function Md = som_mdist(D,q,mask,Ne)% SOM_MDIST Mutual (or pairwise) distance matrix for the given data.% %   Md = som_mdist(D,[q],[mask],[Ne])%%    Md = som_mdist(D); %    Md = som_mdist(D,Inf); %    Md = som_mdist(D,2,Ne); %%  Input and output arguments ([]'s are optional):%   D        (matrix) size dlen x dim, the data set%            (struct) map or data struct%   [q]      (scalar) distance norm, default = 2%   [mask]   (vector) size dim x 1, the weighting mask%   [Ne]     (matrix) size dlen x dlen, sparse matrix %                     indicating which distances should be %                     calculated (ie. less than Infinite) %% See also PDIST. % 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 220800%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% maskif nargin<3, mask = []; end% the dataif isstruct(D),   switch D.type,    case 'som_map', if isempty(mask), mask = D.mask; end, D = D.codebook;    case 'som_data', D = D.data;    otherwise, error('Bad first argument');  endendnans = sum(isnan(D),2);if any(nans>0),   D(find(nans>0),:) = 0;   warning('Distances of vectors with NaNs are not calculated.'); end[dlen dim] = size(D);% distance normif nargin<2 | isempty(q) | isnan(q), q = 2; end% maskif isempty(mask), mask = ones(dim,1); end% connections if nargin<4, Ne = []; endif ~isempty(Ne),   l = size(Ne,1); Ne([0:l-1]*l+[1:l]) = 1; % set diagonal elements = 1end%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%m = mask; o = ones(dlen,1); l = dlen; Md = zeros(dlen);calculate_all = isempty(Ne); if ~calculate_all, Md(Ne==0) = Inf; endfor i=1:l-1,  j=(i+1):l;   if ~calculate_all, j=find(Ne(i,j))+i; end  C=D(j,:)-D(i*o(1:length(j)),:);  switch q,    case 1,    Md(j,i)=abs(C)*m;   case 2,    Md(j,i)=sqrt((C.^2)*m);     case Inf,  Md(j,i)=max(diag(m)*abs(C),[],2);   otherwise, Md(j,i)=((abs(C).^q)*m).^(1/q);  end     Md(i,j) = Md(j,i)';endMd(find(nans>0),:) = NaN; Md(:,find(nans>0)) = NaN; return;%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%