Daniel@0: function sM  = som_supervised(sData,varargin)
Daniel@0: 
Daniel@0: %SOM_SUPERVISED SOM training which utilizes class information.
Daniel@0: %
Daniel@0: % sM = som_supervised(sData, [ArgID, value,...]))
Daniel@0: %
Daniel@0: %  Input and output arguments ([]'s are optional)
Daniel@0: %   sData    (struct) data struct, the class information is 
Daniel@0: %                     taken from the first column of .labels field
Daniel@0: %   [argID,  (string) See below. These are given as 
Daniel@0: %    value]  (varies) 'argID', value -pairs.
Daniel@0: %
Daniel@0: %   sMap     (struct) map struct
Daniel@0: %
Daniel@0: %  Here are the argument IDs and corresponding values: 
Daniel@0: %  'munits'     (scalar) the preferred number of map units
Daniel@0: %  'msize'      (vector) map grid size
Daniel@0: %  'mask'       (vector) BMU search mask, size dim x 1
Daniel@0: %  'name'       (string) map name
Daniel@0: %  'comp_names' (string array / cellstr) component names, size dim x 1
Daniel@0: %  'tracking'   (scalar) how much to report, default = 1
Daniel@0: %  The following values are unambiguous and can therefore
Daniel@0: %  be given without the preceeding argument ID:
Daniel@0: %  'algorithm'  (string) training algorithm: 'seq' or 'batch'
Daniel@0: %  'mapsize'    (string) do you want a 'small', 'normal' or 'big' map
Daniel@0: %               Any explicit settings of munits or msize override this.
Daniel@0: %  'topol'      (struct) topology struct
Daniel@0: %  'som_topol','sTopol' = 'topol'
Daniel@0: %  'lattice'    (string) map lattice, 'hexa' or 'rect'
Daniel@0: %  'shape'      (string) map shape, 'sheet', 'cyl' or 'toroid'
Daniel@0: %  'neigh'      (string) neighborhood function, 'gaussian', 'cutgauss',
Daniel@0: %                       'ep' or 'bubble'
Daniel@0: %
Daniel@0: % For more help, try 'type som_supervised', or check out online documentation.
Daniel@0: % See also SOM_MAKE, SOM_AUTOLABEL.
Daniel@0: 
Daniel@0: %%%%%%%%%%%%% DETAILED DESCRIPTION %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Daniel@0: %
Daniel@0: % som_supervised
Daniel@0: %
Daniel@0: % PURPOSE
Daniel@0: %
Daniel@0: % Creates, initializes and trains a supervised SOM by taking the 
Daniel@0: % class-identity into account.
Daniel@0: %
Daniel@0: % SYNTAX
Daniel@0: %
Daniel@0: % sMap = som_supervised(sData);
Daniel@0: % sMap = som_supervised(...,'argID',value,...)
Daniel@0: % sMap = som_make(...,value,...);
Daniel@0: %
Daniel@0: % DESCRIPTION
Daniel@0: %
Daniel@0: % Creates, initializes and trains a supervised SOM. It constructs the
Daniel@0: % training data by adding 1-of-N -coded matrix to the original data
Daniel@0: % based on the class information in the .labels field. The dimension
Daniel@0: % of vectors after the process is (the old dimension + number of
Daniel@0: % different classes). In each vector, one of the new components has
Daniel@0: % value '1' (this depends on the class of the vector), and others '0'.
Daniel@0: % Calls SOM_MAKE to construct the map. Then the class of each map unit
Daniel@0: % is determined by taking maximum over these added components, and a
Daniel@0: % label is give accordingly. Finally, the extra components (the
Daniel@0: % 1-of-N -coded ones) are removed.
Daniel@0: %
Daniel@0: % REFERENCES
Daniel@0: %
Daniel@0: % Kohonen, T., "Self-Organizing Map", 2nd ed., Springer-Verlag, 
Daniel@0: %    Berlin, 1995, pp. 160-161.
Daniel@0: % Kohonen, T., Mäkivasara, K., Saramäki, T., "Phonetic Maps - 
Daniel@0: %    Insightful Representation of Phonological Features For 
Daniel@0: %    Speech Recognition", In proceedings of International
Daniel@0: %    Conference on Pattern Recognition (ICPR), Montreal, Canada, 
Daniel@0: %    1984, pp. 182-185.
Daniel@0: %
Daniel@0: % REQUIRED INPUT ARGUMENTS
Daniel@0: %
Daniel@0: % sData           The data to use in the training.
Daniel@0: %        (struct) A data struct. '.comp_names' as well as '.name' 
Daniel@0: %                 is copied to the map. The class information is 
Daniel@0: %                 taken from the first column of '.labels' field.
Daniel@0: %
Daniel@0: % OPTIONAL INPUT ARGUMENTS 
Daniel@0: %
Daniel@0: %  argID (string) Argument identifier string (see below).
Daniel@0: %  value (varies) Value for the argument (see below).
Daniel@0: %
Daniel@0: %  The optional arguments can be given as 'argID',value -pairs. If an
Daniel@0: %  argument is given value multiple times, the last one is used. 
Daniel@0: %  Here are the argument IDs and corresponding values: 
Daniel@0: %   'munits'     (scalar) the preferred number of map units - this may 
Daniel@0: %                 change a bit, depending on the properties of the data
Daniel@0: %   'msize'      (vector) map grid size
Daniel@0: %   'mask'       (vector) BMU search mask, size dim x 1
Daniel@0: %   'name'       (string) map name
Daniel@0: %   'comp_names' (string array / cellstr) component names, size dim x 1
Daniel@0: %   'tracking'   (scalar) how much to report, default = 1. This parameter 
Daniel@0: %                 is also passed to the training functions. 
Daniel@0: %   The following values are unambiguous and can therefore
Daniel@0: %   be given without the preceeding argument ID:
Daniel@0: %   'algorithm'  (string) training algorithm: 'seq' or 'batch' (default)
Daniel@0: %   'mapsize'    (string) do you want a 'small', 'normal' or 'big' map
Daniel@0: %                 Any explicit settings of munits or msize (or topol) 
Daniel@0: %                 override this.
Daniel@0: %   'topol'      (struct) topology struct
Daniel@0: %   'som_topol','sTopol' = 'topol'
Daniel@0: %   'lattice'    (string) map lattice, 'hexa' or 'rect'
Daniel@0: %   'shape'      (string) map shape, 'sheet', 'cyl' or 'toroid'
Daniel@0: %   'neigh'      (string) neighborhood function, 'gaussian', 'cutgauss',
Daniel@0: %                 'ep' or 'bubble'
Daniel@0: %
Daniel@0: % OUTPUT ARGUMENTS
Daniel@0: % 
Daniel@0: %  sMap (struct)  SOM -map struct
Daniel@0: %
Daniel@0: % EXAMPLES
Daniel@0: %
Daniel@0: %  To simply train a map with default parameters:
Daniel@0: %
Daniel@0: %   sMap = som_supervised(sData);
Daniel@0: %
Daniel@0: %  With the optional arguments, the initialization and training can be
Daniel@0: %  influenced. To change map size, use 'msize', 'munits' or 'mapsize'
Daniel@0: %  arguments:  
Daniel@0: %
Daniel@0: %   sMap = som_supervised(D,'mapsize','big'); or 
Daniel@0: %   sMap = som_supervised(D,'big');
Daniel@0: %   sMap = som_supervised(D,'munits', 100);
Daniel@0: %   sMap = som_supervised(D,'msize', [20 10]); 
Daniel@0: %
Daniel@0: %  Argument 'algorithm' can be used to switch between 'seq' and 'batch'
Daniel@0: %  algorithms. 'batch' is the default, so to use 'seq' algorithm: 
Daniel@0: %
Daniel@0: %   sMap = som_supervised(D,'algorithm','seq'); or 
Daniel@0: %   sMap = som_supervised(D,'seq'); 
Daniel@0: %
Daniel@0: %  The 'tracking' argument can be used to control the amout of reporting
Daniel@0: %  during training. The argument is used in this function, and it is
Daniel@0: %  passed to the training functions. To make the function work silently
Daniel@0: %  set it to 0.
Daniel@0: %
Daniel@0: %   sMap = som_supervised(D,'tracking',0); 
Daniel@0: %
Daniel@0: % SEE ALSO
Daniel@0: % 
Daniel@0: %  som_make         Create, initialize and train Self-Organizing map.
Daniel@0: %  som_autolabel    Label SOM/data set based on another SOM/data set.
Daniel@0: 
Daniel@0: % Contributed to SOM Toolbox vs2, Feb 2nd, 2000 by Juha Parhankangas
Daniel@0: % Copyright (c) by Juha Parhankangas
Daniel@0: % http://www.cis.hut.fi/projects/somtoolbox/
Daniel@0: 
Daniel@0: % Juha Parhankangas 050100
Daniel@0: 
Daniel@0: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Daniel@0: 
Daniel@0: D0 = sData.data;
Daniel@0: [c,n,classlabels] = class2num(sData.labels(:,1));
Daniel@0: 
Daniel@0: %%%%%%%% Checking arguments %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Daniel@0: 
Daniel@0: if ~isstruct(sData)
Daniel@0:   error('Argument ''sData'' must be a ''som_data'' -struct.');
Daniel@0: else
Daniel@0:   data_name = sData.name;
Daniel@0:   comp_names = sData.comp_names;
Daniel@0:   comp_norm = sData.comp_norm;
Daniel@0: end
Daniel@0: 
Daniel@0: [dlen,dim] = size(sData.data);
Daniel@0: 
Daniel@0: % defaults
Daniel@0: 
Daniel@0: mapsize = '';
Daniel@0: sM = som_map_struct(dim+n); 
Daniel@0: sTopol = sM.topol;
Daniel@0: munits = prod(sTopol.msize); % should be zero
Daniel@0: mask = sM.mask; 
Daniel@0: name = sM.name; 
Daniel@0: neigh = sM.neigh; 
Daniel@0: tracking = 1;
Daniel@0: algorithm = 'batch'; 
Daniel@0: 
Daniel@0: %%%% changes to defaults (checking varargin) %%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Daniel@0: 
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',       
Daniel@0:       i=i+1; 
Daniel@0:       mask = varargin{i}; 
Daniel@0:      case 'munits',     
Daniel@0:       i=i+1; 
Daniel@0:       munits = varargin{i}; 
Daniel@0:      case 'msize',      
Daniel@0:       i=i+1; 
Daniel@0:       sTopol.msize = varargin{i}; 
Daniel@0:       munits = prod(sTopol.msize); 
Daniel@0:      case 'mapsize',    
Daniel@0:       i=i+1; 
Daniel@0:       mapsize = varargin{i}; 
Daniel@0:      case 'name',       
Daniel@0:       i=i+1; 
Daniel@0:       name = varargin{i};
Daniel@0:      case 'comp_names', 
Daniel@0:       i=i+1; 
Daniel@0:       comp_names = varargin{i}; 
Daniel@0:      case 'lattice',    
Daniel@0:       i=i+1; 
Daniel@0:       sTopol.lattice = varargin{i};
Daniel@0:      case 'shape',      
Daniel@0:       i=i+1; 
Daniel@0:       sTopol.shape = varargin{i}; 
Daniel@0:      case {'topol','som_topol','sTopol'}, 
Daniel@0:       i=i+1; 
Daniel@0:       sTopol = varargin{i}; 
Daniel@0:       munits = prod(sTopol.msize); 
Daniel@0:      case 'neigh',      
Daniel@0:       i=i+1; 
Daniel@0:       neigh = varargin{i};
Daniel@0:      case 'tracking',   
Daniel@0:       i=i+1; 
Daniel@0:       tracking = varargin{i};
Daniel@0:      case 'algorithm',  
Daniel@0:       i=i+1; 
Daniel@0:       algorithm = varargin{i}; 
Daniel@0:   % unambiguous values
Daniel@0:      case {'hexa','rect'}, 
Daniel@0:       sTopol.lattice = varargin{i};
Daniel@0:      case {'sheet','cyl','toroid'}, 
Daniel@0:       sTopol.shape = varargin{i}; 
Daniel@0:      case {'gaussian','cutgauss','ep','bubble'}, 
Daniel@0:       neigh = varargin{i};
Daniel@0:      case {'seq','batch'}, 
Daniel@0:       algorithm = varargin{i}; 
Daniel@0:      case {'small','normal','big'}, 
Daniel@0:       mapsize = varargin{i}; 
Daniel@0:      otherwise argok=0; 
Daniel@0:     end
Daniel@0:   elseif isstruct(varargin{i}) & isfield(varargin{i},'type'), 
Daniel@0:     switch varargin{i}(1).type, 
Daniel@0:       case 'som_topol', 
Daniel@0:        sTopol = 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_supervised) Ignoring invalid argument #' num2str(i+1)]); 
Daniel@0:   end
Daniel@0:   i = i+1; 
Daniel@0: end
Daniel@0: 
Daniel@0: %%%%%%%% Action %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Daniel@0: 
Daniel@0: 
Daniel@0: 
Daniel@0: % constructing the training data by adding 1-of-N -coded matrix to the
Daniel@0: % original data.
Daniel@0: 
Daniel@0: [dlen,dim] = size(D0);
Daniel@0: 
Daniel@0: Dc = zeros(dlen,n);
Daniel@0: 
Daniel@0: for i=1:dlen 
Daniel@0:   if c(i)
Daniel@0:     Dc(i,c(i)) = 1;
Daniel@0:   end
Daniel@0: end
Daniel@0: 
Daniel@0: D = [D0, Dc];
Daniel@0: 
Daniel@0: % initialization and training 
Daniel@0: 
Daniel@0: sD = som_data_struct(D,...
Daniel@0:                      'name',data_name);
Daniel@0: 
Daniel@0: sM = som_make(sD,...
Daniel@0:               'mask',mask,...
Daniel@0:               'munits',munits,...
Daniel@0:               'name',data_name,...
Daniel@0:               'tracking',tracking,...
Daniel@0:               'algorithm',algorithm,...
Daniel@0:               'mapsize',mapsize,...
Daniel@0:               'topol',sTopol,...
Daniel@0:               'neigh',neigh);
Daniel@0: 
Daniel@0: % add labels
Daniel@0: 
Daniel@0: for i=1:prod(sM.topol.msize), 
Daniel@0:   [dummy,class] = max(sM.codebook(i,dim+[1:n]));
Daniel@0:   sM.labels{i} = classlabels{class};
Daniel@0: end
Daniel@0: 
Daniel@0: %sD.labels = sData.labels;
Daniel@0: %sM = som_autolabel(sM,sD,'vote');
Daniel@0: 
Daniel@0: % remove extra components and modify map -struct
Daniel@0: 
Daniel@0: sM.codebook = sM.codebook(:,1:dim);
Daniel@0: sM.mask = sM.mask(1:dim);
Daniel@0: sM.comp_names = sData.comp_names;
Daniel@0: sM.comp_norm = sData.comp_norm;
Daniel@0: 
Daniel@0: % remove extras from sM.trainhist
Daniel@0: 
Daniel@0: for i=1:length(sM.trainhist)
Daniel@0:   if sM.trainhist(i).mask
Daniel@0:     sM.trainhist(i).mask = sM.trainhist(i).mask(1:dim);
Daniel@0:   end
Daniel@0: end
Daniel@0: 
Daniel@0: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Daniel@0: 
Daniel@0: function [numbers, n, names] = class2num(class)
Daniel@0: 
Daniel@0: names = {};
Daniel@0: numbers = zeros(length(class),1);
Daniel@0: 
Daniel@0: for i=1:length(class)
Daniel@0:   if ~isempty(class{i}) & ~any(strcmp(class{i},names))
Daniel@0:     names=cat(1,names,class(i));
Daniel@0:   end
Daniel@0: end
Daniel@0: 
Daniel@0: n=length(names);
Daniel@0: 
Daniel@0: tmp_numbers = (1:n)';
Daniel@0: 
Daniel@0: for i=1:length(class)
Daniel@0:   if ~isempty(class{i})
Daniel@0:     numbers(i,1) = find(strcmp(class{i},names));    
Daniel@0:   end
Daniel@0: end