diff toolboxes/MIRtoolbox1.3.2/somtoolbox/som_map_struct.m @ 0:e9a9cd732c1e tip

first hg version after svn

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/toolboxes/MIRtoolbox1.3.2/somtoolbox/som_map_struct.m	Tue Feb 10 15:05:51 2015 +0000
@@ -0,0 +1,231 @@
+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);
+
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%