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