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function sMap = som_map_struct(dim, varargin)
%SOM_MAP_STRUCT Create map struct.
%
% sMap = som_map_struct(dim, [[argID,] value, ...])
%
% sMap = som_map_struct(4);
% sMap = som_map_struct(4,'msize',[3 4],'hexa','sheet');
% sMap = som_map_struct(4,'msize',[3 4 5],'rect','name','a 3D-SOM');
% sMap = som_map_struct(4,'msize',[3 4],'bubble','mask',[1 1 1 0]);
%
% Input and output arguments ([]'s are optional):
% dim (scalar) input space dimension
% [argID, (string) See below. The values which are unambiguous can
% value] (varies) be given without the preceeding argID.
%
% sMap (struct) self-organizing map struct
%
% Here are the valid argument IDs and corresponding values. The values
% which are unambiguous (marked with '*') can be given without the
% preceeding argID.
% 'mask' (vector) BMU search mask, size dim x 1
% 'msize' (vector) map grid size, default is [0]
% 'labels' (string array / cellstr) labels for each map unit,
% length=prod(msize)
% 'name' (string) map name
% 'comp_names' (string array / cellstr) component names, size dim x 1
% 'comp_norm' (cell array) normalization operations for each
% component, size dim x 1. Each cell is either empty,
% or a cell array of normalization structs.
% 'topol' *(struct) topology struct
% 'som_topol','sTopol' = 'topol'
% 'lattice' *(string) map lattice, 'hexa' or 'rect'
% 'shape' *(string) map shape, 'sheet', 'cyl' or 'toroid'
% 'neigh' *(string) neighborhood function, 'gaussian', 'cutgauss',
% 'ep' or 'bubble'
%
% For more help, try 'type som_map_struct' or check out online documentation.
% See also SOM_SET, SOM_INFO, SOM_DATA_STRUCT, SOM_TOPOL_STRUCT, SOM_MAKE.
%%%%%%%%%%%%% DETAILED DESCRIPTION %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% som_map_struct
%
% PURPOSE
%
% Creates a self-organizing map structure.
%
% SYNTAX
%
% sM = som_map_struct(dim)
% sM = som_map_struct(...,'argID',value,...);
% sM = som_map_struct(...,value,...);
%
% DESCRIPTION
%
% Creates a self-organizing map struct. The struct contains the map
% codebook, labels, topology, information on normalization and training,
% as well as component names and a name for the map. The obligatory
% parameter is the map dimension. Most of the other fields can be
% given values using optional arguments. If they are left unspecified,
% default values are used.
%
% Field Type Size / default value (munits = prod(msize))
% ------------------------------------------------------------------------
% .type (string) 'som_map'
% .name (string) 'SOM date'
% .codebook (matrix) rand(munits, dim)
% .topol (struct) topology struct, with the following fields
% .type (string) 'som_topol'
% .msize (vector) size k x 1, [0]
% .lattice (string) 'hexa'
% .shape (string) 'sheet'
% .labels (cellstr) size munits x m, {''; ''; ... ''}
% .neigh (string) 'gaussian'
% .mask (vector) size dim x 1, [1; 1; ...; 1]
% .trainhist (cell array) size tl x 1, []
% .comp_names (cellstr) size dim x 1, {'Variable1', 'Variable2', ...}
% .comp_norm (cell array) size dim x 1, {[], [], ... []}
%
% '.type' field is the struct identifier. Do not change it.
% '.name' field is the identifier for the whole map struct
% '.codebook' field is the codebook matrix, each row corresponds to one unit
% '.topol' field is the topology of the map. This struct has three fields:
% '.msize' field is the dimensions of the map grid. Note that the
% matrix notation of indeces is used.
% '.lattice' field is the map grid lattice
% '.shape' field is the map grid shape
% '.labels' field contains the labels for each of the vectors. The ith row
% of '.labels' contains the labels for ith map unit. Note that
% if some vectors have more labels than others, the others are
% are given empty labels ('') to pad the '.labels' array up.
% '.neigh' field is the neighborhood function.
% '.mask' field is the BMU search mask.
% '.trainhist' field contains information on the training. It is a cell
% array of training structs. The first training struct contains
% information on initialization, the others on actual trainings.
% If the map has not been initialized, '.trainhist' is empty ([]).
% '.comp_names' field contains the names of the vector components
% '.comp_norm' field contains normalization information for each
% component. Each cell of '.comp_norm' is itself a cell array of
% normalization structs. If no normalizations are performed for
% the particular component, the cell is empty ([]).
%
% REQUIRED INPUT ARGUMENTS
%
% dim (scalar) Input space dimension.
%
% OPTIONAL INPUT ARGUMENTS
%
% argID (string) Argument identifier string (see below).
% value (varies) Value for the argument (see below).
%
% The optional arguments are given as 'argID',value -pairs. If the
% value is unambiguous (marked below with '*'), it can be given
% without the preceeding argID. If an argument is given value
% multiple times, the last one is used.
%
% 'mask' (vector) BMU search mask, size dim x 1
% 'msize' (vector) map grid size, default is [0]
% 'labels' (string array / cellstr) labels for each map unit,
% length=prod(msize)
% 'name' (string) map name
% 'comp_names' (string array / cellstr) component names, size dim x 1
% 'comp_norm' (cell array) normalization operations for each
% component, size dim x 1. Each cell is either empty,
% or a cell array of normalization structs.
% 'lattice' *(string) map lattice, 'hexa' or 'rect'
% 'shape' *(string) map shape, 'sheet', 'cyl' or 'toroid'
% 'topol' *(struct) topology struct, sets msize, lattice and shape
% 'som_topol','sTopol' = 'topol'
% 'neigh' *(string) neighborhood function, 'gaussian', 'cutgauss',
% 'ep' or 'bubble'
%
% OUTPUT ARGUMENTS
%
% sMap (struct) the map struct
%
% EXAMPLES
%
% Simplest case:
% sMap = som_map_struct(3);
%
% With optional arguments, the other fields can be given values:
% sTo = som_set('som_topol','msize',[10 5]);
% labs = cell(50, 1); labs{1, 1} = 'first_unit';
% cnames = {'first'; 'second'; 'third'};
% sN = som_set('som_norm');
% csN = {sN; sN; sN};
%
% sMap = som_map_struct(3,'msize',[10 5],'rect');
% sMap = som_map_struct(3,'msize',[10 5],'lattice','rect');
% sMap = som_map_struct(3,sTo,'bubble','labels',labs);
% sMap = som_map_struct(3,sTo,'comp_names',cnames);
% sMap = som_map_struct(3,sTo,'name','a data struct');
% sMap = som_map_struct(3,sTo,'comp_norm',csN,'mask',[1 0 0.5]);
%
% SEE ALSO
%
% som_set Set values and create SOM Toolbox structs.
% som_data_struct Create a data struct.
% som_make Initialize and train self-organizing map.
% som_topol_struct Default values for map topology.
% Copyright (c) 1997-2000 by the SOM toolbox programming team.
% http://www.cis.hut.fi/projects/somtoolbox/
% Version 1.0beta ecco 100997
% Version 2.0beta juuso 101199 130300
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% default values
sTopol = som_set('som_topol','lattice','hexa','shape','sheet');
neigh = 'gaussian';
mask = ones(dim,1);
name = sprintf('SOM %s', datestr(now, 1));
labels = cell(prod(sTopol.msize),1);
for i=1:length(labels), labels{i} = ''; end
comp_names = cell(dim,1);
for i = 1:dim, comp_names{i} = sprintf('Variable%d', i); end
comp_norm = cell(dim,1);
% varargin
i=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 'msize', i=i+1; sTopol.msize = varargin{i};
case 'labels', i=i+1; labels = varargin{i};
case 'name', i=i+1; name = varargin{i};
case 'comp_names', i=i+1; comp_names = varargin{i};
case 'comp_norm', i=i+1; comp_norm = varargin{i};
case 'lattice', i=i+1; sTopol.lattice = varargin{i};
case 'shape', i=i+1; sTopol.shape = varargin{i};
case {'topol','som_topol','sTopol'}, i=i+1; sTopol = varargin{i};
case 'neigh', i=i+1; neigh = varargin{i};
% unambiguous values
case {'hexa','rect'}, sTopol.lattice = varargin{i};
case {'sheet','cyl','toroid'}, sTopol.shape = varargin{i};
case {'gaussian','cutgauss','ep','bubble'}, neigh = varargin{i};
otherwise argok=0;
end
elseif isstruct(varargin{i}) & isfield(varargin{i},'type'),
switch varargin{i}(1).type,
case 'som_topol', sTopol = varargin{i};
otherwise argok=0;
end
else
argok = 0;
end
if ~argok,
disp(['(som_map_struct) Ignoring invalid argument #' num2str(i+1)]);
end
i = i+1;
end
% create the SOM
codebook = rand(prod(sTopol.msize),dim);
sTrain = som_set('som_train','time',datestr(now,0),'mask',mask);
sMap = som_set('som_map','codebook',codebook,'topol',sTopol,...
'neigh',neigh,'labels',labels,'mask',mask,...
'comp_names',comp_names,'name',name,...
'comp_norm',comp_norm,'trainhist',sTrain);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%