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

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first hg version after svn
author wolffd
date Tue, 10 Feb 2015 15:05:51 +0000
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1 function sMap = som_map_struct(dim, varargin)
2
3 %SOM_MAP_STRUCT Create map struct.
4 %
5 % sMap = som_map_struct(dim, [[argID,] value, ...])
6 %
7 % sMap = som_map_struct(4);
8 % sMap = som_map_struct(4,'msize',[3 4],'hexa','sheet');
9 % sMap = som_map_struct(4,'msize',[3 4 5],'rect','name','a 3D-SOM');
10 % sMap = som_map_struct(4,'msize',[3 4],'bubble','mask',[1 1 1 0]);
11 %
12 % Input and output arguments ([]'s are optional):
13 % dim (scalar) input space dimension
14 % [argID, (string) See below. The values which are unambiguous can
15 % value] (varies) be given without the preceeding argID.
16 %
17 % sMap (struct) self-organizing map struct
18 %
19 % Here are the valid argument IDs and corresponding values. The values
20 % which are unambiguous (marked with '*') can be given without the
21 % preceeding argID.
22 % 'mask' (vector) BMU search mask, size dim x 1
23 % 'msize' (vector) map grid size, default is [0]
24 % 'labels' (string array / cellstr) labels for each map unit,
25 % length=prod(msize)
26 % 'name' (string) map name
27 % 'comp_names' (string array / cellstr) component names, size dim x 1
28 % 'comp_norm' (cell array) normalization operations for each
29 % component, size dim x 1. Each cell is either empty,
30 % or a cell array of normalization structs.
31 % 'topol' *(struct) topology struct
32 % 'som_topol','sTopol' = 'topol'
33 % 'lattice' *(string) map lattice, 'hexa' or 'rect'
34 % 'shape' *(string) map shape, 'sheet', 'cyl' or 'toroid'
35 % 'neigh' *(string) neighborhood function, 'gaussian', 'cutgauss',
36 % 'ep' or 'bubble'
37 %
38 % For more help, try 'type som_map_struct' or check out online documentation.
39 % See also SOM_SET, SOM_INFO, SOM_DATA_STRUCT, SOM_TOPOL_STRUCT, SOM_MAKE.
40
41 %%%%%%%%%%%%% DETAILED DESCRIPTION %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
42 %
43 % som_map_struct
44 %
45 % PURPOSE
46 %
47 % Creates a self-organizing map structure.
48 %
49 % SYNTAX
50 %
51 % sM = som_map_struct(dim)
52 % sM = som_map_struct(...,'argID',value,...);
53 % sM = som_map_struct(...,value,...);
54 %
55 % DESCRIPTION
56 %
57 % Creates a self-organizing map struct. The struct contains the map
58 % codebook, labels, topology, information on normalization and training,
59 % as well as component names and a name for the map. The obligatory
60 % parameter is the map dimension. Most of the other fields can be
61 % given values using optional arguments. If they are left unspecified,
62 % default values are used.
63 %
64 % Field Type Size / default value (munits = prod(msize))
65 % ------------------------------------------------------------------------
66 % .type (string) 'som_map'
67 % .name (string) 'SOM date'
68 % .codebook (matrix) rand(munits, dim)
69 % .topol (struct) topology struct, with the following fields
70 % .type (string) 'som_topol'
71 % .msize (vector) size k x 1, [0]
72 % .lattice (string) 'hexa'
73 % .shape (string) 'sheet'
74 % .labels (cellstr) size munits x m, {''; ''; ... ''}
75 % .neigh (string) 'gaussian'
76 % .mask (vector) size dim x 1, [1; 1; ...; 1]
77 % .trainhist (cell array) size tl x 1, []
78 % .comp_names (cellstr) size dim x 1, {'Variable1', 'Variable2', ...}
79 % .comp_norm (cell array) size dim x 1, {[], [], ... []}
80 %
81 % '.type' field is the struct identifier. Do not change it.
82 % '.name' field is the identifier for the whole map struct
83 % '.codebook' field is the codebook matrix, each row corresponds to one unit
84 % '.topol' field is the topology of the map. This struct has three fields:
85 % '.msize' field is the dimensions of the map grid. Note that the
86 % matrix notation of indeces is used.
87 % '.lattice' field is the map grid lattice
88 % '.shape' field is the map grid shape
89 % '.labels' field contains the labels for each of the vectors. The ith row
90 % of '.labels' contains the labels for ith map unit. Note that
91 % if some vectors have more labels than others, the others are
92 % are given empty labels ('') to pad the '.labels' array up.
93 % '.neigh' field is the neighborhood function.
94 % '.mask' field is the BMU search mask.
95 % '.trainhist' field contains information on the training. It is a cell
96 % array of training structs. The first training struct contains
97 % information on initialization, the others on actual trainings.
98 % If the map has not been initialized, '.trainhist' is empty ([]).
99 % '.comp_names' field contains the names of the vector components
100 % '.comp_norm' field contains normalization information for each
101 % component. Each cell of '.comp_norm' is itself a cell array of
102 % normalization structs. If no normalizations are performed for
103 % the particular component, the cell is empty ([]).
104 %
105 % REQUIRED INPUT ARGUMENTS
106 %
107 % dim (scalar) Input space dimension.
108 %
109 % OPTIONAL INPUT ARGUMENTS
110 %
111 % argID (string) Argument identifier string (see below).
112 % value (varies) Value for the argument (see below).
113 %
114 % The optional arguments are given as 'argID',value -pairs. If the
115 % value is unambiguous (marked below with '*'), it can be given
116 % without the preceeding argID. If an argument is given value
117 % multiple times, the last one is used.
118 %
119 % 'mask' (vector) BMU search mask, size dim x 1
120 % 'msize' (vector) map grid size, default is [0]
121 % 'labels' (string array / cellstr) labels for each map unit,
122 % length=prod(msize)
123 % 'name' (string) map name
124 % 'comp_names' (string array / cellstr) component names, size dim x 1
125 % 'comp_norm' (cell array) normalization operations for each
126 % component, size dim x 1. Each cell is either empty,
127 % or a cell array of normalization structs.
128 % 'lattice' *(string) map lattice, 'hexa' or 'rect'
129 % 'shape' *(string) map shape, 'sheet', 'cyl' or 'toroid'
130 % 'topol' *(struct) topology struct, sets msize, lattice and shape
131 % 'som_topol','sTopol' = 'topol'
132 % 'neigh' *(string) neighborhood function, 'gaussian', 'cutgauss',
133 % 'ep' or 'bubble'
134 %
135 % OUTPUT ARGUMENTS
136 %
137 % sMap (struct) the map struct
138 %
139 % EXAMPLES
140 %
141 % Simplest case:
142 % sMap = som_map_struct(3);
143 %
144 % With optional arguments, the other fields can be given values:
145 % sTo = som_set('som_topol','msize',[10 5]);
146 % labs = cell(50, 1); labs{1, 1} = 'first_unit';
147 % cnames = {'first'; 'second'; 'third'};
148 % sN = som_set('som_norm');
149 % csN = {sN; sN; sN};
150 %
151 % sMap = som_map_struct(3,'msize',[10 5],'rect');
152 % sMap = som_map_struct(3,'msize',[10 5],'lattice','rect');
153 % sMap = som_map_struct(3,sTo,'bubble','labels',labs);
154 % sMap = som_map_struct(3,sTo,'comp_names',cnames);
155 % sMap = som_map_struct(3,sTo,'name','a data struct');
156 % sMap = som_map_struct(3,sTo,'comp_norm',csN,'mask',[1 0 0.5]);
157 %
158 % SEE ALSO
159 %
160 % som_set Set values and create SOM Toolbox structs.
161 % som_data_struct Create a data struct.
162 % som_make Initialize and train self-organizing map.
163 % som_topol_struct Default values for map topology.
164
165 % Copyright (c) 1997-2000 by the SOM toolbox programming team.
166 % http://www.cis.hut.fi/projects/somtoolbox/
167
168 % Version 1.0beta ecco 100997
169 % Version 2.0beta juuso 101199 130300
170
171 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
172
173 % default values
174 sTopol = som_set('som_topol','lattice','hexa','shape','sheet');
175 neigh = 'gaussian';
176 mask = ones(dim,1);
177 name = sprintf('SOM %s', datestr(now, 1));
178 labels = cell(prod(sTopol.msize),1);
179 for i=1:length(labels), labels{i} = ''; end
180 comp_names = cell(dim,1);
181 for i = 1:dim, comp_names{i} = sprintf('Variable%d', i); end
182 comp_norm = cell(dim,1);
183
184 % varargin
185 i=1;
186 while i<=length(varargin),
187 argok = 1;
188 if ischar(varargin{i}),
189 switch varargin{i},
190 % argument IDs
191 case 'mask', i=i+1; mask = varargin{i};
192 case 'msize', i=i+1; sTopol.msize = varargin{i};
193 case 'labels', i=i+1; labels = varargin{i};
194 case 'name', i=i+1; name = varargin{i};
195 case 'comp_names', i=i+1; comp_names = varargin{i};
196 case 'comp_norm', i=i+1; comp_norm = varargin{i};
197 case 'lattice', i=i+1; sTopol.lattice = varargin{i};
198 case 'shape', i=i+1; sTopol.shape = varargin{i};
199 case {'topol','som_topol','sTopol'}, i=i+1; sTopol = varargin{i};
200 case 'neigh', i=i+1; neigh = varargin{i};
201 % unambiguous values
202 case {'hexa','rect'}, sTopol.lattice = varargin{i};
203 case {'sheet','cyl','toroid'}, sTopol.shape = varargin{i};
204 case {'gaussian','cutgauss','ep','bubble'}, neigh = varargin{i};
205 otherwise argok=0;
206 end
207 elseif isstruct(varargin{i}) & isfield(varargin{i},'type'),
208 switch varargin{i}(1).type,
209 case 'som_topol', sTopol = varargin{i};
210 otherwise argok=0;
211 end
212 else
213 argok = 0;
214 end
215 if ~argok,
216 disp(['(som_map_struct) Ignoring invalid argument #' num2str(i+1)]);
217 end
218 i = i+1;
219 end
220
221 % create the SOM
222 codebook = rand(prod(sTopol.msize),dim);
223 sTrain = som_set('som_train','time',datestr(now,0),'mask',mask);
224 sMap = som_set('som_map','codebook',codebook,'topol',sTopol,...
225 'neigh',neigh,'labels',labels,'mask',mask,...
226 'comp_names',comp_names,'name',name,...
227 'comp_norm',comp_norm,'trainhist',sTrain);
228
229
230
231 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%