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

first hg version after svn

+function sC = som_clstruct(Z,varargin)
+
+%SOM_CLSTRUCT Create a clustering struct or set its field values.
+%
+%  sC = som_clstruct(Z, [argID, value, ...]) 
+%
+%    Z  = linkage(pdist(sM.codebook));
+%    sC = som_clstruct(Z); 
+%    sC = som_clstruct(sC,'coord',som_vis_coords(lattice,msize));
+%    sC = som_clstruct(sC,'color',som_colorcode(sM));
+%    sC = som_clstruct(sC,'base',sC.base(som_bmus(sM,sD)));
+%
+%  Input and output arguments ([]'s are optional): 
+%   Z         (matrix) size clen-1 x 3, where clen is the number of 
+%                      base clusters. This is a clustering matrix 
+%                      similar to that produced by LINKAGE in 
+%                      Statistical Toolbox. See SOM_LINKAGE.
+%             (struct) clustering struct (as produced by this function)
+%   [argID,   (string) See below. Each pair is the fieldname and 
+%    value]   (varies) the value to be given to that field.
+%
+%   sC        (struct) clustering struct
+% 
+%   The clustering struct is based on the assumption that there 
+%   is a base partitioning of the SOM (or data) which is saved in 
+%   the .base field of the struct. Then a hierarchical clustering
+%   is applied to this base partitioning. The results are saved to 
+%   .tree field of the struct. Each cluster (base and combined)
+%   has also three properties: height, coordinate and color, which 
+%   are used in the visualizations. The fields of the struct are:
+%     .type   (string) 'som_clustering'
+%     .name   (string) Identifier for the clustering.
+%     .tree   (matrix) Size clen-1 x 3, as argument Z above. 
+%     .base   (vector) Size dlen x 1, the basic groups of data 
+%                      forming the base clusters, e.g. as a result 
+%                      of partitive clustering. Allowed values are 
+%                       1:clen indicating the base cluster
+%                              to which the data belongs to. 
+%                       NaN    indicating that the data has
+%                              been ignored in the clustering
+%                      By default [1:clen]. 
+%     .height (vector) Size 2*clen-1 x 1, (clustering) height for each 
+%                      cluster. By default 0 for each base cluster and
+%                      .tree(:,3) for the others.
+%     .coord  (matrix) Size 2*clen-1 x *, coordinate for each cluster, 
+%                      By default the coordinates are set so that 
+%                      the base clusters are ordered on a line, and the
+%                      position of each combined cluster is average of 
+%                      the base clusters that constitute it.
+%     .color  (matrix) Size 2*clen-1 x 3, color for each cluster. 
+%                      By default the colors are set so that the 
+%                      base clusters are ordered on a line, like above,
+%                      and then colors are assigned from the 'hsv' 
+%                      colormap to the base clusters. The color
+%                      of each combined cluster is average as above.
+%
+% Height, coord and color can also be specified in alternate forms:
+%   'height' (vector) size 2*clen-1 x 1, if given explicitly
+%                     size clen-1 x 1, specified heights of the 
+%                          combined clusters (the base cluster heights
+%                          are all = 0)
+%                     size 0 x 0, default value is used
+%   'coord'  (matrix) size 2*clen-1 x *, if given explicitly
+%                     size clen x *, to give coordinates for base 
+%                          clusters; the coordinate of combined clusters
+%                          are averaged from these
+%                     size dlen x *, to give coordinates of the 
+%                          original data: the cluster coordinates are
+%                          averaged from these based on base clusters
+%                     size 0 x 0, default value is used
+%   'color'  (matrix) as 'coord'
+%
+% See also  SOM_CLPLOT, SOM_CLVALIDITY, SOM_CLGET, SOM_CLLINKAGE.
+
+% Copyright (c) 2000 by the SOM toolbox programming team.
+% Contributed to SOM Toolbox on XXX by Juha Vesanto
+% http://www.cis.hut.fi/projects/somtoolbox/
+
+% Version 2.0beta juuso 180800
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+if isstruct(Z), 
+  base = Z.base; 
+  color = Z.color; 
+  coord = Z.coord; 
+  height = Z.height; 
+  name = Z.name; 
+  Z = Z.tree; 
+else
+  base  = []; 
+  color = []; 
+  coord = []; 
+  height = []; 
+  name = ''; 
+end    
+clen  = size(Z,1)+1; 
+
+i=1; 
+while i<=length(varargin), 
+  argok = 1; 
+  if ischar(varargin{i}), 
+    switch varargin{i}, 
+     case 'tree',   i=i+1; Z = varargin{i}; clen = size(Z,1)+1;
+     case 'base',   i=i+1; base = varargin{i}; 
+     case 'color',  i=i+1; color = varargin{i}; 
+     case 'coord',  i=i+1; coord = varargin{i}; 
+     case 'height', i=i+1; height = varargin{i}; 
+     case 'name',   i=i+1; name = varargin{i}; 
+     otherwise argok=0; 
+    end
+  else argok = 0; 
+  end
+  if ~argok, disp(['(som_clstruct) Ignoring invalid argument #' num2str(i+1)]); end
+  i = i+1; 
+end
+
+if isempty(base), 
+  dlen = clen; 
+  base = 1:dlen; 
+else
+  dlen = length(base); 
+  if any(base)>clen | any(base)<1, error('Incorrect base partition vector.'); end
+end
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%% analysis of hierarchy
+
+% order of base clusters
+order = 2*clen-1; 
+nonleaves = 1; 
+while any(nonleaves), 
+  j = nonleaves(1); 
+  ch = Z(order(j)-clen,1:2);
+  if j==1, oleft = []; else oleft = order(1:(j-1)); end
+  if j==length(order), oright = []; else oright = order((j+1):length(order)); end
+  order = [oleft, ch, oright];
+  nonleaves = find(order>clen); 
+end
+
+% base cluster indeces for each non-base cluster
+basecl = cell(clen-1,1); 
+for i=1:clen-1, 
+  c1 = Z(i,1); if c1>clen, c1 = basecl{c1-clen}; end
+  c2 = Z(i,2); if c2>clen, c2 = basecl{c2-clen}; end
+  basecl{i} = [c1 c2];   
+end
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%% set coordinates, color and height and make the struct
+
+% coordinates
+if size(coord,1)==2*clen-1, % this is ok already
+else
+  if size(coord,1)==0, % the default    
+    [dummy,coord] = sort(order); 
+    coord = coord'; 
+  elseif size(coord,1)==dlen & dlen>clen, % coordinates given for original data
+    codata = coord; 
+    coord = zeros(clen,size(coord,2)); 
+    for i=1:clen, coord(i,:) = mean(codata(find(base==i),:),1); end  
+  end
+  if size(coord,1)==clen, % average from base clusters
+    coord = [coord; zeros(clen-1,size(coord,2))]; 
+    for i=1:clen-1, coord(i+clen,:) = mean(coord(basecl{i},:),1); end
+  else
+    error('Incorrect coordinate matrix.'); 
+  end
+end
+
+% color
+if size(color,1)==2*clen-1, % this is ok already
+else
+  if size(color,1)==0, % the default
+    color(order,:) = hsv(length(order)); 
+  elseif size(color,1)==dlen & dlen>clen, % colors given for original data
+    codata = color; 
+    color = zeros(clen,3); 
+    for i=1:clen, color(i,:) = mean(codata(find(base==i),:),1); end  
+  end
+  if size(color,1)==clen, % average from base clusters
+    color = [color; zeros(clen-1,3)]; 
+    for i=1:clen-1, color(i+clen,:) = mean(color(basecl{i},:),1); end
+  else
+    error('Incorrect color matrix.'); 
+  end
+end
+
+% height 
+if isempty(height), 
+  height = [zeros(clen,1); Z(:,3)]; 
+elseif length(height)==clen-1, 
+  if size(height,2)==clen-1, height = height'; end
+  height = [zeros(clen,1); height]; 
+elseif length(height)~=2*clen-1, 
+  error('Incorrect height vector.'); 
+end
+
+% make the struct
+sC = struct('type','som_clustering',...
+	    'name',name,'base',base,'tree',Z,...
+	    'color',color,'coord',coord,'height',height); 
+return; 
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%  
+