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author wolffd
date Tue, 10 Feb 2015 15:05:51 +0000
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1 % SOM Toolbox
2 % Version 2.0beta, May 30 2002
3 %
4 % Copyright 1997-2000 by
5 % Esa Alhoniemi, Johan Himberg, Juha Parhankangas and Juha Vesanto
6 % Contributed files may contain copyrights of their own.
7 %
8 % SOM Toolbox comes with ABSOLUTELY NO WARRANTY; for details
9 % see License.txt in the program package. This is free software,
10 % and you are welcome to redistribute it under certain conditions;
11 % see License.txt for details.
12 %
13 %
14 % Demos
15 %
16 % som_demo1 SOM Toolbox demo 1: basic properties
17 % som_demo2 SOM Toolbox demo 2: basic usage
18 % som_demo3 SOM Toolbox demo 3: visualization
19 % som_demo4 SOM Toolbox demo 4: data analysis
20 %
21 % Creation of structs
22 %
23 % som_set create & set (& check) values to structs
24 % som_info print out information on a given struct
25 % som_data_struct create & initialize a data struct
26 % som_map_struct create & initialize a map struct
27 % som_topol_struct create & initialize a topology struct
28 % som_train_struct create & initialize a train struct
29 % som_clstruct create a cluster struct
30 % som_clset set properties in a cluster struct
31 % som_clget get stuff from a cluster struct
32 %
33 % Struct conversion and file I/O
34 %
35 % som_vs1to2 converts a version 1.0 struct to version 2.0 struct
36 % som_vs2to1 converts a version 2.0 struct to version 1.0 struct
37 % som_read_data reads a (SOM_PAK format) ASCII data file
38 % som_write_data writes a SOM_PAK format codebook file
39 % som_write_cod writes a SOM_PAK format data file
40 % som_read_cod reads a SOM_PAK format codebook file
41 %
42 % Data preprocessing
43 %
44 % som_normalize normalize data set
45 % som_denormalize denormalize data set
46 % som_norm_variable (de)normalize one variable
47 % preprocess preprocessing GUI
48 %
49 % Initialization and training functions
50 %
51 % som_make create, initialize and train a SOM
52 % som_randinit random initialization algorithm
53 % som_lininit linear initialization algorithm
54 % som_seqtrain sequential training algorithm
55 % som_batchtrain batch training algorithm
56 % som_gui SOM initialization and training GUI
57 % som_prototrain a simple version of sequential training: easy to modify
58 %
59 % Clustering algorithms
60 %
61 % som_kmeans k-means algorithm (was earlier kmeans)
62 % kmeans_clusters try and evaluate several k-means clusterings
63 % neural_gas neural gas vector quantization algorithm
64 % som_linkage hierarchical clustering algorithms
65 % som_cllinkage hierarchical clustering of SOM
66 % som_dmatminima local minima from distance (or U-) matrix
67 % som_dmatclusters distance (or U-) matrix based clustering
68 % som_clspread spreads clusters to unassinged map units
69 % som_cldist calculate distances between clusters
70 % som_gapindex gap validity index of clustering
71 % db_index Davies-Bouldin validity index of clustering
72 %
73 % Supervised/classification algorithms
74 %
75 % som_supervised supervised SOM algorithm
76 % lvq1 LVQ1 algorithm
77 % lvq3 LVQ3 algorithm
78 % knn k-NN classification algorithm
79 % knn_old k-NN classification algorithm (old version)
80 %
81 % SOM error measures
82 %
83 % som_quality quantization and topographic error of SOM
84 % som_distortion SOM distortion measure
85 % som_distortion3 elements of the SOM distortion measure
86 %
87 % Auxiliary functions
88 %
89 % som_bmus calculates BMUs for given data vectors
90 % som_eucdist2 pairwise squared euclidian distances between vectors
91 % som_mdist calculates pairwise distances between vectors
92 % som_divide extract subsets of data based on map
93 % som_label give labels to map units
94 % som_label2num rcodes string data labels to interger class labels
95 % som_autolabel automatically labels the SOM based on given data
96 % som_unit_coords calculates coordinates in output space for map units
97 % som_unit_dists distances in output space between map units
98 % som_unit_neighs units in 1-neighborhood for each map unit
99 % som_neighborhood calculates neighborhood matrix for the given map
100 % som_neighbors calculates different kinds of neighborhoods
101 % som_neighf calculates neighborhood function values
102 % som_select GUI for manual selection of map units
103 % som_estimate_gmm create Gaussian mixture model on top of SOM
104 % som_probability_gmm evaluate Gaussian mixture model
105 % som_ind2sub from linear index to subscript index
106 % som_sub2ind from subscript index to linear index
107 % som_ind2cod from linear index to SOM_PAK linear index
108 % som_cod2ind from SOM_linear index to SOM_PAK linear index
109 % nanstats mean, std and median which ignore NaNs
110 % som_modify_dataset add, remove, or extract samples and components
111 % som_fillnans fill NaNs in a data set based on given SOM
112 % som_stats statistics of a data set
113 % som_drmake calculate descriptive rules for a cluster
114 % som_dreval evaluate descriptive rules for a cluster
115 % som_drsignif rule significance measures
116 %
117 % Using SOM_PAK from Matlab
118 %
119 % som_sompaktrain uses SOM_PAK to train a map
120 % sompak_gui GUI for using SOM_PAK from Matlab
121 % sompak_init call SOM_PAK's initialization programs from Matlab
122 % sompak_init_gui GUI for using SOM_PAK's initialization from Matlab
123 % sompak_rb_control an auxiliary function for sompak_*_gui functions.
124 % sompak_sammon call SOM_PAK's Sammon program from Matlab
125 % sompak_sammon_gui GUI for using SOM_PAK's Sammon program from Matlab
126 % sompak_train call SOM_PAK's training program from Matlab
127 % sompak_train_gui GUI for using SOM_PAK's training program from Matlab
128 %
129 % Visualization
130 %
131 % som_show basic visualization
132 % som_show_add add labels, hits and trajectories
133 % som_show_clear remove extra markers
134 % som_recolorbar refresh/reconfigure colorbars
135 % som_show_gui GUI for using som_show and associated functions
136 % som_grid visualization of SOM grid
137 % som_cplane component planes and U-matrices
138 % som_barplane bar chart visualization of map
139 % som_pieplane pie chart visualization of map
140 % som_plotplane plot chart visualization of map
141 % som_trajectory launches a GUI for presenting comet-trajectories
142 % som_dendrogram visualization of clustering tree
143 % som_plotmatrix pairwise scatter plots and histograms
144 % som_order_cplanes order and visualize the component planes
145 % som_clplot plots of clusters (based on cluster struct)
146 % som_projections_plot projections plots (see som_projections)
147 % som_stats_plot plots of statistics (see som_stats)
148 %
149 % Auxiliary functions for visualization
150 %
151 % hits calculates hits, or sum of values for each map unit
152 % som_hits calculates the response of data on the map
153 % som_umat calculates the U-matrix
154 % cca curvilinear component analysis projection algorithm
155 % pcaproj principal component projection algorithm
156 % sammon Sammon's mapping projection algorithm
157 % som_connection connection matrix for map
158 % som_vis_coords map unit coordinates used in visualizations
159 % som_colorcode create color coding for map/2D data
160 % som_bmucolor colors of the BMUs from a given map color code
161 % som_normcolor simulate indexed colormap
162 % som_clustercolor color coding which depends on clustering structure
163 % som_kmeanscolor color coding according to k-means clustering
164 % som_kmeanscolor2 a newer version of the som_kmeanscolor function
165 % som_fuzzycolor a fuzzy color coding
166 % som_coloring a SOM-based color coding
167 % som_projections calculates a default set of projections
168 %
169 % Report generation stuff
170 %
171 % som_table_struct creates a table struct
172 % som_table_modify modifies a table struct
173 % som_table_print print a table in various formats
174 % rep_utils various utilities for printing report elements
175 % som_stats_table a table of data set statistics
176 % som_stats_report report on data set statistics
177 %
178 % Low level routines used by visualization functions
179 %
180 % vis_patch defines hexagonal and rectangular patches
181 % vis_som_show_data returns UserData and subplot handles stored by som_show.m
182 % vis_valuetype used for type checks
183 % vis_footnote adds a movable text to the current figure
184 % vis_trajgui the actual GUI started by som_trajectory.m
185 % vis_PlaneAxisProperties set axis properties in visualization functions
186 % vis_footnoteButtonDownFcn callback function for vis_footnote.m
187 % vis_planeGetArgs converts topol struct to lattice, msize argument pair
188 % vis_show_gui_comp internal function used by som_show_gui.m
189 % vis_show_gui_tool internal function used by som_show_gui.m
190 %
191 % Other
192 %
193 % somtoolbox this file
194 % iris.data IRIS data set (used in demos)
195 % License.txt GNU General Public License
196 % Copyright.txt Copyright notice