diff toolboxes/MIRtoolbox1.3.2/somtoolbox/som_cllinkage.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_cllinkage.m	Tue Feb 10 15:05:51 2015 +0000
@@ -0,0 +1,272 @@
+function sC = som_cllinkage(sM,varargin)
+
+%SOM_CLLINKAGE Make a hierarchical linkage of the SOM map units.
+%
+% sC = som_cllinkage(sM, [[argID,] value, ...])
+%  
+%  sC = som_cllinkage(sM);
+%  sC = som_cllinkage(D,'complete');
+%  sC = som_cllinkage(sM,'single','ignore',find(~som_hits(sM,D)));
+%  sC = som_cllinkage(sM,pdist(sM.codebook,'mahal'));
+%  som_clplot(sC); 
+%
+%  Input and output arguments ([]'s are optional):
+%   sM       (struct) map or data struct to be clustered
+%            (matrix) size dlen x dim, a data set: the matrix must not
+%                     contain any NaN's!
+%   [argID,  (string) See below. The values which are unambiguous can 
+%    value]  (varies) be given without the preceeding argID.
+%
+%   sC       (struct) a clustering struct with e.g. the following fields
+%                     (for more information see SOMCL_STRUCT)
+%     .base  (vector) if base partitioning is given, this is a newly 
+%                     coded version of it so that the cluster indices
+%                     go from 1 to the number of clusters. 
+%     .tree  (matrix) size clen-1 x 3, the linkage info
+%                     Z(i,1) and Z(i,2) hold the indeces of clusters 
+%                     combined on level i (starting from bottom). The new
+%                     cluster has index dlen+i. The initial cluster 
+%                     index of each unit is its linear index in the 
+%                     original data matrix. Z(i,3) is the distance
+%                     between the combined clusters. See LINKAGE
+%                     function in the Statistics Toolbox.
+%     
+% Here are the valid argument IDs and corresponding values. The values 
+% which are unambiguous (marked with '*') can be given without the
+% preceeding argID.
+%   'topol'   *(struct) topology struct
+%   'connect' *(string) 'neighbors' or 'any' (default), whether the
+%                       connections should be allowed only between 
+%                       neighbors or between any vectors
+%              (matrix) size dlen x dlen indicating the connections
+%                       between vectors
+%   'linkage' *(string) the linkage criteria to use: 'single' (the
+%                       default), 'average', 'complete', 'centroid', or 'ward' 
+%   'dist'     (matrix) size dlen x dlen, pairwise distance matrix to 
+%                       be used instead of euclidian distances
+%              (vector) as the output of PDIST function
+%              (scalar) distance norm to use (default is euclidian = 2)
+%   'mask'     (vector) size dim x 1, the search mask used to 
+%                       weight distance calculation. By default 
+%                       sM.mask or a vector of ones is used.
+%   'base'     (vector) giving the base partitioning of the data: 
+%                       base(i) = j denotes that vector i belongs to
+%                       base cluster j, and base(i) = NaN that vector
+%                       i does not belong to any cluster, but should be
+%                       ignored. At the beginning of the clustering, the 
+%                       vector of each cluster are averaged, and these
+%                       averaged vectors are then clustered using 
+%                       hierarchical clustering.
+%   'ignore'   (vector) units to be ignored (in addition to those listed
+%                       in base argument)
+%   'tracking' (scalar) 1 or 0: whether to show tracking bar or not (default = 0)
+%
+% Note that if 'connect'='neighbors' and some vector are ignored (as denoted
+% by NaNs in the base vector), there may be areas on the map which will
+% never be connected: connections across the ignored map units simply do not
+% exist. In such a case, the neighborhood is gradually increased until 
+% the areas can be connected.
+%
+% See also KMEANS_CLUSTERS, LINKAGE, PDIST, DENDROGRAM. 
+
+% Copyright (c) 2000 by Juha Vesanto
+% Contributed to SOM Toolbox on XXX by Juha Vesanto
+% http://www.cis.hut.fi/projects/somtoolbox/
+ 
+% Version 2.0beta juuso 160600 250800
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%% input arguments
+
+% the data
+if isstruct(sM), 
+  switch sM.type, 
+   case 'som_map', M = sM.codebook; sT = sM.topol; mask = sM.mask; data_name = sM.name; sTr = sM.trainhist(end); 
+   case 'som_data', M = sM.data; sT = []; mask = []; data_name = sM.name; sTr = [];
+   case 'som_topol', M = []; sT = sM; mask = []; data_name = inputname(1); 
+                     sTr = som_set('som_train','neigh','gaussian','radius_fin',1);
+   otherwise, error('Bad first argument');
+  end
+else M = sM; sT = []; mask = []; data_name = inputname(1); sTr = []; 
+end
+[dlen dim] = size(M);
+if isempty(mask), mask = ones(dim,1); end
+if any(isnan(M(:))), error('Data matrix must not have any NaNs.'); end
+
+% varargin
+q = 2; 
+Md = []; 
+linkage = 'single';
+ignore = []; 
+Ne = 'any';
+base = []; 
+tracking = 0; 
+i=1; 
+while i<=length(varargin), 
+  argok = 1; 
+  if ischar(varargin{i}), 
+    switch varargin{i}, 
+      % argument IDs
+     case {'topol','som_topol','sTopol'}, i=i+1; sT = varargin{i};
+     case 'connect', i=i+1; Ne = varargin{i};
+     case 'ignore',  i=i+1; ignore = varargin{i}; 
+     case 'dist',    i=i+1; Md = varargin{i};
+     case 'linkage', i=i+1; linkage = varargin{i};
+     case 'mask',    i=i+1; mask = varargin{i};
+     case 'tracking',i=i+1; tracking = varargin{i}; 
+     case 'base',    i=i+1; base = varargin{i};
+      % unambiguous values
+     case 'neighbors', Ne = varargin{i};
+     case 'any',       Ne = varargin{i};
+     case {'single','average','complete','neighf','centroid','ward'}, linkage = varargin{i};
+     otherwise argok=0; 
+    end
+  elseif isstruct(varargin{i}) & isfield(varargin{i},'type'), 
+    switch varargin{i}(1).type, 
+     case 'som_topol', sT = varargin{i}; 
+     otherwise argok=0; 
+    end
+  else
+    argok = 0; 
+  end
+  if ~argok, disp(['(som_cllinkage) Ignoring invalid argument #' num2str(i+1)]); end
+  i = i+1; 
+end
+
+% check distance metric
+if prod(size(Md))==1, q = Md; Md = []; end
+if ~isempty(Md) & prod(size(Md))<dlen^2, Md = squareform(Md); end    
+if prod(size(Md))>0 & any(strcmp(linkage,{'ward','centroid'})),
+  warning(['The linkage method ' linkage ' cannot be performed with precalculated distance matrix.']);
+end
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%% distance matrix and connections between units
+
+% base partition 
+if isempty(base), base = 1:dlen; end
+if ~isempty(ignore), base(ignore) = NaN; end
+cid = unique(base(isfinite(base))); 
+nc = length(cid); 
+if max(cid)>nc | min(cid)<1, 
+  b = base; for i=1:nc, base(find(b==cid(i))) = i; end
+end
+
+% initial clusters
+clinds = cell(nc,1); 
+for i=1:nc, clinds{i} = find(base==i); end
+
+% neighborhood constraint (calculate connection matrix Ne)
+if ischar(Ne),
+  switch Ne, 
+   case 'any', Ne = []; 
+   case 'neighbors', if ischar(Ne), Ne = som_unit_neighs(sT); end  
+   otherwise, error(['Unrecognized connection mode ' Ne]);
+  end
+end
+if ~isempty(Ne), l = size(Ne,1); Ne([0:l-1]*l+[1:l]) = 1; end % diagonal=1
+if all(Ne(:)>0), Ne = []; end
+
+% neighborhood function values
+if strcmp(linkage,'neighf') 
+  if isempty(sTr), error('Cannot use neighf linkage.'); end
+  q = som_unit_dists(sT).^2; 
+  r = sTr.radius_fin^2; 
+  if isnan(r) | isempty(r), r = 1; end 
+  switch sTr.neigh,
+   case 'bubble',   q = (q <= r);
+   case 'gaussian', q = exp(-q/(2*r));
+   case 'cutgauss', q = exp(-q/(2*r)) .* (q <= r);
+   case 'ep',       q = (1-q/r) .* (q <= r);
+  end
+end
+
+% mutual distances and initial cluster distances
+Cd = []; 
+if any(strcmp(linkage,{'single','average','complete','neighf'})), 
+  M = som_mdist(M,2,mask,Ne); 
+  if (nc == dlen & all(base==[1:dlen])), Cd = M; end
+end 
+if isempty(Cd), Cd = som_cldist(M,clinds,[],linkage,q,mask); end
+Cd([0:nc-1]*nc+[1:nc]) = NaN; % NaNs on the diagonal
+			      
+% check out from Ne which of the clusters are not connected
+if ~isempty(Ne) & any(strcmp(linkage,{'centroid','ward'})),
+  Clconn = sparse(nc); 
+  for i=1:nc-1, 
+    for j=i+1:nc, Clconn(i,j) = any(any(Ne(clinds{i},clinds{j}))); end
+    Clconn(i+1:nc,i) = Clconn(i,i+1:nc)'; 
+  end
+  Cd(Clconn==0) = Inf; 
+else
+  Clconn = []; 
+end
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%% construct dendrogram
+
+clen = nc; 
+cid = 1:clen; 
+Z = zeros(nc-1,3)+NaN;     % merged clusters and distance for each step
+if tracking, h = waitbar(0,'Making hierarchical clustering'); end
+
+for i=1:clen-1,
+  if tracking, waitbar(i/clen,h); end
+  
+  % find two closest clusters and combine them
+  [d,c1] = min(min(Cd));          % cluster1
+  [d,c2] = min(Cd(:,c1));         % cluster2
+  i1 = clinds{c1};                % vectors belonging to c1
+  i2 = clinds{c2};                % vectors belonging to c2
+  clinds{c1} = [i1; i2];          % insert clusters to c1 
+  Z(i,:) = [cid(c1), cid(c2), d]; % update tree info   
+  
+  % remove cluster c2
+  notc2 = [1:c2-1,c2+1:nc]; 
+  nc = nc-1; if nc<=1, break; end
+  if c1>c2, c1=c1-1; end 
+  clinds = clinds(notc2); 
+  Cd = Cd(notc2,notc2);
+  cid = cid(notc2);
+  if ~isempty(Clconn), Clconn = Clconn(notc2,notc2); end
+  
+  % update cluster distances
+  notc1 = [1:c1-1,c1+1:nc];   
+  Cd(c1,notc1) = som_cldist(M,clinds(c1),clinds(notc1),linkage,q,mask); 
+  Cd(notc1,c1) = Cd(c1,notc1)'; 
+  if ~isempty(Clconn), 
+    for j=notc1, Clconn(c1,j) = any(any(Ne(clinds{c1},clinds{j}))); end
+    Clconn(notc1,c1) = Clconn(c1,notc1)'; 
+    Cd(Clconn==0) = Inf; 
+  end
+  
+end
+
+if tracking, close(h); end
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%% return values
+
+% to maintain compatibility with Statistics Toolbox, the values in 
+% Z must be yet transformed so that they are similar to the output
+% of LINKAGE function
+
+clen = size(Z,1)+1; 
+Zs = Z;
+current_cluster = 1:clen;
+for i=1:size(Z,1),
+  Zs(i,1) = current_cluster(Z(i,1));
+  Zs(i,2) = current_cluster(Z(i,2));
+  current_cluster(Z(i,[1 2])) = clen+i;  
+end
+Z = Zs;
+
+% make a clustering struct
+name = sprintf('Clustering of %s at %s',data_name,datestr(datenum(now),0)); 
+sC = som_clstruct(Z,'base',base,'name',name); 
+
+return;
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+