Daniel@0: function color=som_clustercolor(m, class, colorcode)
Daniel@0: 
Daniel@0: % SOM_CLUSTERCOLOR Sets map unit coloring according to classification
Daniel@0: %
Daniel@0: % syntax 1: color = som_clustercolor(m, class, [colorcode]) 
Daniel@0: % syntax 2: color = som_clustercolor(class, colormatrix)
Daniel@0: %
Daniel@0: %  Input and output arguments ([]'s are optional):
Daniel@0: %   m           (struct) map or topol struct
Daniel@0: %               (cell array) of form {str,[m1 m2]} where str = 'hexa'
Daniel@0: %                  or 'rect' and [m1 m2] = msize.
Daniel@0: %   class       (matrix) Mxn matrix of integers (class labels)
Daniel@0: %                  where M is the number of map units and each
Daniel@0: %                  column gives some classification for the units. 
Daniel@0: %   colorcode   (string) 'rgb1', 'rgb2' (default), 'rgb3', 'rgb4', 'hsv'.
Daniel@0: %   colormatrix (matrix) Mx3 matrix of RGB triplets giving the
Daniel@0: %                  initial color code for each unit.
Daniel@0: %   color       (matrix) size Mx3xn of RGB triplets giving the
Daniel@0: %                  resulting color code for each unit 
Daniel@0: %    
Daniel@0: % The function gives a color coding by class and location for the
Daniel@0: % map units. The color is determined by calculating the mean of the 
Daniel@0: % initial RGB values of units belonging to the same class. 
Daniel@0: % 
Daniel@0: % Function has two syntaxes: 
Daniel@0: % 
Daniel@0: % * If first argument gives the map topology, i.e. is map or topol struct
Daniel@0: % or cell indicating the topology, the initial color coding of the
Daniel@0: % units may be given by a string ('rgb1','rgb2','rgb3','rgb4', or 'hsv')
Daniel@0: % which describe a predefined coloring scheme. (see SOM_COLORCODE).
Daniel@0: % or an initial color matrix of size Mx3 with RGB triplets as rows.  
Daniel@0: % * Another possibility is to give just the classification vector
Daniel@0: % of size Mx1 and an initial color matrix of size Mx3 with RGB 
Daniel@0: % triplets as rows.  
Daniel@0: %
Daniel@0: % EXAMPLE (requires Matlab Statistics Toolbox)
Daniel@0: %
Daniel@0: % % Do a 10-cluster single linkage hierachical clustering for SOM units
Daniel@0: %    class=cluster(linkage(pdist(sM.codebook),'single'),10);
Daniel@0: % % Color code the clusters 
Daniel@0: %    C=som_clustercolor(sM, class, 'rgb2');
Daniel@0: % % Visualize
Daniel@0: %    som_show(sM,'color',C);
Daniel@0: %
Daniel@0: % See also SOM_COLORCODE, SOM_KMEANSCOLOR, SOM_CPLANE, SOM_SHOW
Daniel@0: 
Daniel@0: % Contributed to SOM Toolbox 2.0, February 11th, 2000 by Johan Himberg
Daniel@0: % Copyright (c) by Johan Himberg
Daniel@0: % http://www.cis.hut.fi/projects/somtoolbox/
Daniel@0: 
Daniel@0: % Version 2.0beta Johan 100200 
Daniel@0: 
Daniel@0: %%% Check arguments %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Daniel@0: 
Daniel@0: error(nargchk(2, 3, nargin));   % check no. of input args is correct
Daniel@0: 
Daniel@0: % Check 1s argument 
Daniel@0: 
Daniel@0: % Class matrix?
Daniel@0: if vis_valuetype(m, {'nxm'});
Daniel@0:    colorcode=class; 
Daniel@0:    class=m;
Daniel@0:    if ~vis_valuetype(colorcode,{'nx3rgb',[size(class,1) 3]},'all'),
Daniel@0:       error(['If map or topol is not specified the colorcode must be a' ...
Daniel@0:             ' [size(class,1) 3] sized RGB matrix.']);
Daniel@0:    end
Daniel@0: else
Daniel@0:    [tmp,ok,tmp]=som_set(m);
Daniel@0:    if isstruct(m) & all(ok)
Daniel@0:       switch m.type
Daniel@0:       case 'som_topol'              % topol? 
Daniel@0:          msize=m.msize;
Daniel@0:          lattice=m.lattice;
Daniel@0:       case 'som_map'   
Daniel@0:          msize=m.topol.msize;         % map?
Daniel@0:          lattice=m.topol.lattice;
Daniel@0:       otherwise
Daniel@0:          error('Invalid map or topol struct.');
Daniel@0:       end
Daniel@0:       % cell?  
Daniel@0:    elseif iscell(m) & vis_valuetype(size(m),{[1 2]}),
Daniel@0:       if vis_valuetype(m{2},{[1 2]}) & vis_valuetype(m{1},{'string'}),
Daniel@0:          lattice=m{1};    
Daniel@0:          msize=m{2}; 
Daniel@0:       else
Daniel@0:          error('Invalid map size information.');
Daniel@0:       end
Daniel@0:    else
Daniel@0:       % not known type
Daniel@0:       error('Invalid first argument!');
Daniel@0:    end
Daniel@0:    % Check map parameters
Daniel@0:    switch lattice                   % lattice  
Daniel@0:    case 'hexa' 
Daniel@0:       ;
Daniel@0:    case 'rect'
Daniel@0:       ;
Daniel@0:    otherwise
Daniel@0:       error('Unknown lattice type');
Daniel@0:    end
Daniel@0:    if length(msize)>2               % dimension
Daniel@0:       error('Only 2D maps allowed!');
Daniel@0:    end
Daniel@0:    % Check colorcode
Daniel@0:    if nargin<3 | isempty(colorcode)
Daniel@0:       colorcode='rgb2';
Daniel@0:    end
Daniel@0: end
Daniel@0: 
Daniel@0: % Check class
Daniel@0: if any(class~=round(class))
Daniel@0:    error('Class labels must be integer numbers.');
Daniel@0: end
Daniel@0: 
Daniel@0: if min(class)<=0 
Daniel@0:    error('Class numbers should be greater than 0');
Daniel@0: end
Daniel@0: 
Daniel@0: if ischar(colorcode),
Daniel@0:    switch colorcode
Daniel@0:    case{'rgb1','rgb2','rgb3','rgb4','hsv'}
Daniel@0:       colorcode=som_colorcode(m, colorcode);
Daniel@0:    otherwise
Daniel@0:       error(['Color code not known: should be ''rgb1'',''rgb2'',' ...
Daniel@0:             ' ''rgb3'',''rgb4'' or ''hsv''.']);
Daniel@0:    end
Daniel@0: elseif ~vis_valuetype(colorcode,{'nx3rgb',[size(class,1) 3]},'all');
Daniel@0:    error(['Invalid colorcode matrix: should be a ' ...
Daniel@0:          '[length(class) 3] sized RGB matrix.']);
Daniel@0: end
Daniel@0: 
Daniel@0: %% Action %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Daniel@0: 
Daniel@0: % Go through all i classifications (columns)
Daniel@0: for i=1:size(class,2), 
Daniel@0:    % Get unique class labels in ith classification
Daniel@0:    c=unique(class(:,i))'; % row vector for loop indexing
Daniel@0:    % Go through all class in ith classification    
Daniel@0:    for j=c;             
Daniel@0:       index=(class(:,i)==j); 
Daniel@0:       N=sum(index);
Daniel@0:       colors=colorcode(index,:);
Daniel@0:       % Calculate the mean color
Daniel@0:       meancolor=repmat(mean(colors,1),N,1);
Daniel@0:       % Select the original color that is closest to this mean
Daniel@0:       dist=sum((meancolor-colors).^2,2);
Daniel@0:       [tmp,min_dist_index]=min(dist);
Daniel@0:       best_color=repmat(colors(min_dist_index,:),N,1);
Daniel@0:       % Set the color to output variable
Daniel@0:       color(index,:,i)=best_color;
Daniel@0:    end
Daniel@0: end