% 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