Daniel@0: function [base,seed] = som_dmatclusters(sM,linkage,neigh,ignore)
Daniel@0: 
Daniel@0: % SOM_DMATCLUSTERS Cluster map based on neighbor distance matrix.
Daniel@0: %
Daniel@0: % base = som_dmatclusters(sM,linkage,neigh,ignore)
Daniel@0: %
Daniel@0: % sM        (struct) map or data struct
Daniel@0: %           (matrix) data matrix, size n x dim
Daniel@0: % [linkage] (string) 'closest', 'single', 'average', 'complete', 
Daniel@0: %                    'centroid', 'ward', and 'neighf' (last for SOM only)
Daniel@0: %                    default is 'centroid'
Daniel@0: % [neigh]   (string) 'kNN' or 'Nk' (which is valid for a SOM only)
Daniel@0: %                    for example '6NN' or 'N1'
Daniel@0: %                    default is '10NN' for a data set and 'N1' for SOM
Daniel@0: %           (matrix) 0/1 matrix of size size n x n, 1=connection exists
Daniel@0: % [ignore]  (vector) indeces of vectors to be ignored in the spreading
Daniel@0: %                    phase, empty vector by default
Daniel@0: %
Daniel@0: % base      (vector) size n x 1, cluster indeces (1...c)
Daniel@0: % seed      (vector) size c x 1, indeces of seed units for the clusters
Daniel@0: %
Daniel@0: % See also  SOM_NEIGHBORS, KMEANS_CLUSTERS, SOM_DMATMINIMA.
Daniel@0: 
Daniel@0: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Daniel@0: %% input arguments
Daniel@0: 
Daniel@0: if nargin<2 | isempty(linkage), linkage = 'centroid'; end
Daniel@0: 
Daniel@0: if nargin<3 | isempty(neigh),
Daniel@0:   if isstruct(sM) & strcmp(sM.type,'som_map'),
Daniel@0:     neigh = 'N1';
Daniel@0:   else
Daniel@0:     neigh = '10NN';
Daniel@0:   end
Daniel@0: end
Daniel@0: 
Daniel@0: if nargin<4, ignore = []; end
Daniel@0: n = size(sM.codebook,1);
Daniel@0: 
Daniel@0: % neighborhoods
Daniel@0: if ischar(neigh),
Daniel@0:   Ne = som_neighbors(sM,neigh);
Daniel@0: else
Daniel@0:   Ne = neigh;
Daniel@0: end
Daniel@0: 
Daniel@0: % find seed points
Daniel@0: seed = som_dmatminima(sM,[],Ne);
Daniel@0: 
Daniel@0: % make partition
Daniel@0: base = zeros(n,1);
Daniel@0: base(seed) = 1:length(seed);
Daniel@0: if any(ignore), base(ignore) = NaN; end
Daniel@0: base = som_clspread(sM,base,linkage,Ne,0);
Daniel@0: 
Daniel@0: % assign the ignored units, too
Daniel@0: base(isnan(base)) = 0;
Daniel@0: if any(base==0), base = som_clspread(sM,base,linkage,Ne,0); end
Daniel@0: 
Daniel@0: return;
Daniel@0: