Daniel@0: function P = som_order_cplanes(sM, varargin)
Daniel@0: 
Daniel@0: %SOM_ORDER_CPLANES Orders and shows the SOM component planes.
Daniel@0: %
Daniel@0: % P = som_order_cplanes(sM, [[argID,] value, ...])
Daniel@0: %
Daniel@0: %  som_order_cplanes(sM);
Daniel@0: %  som_order_cplanes(sM,'comp',1:30,'simil',C,'pca');
Daniel@0: %  P = som_order_cplanes(sM);
Daniel@0: %
Daniel@0: %  Input and output arguments ([]'s are optional): 
Daniel@0: %   sM       (struct) map or data struct
Daniel@0: %            (matrix) a data matrix, size * x dim
Daniel@0: %   [argID,  (string) See below. The values which are unambiguous can
Daniel@0: %    value]  (varies) be given without the preceeding argID.
Daniel@0: %
Daniel@0: %   P        (matrix) size n x * (typically n x 2), the projection coordinates
Daniel@0: %   
Daniel@0: % Here are the valid argument IDs and corresponding values. The values
Daniel@0: % which are unambiguous (marked with '*') can be given without the
Daniel@0: % preceeding argID.
Daniel@0: %   'comp'    (vector) size 1 x n, which components to project, 1:dim by default
Daniel@0: %   'simil'  *(string) similarity measure to use 
Daniel@0: %                      'corr'        linear correlation between component planes
Daniel@0: %                      'abs(corr)'   absolute value of correlation (default)
Daniel@0: %                      'umat'        as 'abs(corr)' but calculated from U-matrices
Daniel@0: %                      'mutu'        mutual information (not implemented yet)
Daniel@0: %             (matrix) size n x n, a similarity matrix to be used             
Daniel@0: %   'proj'   *(string) projection method to use: 'SOM' (default), 
Daniel@0: %                      'pca', 'sammon', 'cca', 'order', 'ring'
Daniel@0: %   'msize'   (vector) size of the SOM that is used for projection
Daniel@0: %   'show'   *(string) how visualization is done: 'planes' (default), 
Daniel@0: %                      'names', or 'none'
Daniel@0: %   'mask'    (vector) dim x 1, the mask to use, ones(dim,1) by default
Daniel@0: %   'comp_names' (cell array) of strings, size dim x 1, the component names
Daniel@0: %
Daniel@0: % The visualized objects have a callback associated with them: by
Daniel@0: % clicking on the object, the index and name of the component are printed
Daniel@0: % to the standard output.
Daniel@0: % 
Daniel@0: % See also SOM_SHOW.
Daniel@0: 
Daniel@0: % Copyright (c) 2000 by the SOM toolbox programming team.
Daniel@0: % Contributed to SOM Toolbox on June 16th, 2000 by Juha Vesanto
Daniel@0: % http://www.cis.hut.fi/projects/somtoolbox/
Daniel@0: 
Daniel@0: % Version 2.0beta juuso 120600 070601
Daniel@0: 
Daniel@0: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Daniel@0: %% check arguments
Daniel@0: 
Daniel@0: % sM
Daniel@0: if isstruct(sM), 
Daniel@0:   switch sM.type
Daniel@0:   case 'som_map', 
Daniel@0:     D = sM.codebook; dim = size(D,2); cnames = sM.comp_names; mask = sM.mask; 
Daniel@0:     ismap = 1; 
Daniel@0:   case 'som_data', 
Daniel@0:     D = sM.data; dim = size(D,2); cnames = sM.comp_names; mask = ones(dim,1); 
Daniel@0:     ismap = 0; 
Daniel@0:   otherwise, error('Invalid first argument.');
Daniel@0:   end                  
Daniel@0: else
Daniel@0:   D = sM; 
Daniel@0:   dim = size(D,2); mask = ones(dim,1);
Daniel@0:   cnames = cell(dim,1); 
Daniel@0:   for i = 1:dim, cnames{i} = sprintf('Variable%d',i); end
Daniel@0:   ismap = 0; 
Daniel@0: end
Daniel@0: 
Daniel@0: % defaults
Daniel@0: comps = 1:dim; 
Daniel@0: simil = 'abs(corr)';
Daniel@0: proj = 'SOM'; 
Daniel@0: show = 'planes'; 
Daniel@0: mapsize = NaN;
Daniel@0: 
Daniel@0: % varargin
Daniel@0: i=1;
Daniel@0: while i<=length(varargin),
Daniel@0:   argok = 1;
Daniel@0:   if ischar(varargin{i}),
Daniel@0:     switch varargin{i},
Daniel@0:      % argument IDs
Daniel@0:      case 'mask',       i=i+1; mask = varargin{i};
Daniel@0:      case 'comp_names', i=i+1; cnames = varargin{i};
Daniel@0:      case 'comp',       i=i+1; comps = varargin{i}; 
Daniel@0:      case 'proj',       i=i+1; proj = varargin{i}; 
Daniel@0:      case 'show',       i=i+1; show = varargin{i}; 
Daniel@0:      case 'simil',      i=i+1; simil = varargin{i}; 
Daniel@0:      case 'msize',      i=i+1; mapsize = varargin{i};
Daniel@0:      % unambiguous values
Daniel@0:      case {'corr','abs(corr)','umat','mutu'}, simil = varargin{i}; 
Daniel@0:      case {'SOM','pca','sammon','cca','order','ring'}, proj = varargin{i}; 
Daniel@0:      case {'planes','names','none'}, show = varargin{i}; 
Daniel@0:      otherwise argok=0;
Daniel@0:     end
Daniel@0:   else
Daniel@0:     argok = 0;
Daniel@0:   end
Daniel@0:   if ~argok,
Daniel@0:     disp(['(som_order_cplanes) Ignoring invalid argument #' num2str(i+1)]);
Daniel@0:   end
Daniel@0:   i = i+1;
Daniel@0: end
Daniel@0: 
Daniel@0: if strcmp(show,'planes') & ~ismap, 
Daniel@0:   warning('Given data is not a map: using ''names'' visualization.'); 
Daniel@0:   show = 'names'; 
Daniel@0: end
Daniel@0: 
Daniel@0: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Daniel@0: %% similarity matrix
Daniel@0: 
Daniel@0: fprintf(1,'Calculating similarity matrix\n');
Daniel@0: 
Daniel@0: % use U-matrix
Daniel@0: if strcmp(simil,'umat'), 
Daniel@0:   if ~ismap, error('Given data is not a map: cannot use U-matrix similarity.'); end
Daniel@0:   U = som_umat(sM);
Daniel@0:   D = zeros(prod(size(U)),dim); 
Daniel@0:   m = zeros(dim,1);
Daniel@0:   for i=1:dim, m=m*0; m(i)=1; U = som_umat(sM,'mask',m); D(:,i) = U(:); end
Daniel@0: end
Daniel@0: 
Daniel@0: % components
Daniel@0: D = D(:,comps); 
Daniel@0: cnames = cnames(comps);
Daniel@0: mask = mask(comps);
Daniel@0: dim = length(comps);
Daniel@0:   
Daniel@0: % similarity matrix
Daniel@0: if ischar(simil), 
Daniel@0:   switch simil, 
Daniel@0:   case {'corr','abs(corr)','umat'}, 
Daniel@0:     A = zeros(dim);
Daniel@0:     me = zeros(1,dim);
Daniel@0:     for i=1:dim, 
Daniel@0:         me(i) = mean(D(isfinite(D(:,i)),i)); D(:,i) = D(:,i) - me(i); 
Daniel@0:     end  
Daniel@0:     for i=1:dim, 
Daniel@0:       for j=i:dim, 
Daniel@0:         c = D(:,i).*D(:,j); c = c(isfinite(c));
Daniel@0:         A(i,j) = sum(c)/length(c); A(j,i) = A(i,j); 
Daniel@0:       end
Daniel@0:     end
Daniel@0:     s = diag(A); 
Daniel@0:     A = A./sqrt(s*s');
Daniel@0:     switch simil, 
Daniel@0:     case {'abs(corr)','umat'}, A = abs(A); 
Daniel@0:     case 'corr', A = A + 1; 
Daniel@0:     end
Daniel@0:   case 'mutu', 
Daniel@0:     error('Mutual information not implemented yet.');
Daniel@0:   end
Daniel@0: else
Daniel@0:   A = simil; 
Daniel@0: end
Daniel@0: 
Daniel@0: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Daniel@0: %% projection
Daniel@0: 
Daniel@0: fprintf(1,'Projection\n');
Daniel@0: 
Daniel@0: mu = 2*dim; 
Daniel@0: 
Daniel@0: switch proj, 
Daniel@0:  case 'SOM',
Daniel@0: 
Daniel@0:   if isnan(mapsize), 
Daniel@0:     sMtmp = som_randinit(A,'munits',mu); 
Daniel@0:     msize = sMtmp.topol.msize; 
Daniel@0:   else 
Daniel@0:     msize = mapsize; 
Daniel@0:   end
Daniel@0: 
Daniel@0:   sM2 = som_make(A,'msize',msize,'rect','tracking',0);
Daniel@0:   bm  = assign_unique_bm(sM2,A);
Daniel@0:   Co  = som_unit_coords(sM2);
Daniel@0:   P   = Co(bm,:);
Daniel@0: 
Daniel@0:  case 'ring', 
Daniel@0: 
Daniel@0:   if isnan(mapsize), msize = [1 mu]; else msize = mapsize; end
Daniel@0: 
Daniel@0:   sM2 = som_make(A,'msize',msize,'cyl','rect','tracking',0);
Daniel@0:   bm  = assign_unique_bm(sM2,A);
Daniel@0:   Co  = som_unit_coords(sM2);
Daniel@0:   P   = Co(bm,[1 3]);   
Daniel@0:   
Daniel@0:  case 'order',
Daniel@0: 
Daniel@0:   if isnan(mapsize), msize = [1 mu]; else msize = mapsize; end
Daniel@0: 
Daniel@0:   sM2 = som_make(A,'msize',msize,'tracking',0);
Daniel@0:   bm  = assign_unique_bm(sM2,A);
Daniel@0:   [dummy,i] = sort(bm); 
Daniel@0:   [dummy,P] = sort(i);
Daniel@0:   if size(P,2)>1, P = P'; end
Daniel@0:   if size(P,2)==1, P(:,2) = zeros(length(P),1); end
Daniel@0: 
Daniel@0:  case {'pca','sammon','cca'}, 
Daniel@0:   P = pcaproj(A,2);  
Daniel@0:   if strcmp(proj,'sammon'), P = sammon(A,P,50,'steps');
Daniel@0:   elseif strcmp(proj,'cca'), P = cca(A,P,50);
Daniel@0:   end
Daniel@0: 
Daniel@0: end
Daniel@0: 
Daniel@0: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Daniel@0: %% visualization
Daniel@0: 
Daniel@0: if ~strcmp(show,'none'), 
Daniel@0:   fprintf(1,'Visualization\n');
Daniel@0:   cla
Daniel@0:   hold on
Daniel@0:   if strcmp(show,'planes')
Daniel@0:     s = findscaling(sM.topol.msize,P);
Daniel@0:     for i=1:dim, 
Daniel@0:       C = som_normcolor(D(:,i));
Daniel@0:       if strcmp(simil,'umat'), 
Daniel@0: 	h=som_cplane([sM.topol.lattice 'U'],sM.topol.msize,C,1,s*P(i,:));
Daniel@0:       else
Daniel@0: 	h=som_cplane(sM,C,1,s*P(i,:)); 
Daniel@0:       end 
Daniel@0:       set(h,'edgecolor','none','Userdata',sprintf('[%d] %s',i,cnames{i}));
Daniel@0:       set(h,'ButtonDownFcn','fprintf(1,''%s\n'',get(gco,''UserData''))');
Daniel@0:     end
Daniel@0:   else 
Daniel@0:     s=1; 
Daniel@0:     a=[min(P(:,1))-1 max(P(:,1))+1 min(P(:,2))-1-3 max(P(:,2))+1-3];
Daniel@0:     axis(s*a);
Daniel@0:   end
Daniel@0:   h=text(s*P(:,1),s*P(:,2)-3,cnames);
Daniel@0:   for i=1:length(h), set(h(i),'Userdata',sprintf('[%d] %s',i,cnames{i})); end
Daniel@0:   set(h,'ButtonDownFcn','fprintf(1,''%s\n'',get(gco,''UserData''))');
Daniel@0:   hold off
Daniel@0: 
Daniel@0:   axis on; axis equal; axis tight; set(gca,'XTick',[],'YTick',[],'Box','on');
Daniel@0: end
Daniel@0: 
Daniel@0: return; 
Daniel@0: 
Daniel@0: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%5
Daniel@0: %% subfunctions
Daniel@0: 
Daniel@0: function bm = assign_unique_bm(sM,D)
Daniel@0: 
Daniel@0:   munits = size(sM.codebook,1);
Daniel@0:   [dlen dim] = size(D);
Daniel@0:   margin = max(0,dlen-munits);
Daniel@0: 
Daniel@0:   [bm,qers] = som_bmus(sM,D); 
Daniel@0:   bmi=ones(dim,1);  
Daniel@0:   hits = som_hits(sM,D); 
Daniel@0:   mult = find(hits>1); 
Daniel@0:   while any(mult) & sum(hits(mult))-length(mult)>margin, 
Daniel@0:     choices = find(bm==mult(1)); 
Daniel@0:     while length(choices)>1,
Daniel@0:       [dummy,mv] = max(qers(choices)); mv = choices(mv);
Daniel@0:       [mv_to,q] = som_bmus(sM,D(mv,:),bmi(mv)); 
Daniel@0:       bmi(mv)=bmi(mv)+1; qers(mv) = q; bm(mv) = mv_to;
Daniel@0:       choices = find(bm==mv_to);
Daniel@0:     end
Daniel@0:     for i=1:length(hits), hits(i)=sum(bm==i); end
Daniel@0:     mult = find(hits>1);
Daniel@0:   end
Daniel@0:   return;
Daniel@0:   
Daniel@0: function s = findscaling(msize,P)
Daniel@0: 
Daniel@0:   d1 = median(abs(diff(unique(sort(P(:,1))))));
Daniel@0:   d2 = median(abs(diff(unique(sort(P(:,2))))));
Daniel@0:   if d1>0, s1 = 1.5*msize(2)/d1; else s1 = 0; end
Daniel@0:   if d2>0, s2 = 1.5*msize(1)/d2; else s2 = 0; end
Daniel@0:   s = max(s1,s2);
Daniel@0:   if s==0, s=1; end
Daniel@0:   return; 
Daniel@0: 
Daniel@0: function alternative_SOM_plane_vis(sT,bm,simil,D,cnames)
Daniel@0: 
Daniel@0:   clf
Daniel@0:   for i=1:size(D,2), 
Daniel@0:     subplot(sT.msize(2),sT.msize(1),bm(i));
Daniel@0:     if strcmp(simil,'umat'), h=som_cplane([sT.lattice 'U'],sT.msize,D(:,i));
Daniel@0:     else h=som_cplane(sT,D(:,i)); 
Daniel@0:     end
Daniel@0:     set(h,'edgecolor','none');
Daniel@0:     title(cnames{i});
Daniel@0:     axis off
Daniel@0:   end    
Daniel@0:   return;
Daniel@0: