% SOM Toolbox% Version 2.0beta, May 30 2002% % Copyright 1997-2000 by% Esa Alhoniemi, Johan Himberg, Juha Parhankangas and Juha Vesanto% Contributed files may contain copyrights of their own.% % SOM Toolbox comes with ABSOLUTELY NO WARRANTY; for details% see License.txt in the program package. This is free software,% and you are welcome to redistribute it under certain conditions;% see License.txt for details.% % % Demos% %            som_demo1   SOM Toolbox demo 1: basic properties%            som_demo2   SOM Toolbox demo 2: basic usage%            som_demo3   SOM Toolbox demo 3: visualization%            som_demo4   SOM Toolbox demo 4: data analysis% % Creation of structs% %              som_set   create & set (& check) values to structs%             som_info   print out information on a given struct  %      som_data_struct   create & initialize a data struct %       som_map_struct   create & initialize a map struct %     som_topol_struct   create & initialize a topology struct %     som_train_struct   create & initialize a train struct %         som_clstruct   create a cluster struct%            som_clset   set properties in a cluster struct%            som_clget   get stuff from a cluster struct% % Struct conversion and file I/O% %           som_vs1to2   converts a version 1.0 struct to version 2.0 struct%           som_vs2to1   converts a version 2.0 struct to version 1.0 struct%        som_read_data   reads a (SOM_PAK format) ASCII data file%       som_write_data   writes a SOM_PAK format codebook file%        som_write_cod   writes a SOM_PAK format data file%         som_read_cod   reads a SOM_PAK format codebook file% % Data preprocessing% %        som_normalize   normalize data set%      som_denormalize   denormalize data set %    som_norm_variable   (de)normalize one variable%           preprocess   preprocessing GUI% % Initialization and training functions% %             som_make   create, initialize and train a SOM%         som_randinit   random initialization algorithm%          som_lininit   linear initialization algorithm%         som_seqtrain   sequential training algorithm%       som_batchtrain   batch training algorithm%              som_gui   SOM initialization and training GUI%       som_prototrain   a simple version of sequential training: easy to modify% % Clustering algorithms% %           som_kmeans   k-means algorithm (was earlier kmeans)%      kmeans_clusters   try and evaluate several k-means clusterings%           neural_gas   neural gas vector quantization algorithm%          som_linkage   hierarchical clustering algorithms%        som_cllinkage   hierarchical clustering of SOM%       som_dmatminima   local minima from distance (or U-) matrix%     som_dmatclusters   distance (or U-) matrix based clustering%         som_clspread   spreads clusters to unassinged map units%           som_cldist   calculate distances between clusters%         som_gapindex   gap validity index of clustering%             db_index   Davies-Bouldin validity index of clustering  % % Supervised/classification algorithms% %       som_supervised   supervised SOM algorithm%                 lvq1   LVQ1 algorithm%                 lvq3   LVQ3 algorithm%                  knn   k-NN classification algorithm %              knn_old   k-NN classification algorithm (old version)% % SOM error measures% %          som_quality   quantization and topographic error of SOM%       som_distortion   SOM distortion measure%      som_distortion3   elements of the SOM distortion measure% % Auxiliary functions% %             som_bmus   calculates BMUs for given data vectors%         som_eucdist2   pairwise squared euclidian distances between vectors%            som_mdist   calculates pairwise distances between vectors %           som_divide   extract subsets of data based on map%            som_label   give labels to map units%        som_label2num   rcodes string data labels to interger class labels %        som_autolabel   automatically labels the SOM based on given data%      som_unit_coords   calculates coordinates in output space for map units%       som_unit_dists   distances in output space between map units%      som_unit_neighs   units in 1-neighborhood for each map unit%     som_neighborhood   calculates neighborhood matrix for the given map%        som_neighbors   calculates different kinds of neighborhoods %           som_neighf   calculates neighborhood function values%           som_select   GUI for manual selection of map units%     som_estimate_gmm   create Gaussian mixture model on top of SOM%  som_probability_gmm   evaluate Gaussian mixture model%          som_ind2sub   from linear index to subscript index %          som_sub2ind   from subscript index to linear index%          som_ind2cod   from linear index to SOM_PAK linear index %          som_cod2ind   from SOM_linear index to SOM_PAK linear index %             nanstats   mean, std and median which ignore NaNs%   som_modify_dataset   add, remove, or extract samples and components%         som_fillnans   fill NaNs in a data set based on given SOM%            som_stats   statistics of a data set%           som_drmake   calculate descriptive rules for a cluster%           som_dreval   evaluate descriptive rules for a cluster%         som_drsignif   rule significance measures% % Using SOM_PAK from Matlab% %      som_sompaktrain   uses SOM_PAK to train a map%           sompak_gui   GUI for using SOM_PAK from Matlab%          sompak_init   call SOM_PAK's initialization programs from Matlab%      sompak_init_gui   GUI for using SOM_PAK's initialization from Matlab%    sompak_rb_control   an auxiliary function for sompak_*_gui functions.%        sompak_sammon   call SOM_PAK's Sammon program from Matlab%    sompak_sammon_gui   GUI for using SOM_PAK's Sammon program from Matlab%         sompak_train   call SOM_PAK's training program from Matlab%     sompak_train_gui   GUI for using SOM_PAK's training program from Matlab % % Visualization% %             som_show   basic visualization%         som_show_add   add labels, hits and trajectories%       som_show_clear   remove extra markers%       som_recolorbar   refresh/reconfigure colorbars%         som_show_gui   GUI for using som_show and associated functions%             som_grid   visualization of SOM grid%           som_cplane   component planes and U-matrices%         som_barplane   bar chart visualization of map%         som_pieplane   pie chart visualization of map%        som_plotplane   plot chart visualization of map%       som_trajectory   launches a GUI for presenting comet-trajectories %       som_dendrogram   visualization of clustering tree%       som_plotmatrix   pairwise scatter plots and histograms%    som_order_cplanes   order and visualize the component planes%           som_clplot   plots of clusters (based on cluster struct)% som_projections_plot   projections plots (see som_projections)%       som_stats_plot   plots of statistics (see som_stats)% % Auxiliary functions for visualization% %                 hits   calculates hits, or sum of values for each map unit%             som_hits   calculates the response of data on the map%             som_umat   calculates the U-matrix%                  cca   curvilinear component analysis projection algorithm%              pcaproj   principal component projection algorithm%               sammon   Sammon's mapping projection algorithm%       som_connection   connection matrix for map %       som_vis_coords   map unit coordinates used in visualizations%        som_colorcode   create color coding for map/2D data%         som_bmucolor   colors of the BMUs from a given map color code%        som_normcolor   simulate indexed colormap%     som_clustercolor   color coding which depends on clustering structure%      som_kmeanscolor   color coding according to k-means clustering%     som_kmeanscolor2   a newer version of the som_kmeanscolor function%       som_fuzzycolor   a fuzzy color coding %         som_coloring   a SOM-based color coding %      som_projections   calculates a default set of projections% % Report generation stuff% %     som_table_struct   creates a table struct%     som_table_modify   modifies a table struct%      som_table_print   print a table in various formats%            rep_utils   various utilities for printing report elements%      som_stats_table   a table of data set statistics%     som_stats_report   report on data set statistics% % Low level routines used by visualization functions% %            vis_patch   defines hexagonal and rectangular patches%    vis_som_show_data   returns UserData and subplot handles stored by som_show.m%        vis_valuetype   used for type checks %         vis_footnote   adds a movable text to the current figure %          vis_trajgui   the actual GUI started by som_trajectory.m % vis_PlaneAxisProperties   set axis properties in visualization functions% vis_footnoteButtonDownFcn   callback function for vis_footnote.m%     vis_planeGetArgs   converts topol struct to lattice, msize argument pair%    vis_show_gui_comp   internal function used by som_show_gui.m%    vis_show_gui_tool   internal function used by som_show_gui.m% % Other% %           somtoolbox   this file%            iris.data   IRIS data set (used in demos)%          License.txt   GNU General Public License %        Copyright.txt   Copyright notice