comparison toolboxes/MIRtoolbox1.3.2/somtoolbox/som_kmeanscolor.m @ 0:e9a9cd732c1e tip

first hg version after svn

+function [color,best,kmeans]=som_kmeanscolor(sM,C,initRGB,contrast)
+
+% SOM_KMEANSCOLOR Map unit color code according to K-means clustering
+%
+% [color, best, kmeans] = som_kmeanscolor(sM, C, [initRGB],[contrast])
+%
+%  color        = som_kmeanscolor(sM,15,som_colorcode(sM,'rgb1'),'enhance');
+%  [color,best] = som_kmeanscolor(sM,15,[],'normal');
+%  
+%  Input and output arguments ([]'s are optional):
+%   sM       (struct) map struct
+%   C        (scalar) maximum number of clusters
+%   initRGB  (string, matrix) color code string accepted by SOM_COLORCODE
+%                     or an Mx3 matrix of RGB triples, where M is the number
+%                     of map units. Default: SOM_COLORCODEs default
+%   contrast (string) 'flat', 'enhanced' color contrast mode, default:
+%                     'enhanced'
+%
+%   color    (matrix) MxCx3 of RGB triples
+%   best     (scalar) index for "best" clustering according to 
+%                     Davies-Boulding index; color(:,:,best) includes the 
+%                     corresponding color code.
+%   kmeans   (cell)   output of KMEANS_CLUSTERS in a cell array.
+% 
+% The function gives a set of color codings according to K-means 
+% clustering. For clustering, it uses function KMEANS_CLUSTERS for map units, 
+% and it calculates color codings for 1,2,...,C clusters. 
+% The idea of coloring is that the color of a cluster is the mean of the 
+% original colors (RGB values) of the map units belonging to that cluster, 
+% see SOM_CLUSTERCOLOR. The original colors are defined by  SOM_COLORCODE
+% by default. Input 'contrast' simply specifies whether or not 
+% to linearly redistribute R,G, and B values so that minimum is 0 and 
+% maximum 1 ('enahanced')  or to use directly the output of 
+% SOM_CLUSTERCOLOR ('flat'). KMEANS_CLUSTERS uses certain heuristics to 
+% select the best of 5 trials for each  number of clusters. Evaluating the 
+% clustering multiple times may take some time. 
+%
+% EXAMPLE
+% 
+%  load iris; % or any other map struct sM 
+%  [color,b]=som_kmeanscolor(sM,10);
+%  som_show(sM,'color',color,'color',{color(:,:,b),'"Best clustering"');
+% 
+% See also SOM_SHOW, SOM_COLORCODE, SOM_CLUSTERCOLOR, KMEANS_CLUSTERS
+
+% Contributed to SOM Toolbox 2.0, April 1st, 2000 by Johan Himberg
+% Copyright (c) by Johan Himberg
+% http://www.cis.hut.fi/projects/somtoolbox/
+
+% corrected help text 11032005 johan
+
+%%% Check number of inputs
+
+error(nargchk(2, 4, nargin));  % check no. of input args
+
+%%% Check input args & set defaults
+
+if isstruct(sM) & isfield(sM,'type') & strcmp(sM.type,'som_map'),
+   [tmp,lattice,msize]=vis_planeGetArgs(sM);
+   munits=prod(msize);
+   if length(msize)>2 
+      error('Does not work with 3D maps.')
+   end
+else
+   error('Map struct requires for first input argument!');
+end
+
+if ~vis_valuetype(C,{'1x1'}),
+   error('Scalar value expect for maximum number of clusters.');
+end
+
+% check initial color coding
+if nargin<3 | isempty(initRGB)
+   initRGB=som_colorcode(sM);
+end
+
+% check contrast checking
+if nargin<4 | isempty(contrast),
+   contrast='enhanced';
+end
+
+if ~ischar(contrast),
+   error('String input expected for input arg. ''contrast''.');
+else
+   switch lower(contrast)
+   case {'flat','enhanced'}
+      ;
+   otherwise 
+      error(['''flat'' or ''enhanced'' expected for '...
+            'input argument ''contrast''.']);
+   end
+end
+
+if ischar(initRGB),
+   try 
+      initRGB=som_colorcode(sM,initRGB);
+   catch
+      error(['Color code ' initRGB ...
+            'was not recognized by SOM_COLORCODE.']);
+   end
+elseif vis_valuetype(initRGB,{'nx3rgb',[munits 3]},'all'),
+   ;
+else
+   error(['The initial color code must be a string '...
+         'or an Mx3 matrix of RGB triples.']);
+end
+
+%%% Action %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+disp('Wait...');
+[c,p,err,ind]=kmeans_clusters(sM,C,5,0); % use 5 trials, verbose off
+
+% Store outputs to kmeans
+kmeans{1}=c; 
+kmeans{2}=p; 
+kmeans{3}=err; 
+kmeans{4}=ind;
+
+%%% Build output
+color=som_clustercolor(sM,cat(2,p{:}),initRGB);
+[tmp,best]=min(ind);
+
+switch contrast
+case 'flat'
+   ;
+case 'enhanced'
+   warning off;
+   ncolor=maxnorm(color);
+   ncolor(~isfinite(ncolor))=color(~isfinite(ncolor));
+   color=ncolor;
+   warning on;
+end
+
+%%% Subfunctions %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+function X=maxnorm(x)
+% normalize columns of x between [0,1]
+
+x=x-repmat(min(x),[size(x,1) 1 1]);
+X=x./repmat(max(x),[size(x,1) 1 1]);