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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;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%