,'median','mask',[1 1 0 1]);
+%  U = som_umat(rand(10,10,4),'hexa','rect'); 
+% 
+% SEE ALSO
+%
+%  som_show    show the selected component planes and the u-matrix
+%  som_cplane  draw a 2D unified distance matrix
+
+% Copyright (c) 1997-2000 by the SOM toolbox programming team.
+% http://www.cis.hut.fi/projects/somtoolbox/
+
+% Version 1.0beta juuso 260997
+% Version 2.0beta juuso 151199, 151299, 200900
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%% check arguments
+
+error(nargchk(1, Inf, nargin));  % check no. of input arguments is correct
+
+% sMap
+if isstruct(sMap), 
+  M = sMap.codebook;
+  sTopol = sMap.topol; 
+  mask = sMap.mask;
+elseif isnumeric(sMap),
+  M = sMap; 
+  si = size(M);
+  dim = si(end);
+  if length(si)>2, msize = si(1:end-1);
+  else msize = [si(1) 1];
+  end
+  munits = prod(msize);
+  sTopol = som_set('som_topol','msize',msize,'lattice','rect','shape','sheet'); 
+  mask = ones(dim,1);
+  M = reshape(M,[munits,dim]);
+end
+mode = 'median';
+
+% varargin
+i=1; 
+while i<=length(varargin), 
+  argok = 1; 
+  if ischar(varargin{i}), 
+    switch varargin{i}, 
+      % argument IDs
+     case 'mask',       i=i+1; mask = varargin{i}; 
+     case 'msize',      i=i+1; sTopol.msize = varargin{i}; 
+     case 'lattice',    i=i+1; sTopol.lattice = varargin{i};
+     case {'topol','som_topol','sTopol'}, i=i+1; sTopol = varargin{i};
+     case 'mode',       i=i+1; mode = varargin{i};
+      % unambiguous values
+     case {'hexa','rect'}, sTopol.lattice = varargin{i};
+     case {'min','mean','median','max'}, mode = varargin{i};
+     otherwise argok=0; 
+    end
+  elseif isstruct(varargin{i}) & isfield(varargin{i},'type'), 
+    switch varargin{i}(1).type, 
+     case 'som_topol', sTopol = varargin{i};
+     case 'som_map',   sTopol = varargin{i}.topol;
+     otherwise argok=0; 
+    end
+  else
+    argok = 0; 
+  end
+  if ~argok, 
+    disp(['(som_umat) Ignoring invalid argument #' num2str(i+1)]); 
+  end
+  i = i+1; 
+end
+
+% check
+[munits dim] = size(M);
+if prod(sTopol.msize)~=munits, 
+  error('Map grid size does not match the number of map units.')
+end
+if length(sTopol.msize)>2, 
+  error('Can only handle 1- and 2-dimensional map grids.')
+end
+if prod(sTopol.msize)==1,
+  warning('Only one codebook vector.'); U = []; return;
+end
+if ~strcmp(sTopol.shape,'sheet'), 
+  disp(['The ' sTopol.shape ' shape of the map ignored. Using sheet instead.']);
+end
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%% initialize variables
+
+y = sTopol.msize(1);
+x = sTopol.msize(2);
+lattice = sTopol.lattice;
+shape = sTopol.shape;
+M = reshape(M,[y x dim]);
+
+ux = 2 * x - 1; 
+uy = 2 * y - 1;
+U  = zeros(uy, ux);
+
+calc = sprintf('%s(a)',mode);
+
+if size(mask,2)>1, mask = mask'; end
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%% u-matrix computation
+
+% distances between map units
+
+if strcmp(lattice, 'rect'), % rectangular lattice
+  
+  for j=1:y, for i=1:x,
+      if i<x, 
+	dx = (M(j,i,:) - M(j,i+1,:)).^2; % horizontal
+	U(2*j-1,2*i) = sqrt(mask'*dx(:));
+      end 
+      if j<y, 
+	dy = (M(j,i,:) - M(j+1,i,:)).^2; % vertical
+	U(2*j,2*i-1) = sqrt(mask'*dy(:));
+      end
+      if j<y & i<x,	
+	dz1 = (M(j,i,:) - M(j+1,i+1,:)).^2; % diagonals
+	dz2 = (M(j+1,i,:) - M(j,i+1,:)).^2;
+	U(2*j,2*i) = (sqrt(mask'*dz1(:))+sqrt(mask'*dz2(:)))/(2 * sqrt(2));
+      end
+    end
+  end
+
+elseif strcmp(lattice, 'hexa') % hexagonal lattice
+
+  for j=1:y, 
+    for i=1:x,
+      if i<x,
+	dx = (M(j,i,:) - M(j,i+1,:)).^2; % horizontal
+	U(2*j-1,2*i) = sqrt(mask'*dx(:));
+      end
+      
+      if j<y, % diagonals
+	dy = (M(j,i,:) - M(j+1,i,:)).^2;
+	U(2*j,2*i-1) = sqrt(mask'*dy(:));	
+	
+	if rem(j,2)==0 & i<x,
+	  dz= (M(j,i,:) - M(j+1,i+1,:)).^2; 
+	  U(2*j,2*i) = sqrt(mask'*dz(:));
+	elseif rem(j,2)==1 & i>1,
+	  dz = (M(j,i,:) - M(j+1,i-1,:)).^2; 
+	  U(2*j,2*i-2) = sqrt(mask'*dz(:));
+	end
+      end
+    end
+  end
+  
+end
+
+% values on the units
+
+if (uy == 1 | ux == 1),
+  % in 1-D case, mean is equal to median 
+
+  ma = max([ux uy]);
+  for i = 1:2:ma,
+    if i>1 & i<ma, 
+      a = [U(i-1) U(i+1)]; 
+      U(i) = eval(calc);
+    elseif i==1, U(i) = U(i+1); 
+    else U(i) = U(i-1); % i==ma
+    end
+  end    
+
+elseif strcmp(lattice, 'rect')
+
+  for j=1:2:uy, 
+    for i=1:2:ux,
+      if i>1 & j>1 & i<ux & j<uy,    % middle part of the map
+	a = [U(j,i-1) U(j,i+1) U(j-1,i) U(j+1,i)];        
+      elseif j==1 & i>1 & i<ux,        % upper edge
+	a = [U(j,i-1) U(j,i+1) U(j+1,i)];
+      elseif j==uy & i>1 & i<ux,       % lower edge
+	a = [U(j,i-1) U(j,i+1) U(j-1,i)];
+      elseif i==1 & j>1 & j<uy,        % left edge
+	a = [U(j,i+1) U(j-1,i) U(j+1,i)];
+      elseif i==ux & j>1 & j<uy,       % right edge
+	a = [U(j,i-1) U(j-1,i) U(j+1,i)];
+      elseif i==1 & j==1,              % top left corner
+	a = [U(j,i+1) U(j+1,i)];
+      elseif i==ux & j==1,             % top right corner
+	a = [U(j,i-1) U(j+1,i)];
+      elseif i==1 & j==uy,             % bottom left corner
+	a = [U(j,i+1) U(j-1,i)];
+      elseif i==ux & j==uy,            % bottom right corner
+	a = [U(j,i-1) U(j-1,i)];
+      else
+	a = 0;
+      end
+      U(j,i) = eval(calc);
+    end
+  end
+
+elseif strcmp(lattice, 'hexa')
+  
+  for j=1:2:uy, 
+    for i=1:2:ux,
+      if i>1 & j>1 & i<ux & j<uy,      % middle part of the map
+	a = [U(j,i-1) U(j,i+1)];
+	if rem(j-1,4)==0, a = [a, U(j-1,i-1) U(j-1,i) U(j+1,i-1) U(j+1,i)];
+	else a = [a, U(j-1,i) U(j-1,i+1) U(j+1,i) U(j+1,i+1)]; end       
+      elseif j==1 & i>1 & i<ux,        % upper edge
+	a = [U(j,i-1) U(j,i+1) U(j+1,i-1) U(j+1,i)];
+      elseif j==uy & i>1 & i<ux,       % lower edge
+	a = [U(j,i-1) U(j,i+1)];
+	if rem(j-1,4)==0, a = [a, U(j-1,i-1) U(j-1,i)];
+	else a = [a, U(j-1,i) U(j-1,i+1)]; end
+      elseif i==1 & j>1 & j<uy,        % left edge
+	a = U(j,i+1);
+	if rem(j-1,4)==0, a = [a, U(j-1,i) U(j+1,i)];
+	else a = [a, U(j-1,i) U(j-1,i+1) U(j+1,i) U(j+1,i+1)]; end
+      elseif i==ux & j>1 & j<uy,       % right edge
+	a = U(j,i-1);
+	if rem(j-1,4)==0, a=[a, U(j-1,i) U(j-1,i-1) U(j+1,i) U(j+1,i-1)];
+	else a = [a, U(j-1,i) U(j+1,i)]; end
+      elseif i==1 & j==1,              % top left corner
+	a = [U(j,i+1) U(j+1,i)];
+      elseif i==ux & j==1,             % top right corner
+	a = [U(j,i-1) U(j+1,i-1) U(j+1,i)];
+      elseif i==1 & j==uy,             % bottom left corner
+	if rem(j-1,4)==0, a = [U(j,i+1) U(j-1,i)];
+	else a = [U(j,i+1) U(j-1,i) U(j-1,i+1)]; end
+      elseif i==ux & j==uy,            % bottom right corner
+	if rem(j-1,4)==0, a = [U(j,i-1) U(j-1,i) U(j-1,i-1)];
+	else a = [U(j,i-1) U(j-1,i)]; end
+      else
+	a=0;
+      end
+      U(j,i) = eval(calc);
+    end
+  end
+end
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%% normalization between [0,1]
+
+% U = U - min(min(U)); 
+% ma = max(max(U)); if ma > 0, U = U / ma; end
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
+