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1 function Md = som_mdist(D,q,mask,Ne)
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2
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3 % SOM_MDIST Mutual (or pairwise) distance matrix for the given data.
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4 %
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5 % Md = som_mdist(D,[q],[mask],[Ne])
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6 %
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7 % Md = som_mdist(D);
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8 % Md = som_mdist(D,Inf);
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9 % Md = som_mdist(D,2,Ne);
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10 %
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11 % Input and output arguments ([]'s are optional):
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12 % D (matrix) size dlen x dim, the data set
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13 % (struct) map or data struct
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14 % [q] (scalar) distance norm, default = 2
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15 % [mask] (vector) size dim x 1, the weighting mask
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16 % [Ne] (matrix) size dlen x dlen, sparse matrix
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17 % indicating which distances should be
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18 % calculated (ie. less than Infinite)
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19 %
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20 % See also PDIST.
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21
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22 % Copyright (c) 2000 by Juha Vesanto
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23 % Contributed to SOM Toolbox on XXX by Juha Vesanto
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24 % http://www.cis.hut.fi/projects/somtoolbox/
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25
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26 % Version 2.0beta juuso 220800
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27
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28 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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29
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30 % mask
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31 if nargin<3, mask = []; end
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32
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33 % the data
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34 if isstruct(D),
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35 switch D.type,
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36 case 'som_map', if isempty(mask), mask = D.mask; end, D = D.codebook;
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37 case 'som_data', D = D.data;
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38 otherwise, error('Bad first argument');
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39 end
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40 end
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41 nans = sum(isnan(D),2);
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42 if any(nans>0),
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43 D(find(nans>0),:) = 0;
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44 warning('Distances of vectors with NaNs are not calculated.');
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45 end
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46 [dlen dim] = size(D);
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47
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48 % distance norm
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49 if nargin<2 | isempty(q) | isnan(q), q = 2; end
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50
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51 % mask
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52 if isempty(mask), mask = ones(dim,1); end
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53
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54 % connections
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55 if nargin<4, Ne = []; end
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56 if ~isempty(Ne),
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57 l = size(Ne,1); Ne([0:l-1]*l+[1:l]) = 1; % set diagonal elements = 1
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58 end
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59
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60 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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61
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62 m = mask;
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63 o = ones(dlen,1);
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64 l = dlen;
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65 Md = zeros(dlen);
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66 calculate_all = isempty(Ne);
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67
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68 if ~calculate_all, Md(Ne==0) = Inf; end
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69
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70 for i=1:l-1,
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71 j=(i+1):l;
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72 if ~calculate_all, j=find(Ne(i,j))+i; end
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73 C=D(j,:)-D(i*o(1:length(j)),:);
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74 switch q,
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75 case 1, Md(j,i)=abs(C)*m;
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76 case 2, Md(j,i)=sqrt((C.^2)*m);
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77 case Inf, Md(j,i)=max(diag(m)*abs(C),[],2);
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78 otherwise, Md(j,i)=((abs(C).^q)*m).^(1/q);
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79 end
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80 Md(i,j) = Md(j,i)';
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81 end
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82
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83 Md(find(nans>0),:) = NaN;
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84 Md(:,find(nans>0)) = NaN;
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85
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86 return;
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87
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88 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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89
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