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