wolffd@0: % SOM Toolbox wolffd@0: % Version 2.0beta, May 30 2002 wolffd@0: % wolffd@0: % Copyright 1997-2000 by wolffd@0: % Esa Alhoniemi, Johan Himberg, Juha Parhankangas and Juha Vesanto wolffd@0: % Contributed files may contain copyrights of their own. wolffd@0: % wolffd@0: % SOM Toolbox comes with ABSOLUTELY NO WARRANTY; for details wolffd@0: % see License.txt in the program package. This is free software, wolffd@0: % and you are welcome to redistribute it under certain conditions; wolffd@0: % see License.txt for details. wolffd@0: % wolffd@0: % wolffd@0: % Demos wolffd@0: % wolffd@0: % som_demo1 SOM Toolbox demo 1: basic properties wolffd@0: % som_demo2 SOM Toolbox demo 2: basic usage wolffd@0: % som_demo3 SOM Toolbox demo 3: visualization wolffd@0: % som_demo4 SOM Toolbox demo 4: data analysis wolffd@0: % wolffd@0: % Creation of structs wolffd@0: % wolffd@0: % som_set create & set (& check) values to structs wolffd@0: % som_info print out information on a given struct wolffd@0: % som_data_struct create & initialize a data struct wolffd@0: % som_map_struct create & initialize a map struct wolffd@0: % som_topol_struct create & initialize a topology struct wolffd@0: % som_train_struct create & initialize a train struct wolffd@0: % som_clstruct create a cluster struct wolffd@0: % som_clset set properties in a cluster struct wolffd@0: % som_clget get stuff from a cluster struct wolffd@0: % wolffd@0: % Struct conversion and file I/O wolffd@0: % wolffd@0: % som_vs1to2 converts a version 1.0 struct to version 2.0 struct wolffd@0: % som_vs2to1 converts a version 2.0 struct to version 1.0 struct wolffd@0: % som_read_data reads a (SOM_PAK format) ASCII data file wolffd@0: % som_write_data writes a SOM_PAK format codebook file wolffd@0: % som_write_cod writes a SOM_PAK format data file wolffd@0: % som_read_cod reads a SOM_PAK format codebook file wolffd@0: % wolffd@0: % Data preprocessing wolffd@0: % wolffd@0: % som_normalize normalize data set wolffd@0: % som_denormalize denormalize data set wolffd@0: % som_norm_variable (de)normalize one variable wolffd@0: % preprocess preprocessing GUI wolffd@0: % wolffd@0: % Initialization and training functions wolffd@0: % wolffd@0: % som_make create, initialize and train a SOM wolffd@0: % som_randinit random initialization algorithm wolffd@0: % som_lininit linear initialization algorithm wolffd@0: % som_seqtrain sequential training algorithm wolffd@0: % som_batchtrain batch training algorithm wolffd@0: % som_gui SOM initialization and training GUI wolffd@0: % som_prototrain a simple version of sequential training: easy to modify wolffd@0: % wolffd@0: % Clustering algorithms wolffd@0: % wolffd@0: % som_kmeans k-means algorithm (was earlier kmeans) wolffd@0: % kmeans_clusters try and evaluate several k-means clusterings wolffd@0: % neural_gas neural gas vector quantization algorithm wolffd@0: % som_linkage hierarchical clustering algorithms wolffd@0: % som_cllinkage hierarchical clustering of SOM wolffd@0: % som_dmatminima local minima from distance (or U-) matrix wolffd@0: % som_dmatclusters distance (or U-) matrix based clustering wolffd@0: % som_clspread spreads clusters to unassinged map units wolffd@0: % som_cldist calculate distances between clusters wolffd@0: % som_gapindex gap validity index of clustering wolffd@0: % db_index Davies-Bouldin validity index of clustering wolffd@0: % wolffd@0: % Supervised/classification algorithms wolffd@0: % wolffd@0: % som_supervised supervised SOM algorithm wolffd@0: % lvq1 LVQ1 algorithm wolffd@0: % lvq3 LVQ3 algorithm wolffd@0: % knn k-NN classification algorithm wolffd@0: % knn_old k-NN classification algorithm (old version) wolffd@0: % wolffd@0: % SOM error measures wolffd@0: % wolffd@0: % som_quality quantization and topographic error of SOM wolffd@0: % som_distortion SOM distortion measure wolffd@0: % som_distortion3 elements of the SOM distortion measure wolffd@0: % wolffd@0: % Auxiliary functions wolffd@0: % wolffd@0: % som_bmus calculates BMUs for given data vectors wolffd@0: % som_eucdist2 pairwise squared euclidian distances between vectors wolffd@0: % som_mdist calculates pairwise distances between vectors wolffd@0: % som_divide extract subsets of data based on map wolffd@0: % som_label give labels to map units wolffd@0: % som_label2num rcodes string data labels to interger class labels wolffd@0: % som_autolabel automatically labels the SOM based on given data wolffd@0: % som_unit_coords calculates coordinates in output space for map units wolffd@0: % som_unit_dists distances in output space between map units wolffd@0: % som_unit_neighs units in 1-neighborhood for each map unit wolffd@0: % som_neighborhood calculates neighborhood matrix for the given map wolffd@0: % som_neighbors calculates different kinds of neighborhoods wolffd@0: % som_neighf calculates neighborhood function values wolffd@0: % som_select GUI for manual selection of map units wolffd@0: % som_estimate_gmm create Gaussian mixture model on top of SOM wolffd@0: % som_probability_gmm evaluate Gaussian mixture model wolffd@0: % som_ind2sub from linear index to subscript index wolffd@0: % som_sub2ind from subscript index to linear index wolffd@0: % som_ind2cod from linear index to SOM_PAK linear index wolffd@0: % som_cod2ind from SOM_linear index to SOM_PAK linear index wolffd@0: % nanstats mean, std and median which ignore NaNs wolffd@0: % som_modify_dataset add, remove, or extract samples and components wolffd@0: % som_fillnans fill NaNs in a data set based on given SOM wolffd@0: % som_stats statistics of a data set wolffd@0: % som_drmake calculate descriptive rules for a cluster wolffd@0: % som_dreval evaluate descriptive rules for a cluster wolffd@0: % som_drsignif rule significance measures wolffd@0: % wolffd@0: % Using SOM_PAK from Matlab wolffd@0: % wolffd@0: % som_sompaktrain uses SOM_PAK to train a map wolffd@0: % sompak_gui GUI for using SOM_PAK from Matlab wolffd@0: % sompak_init call SOM_PAK's initialization programs from Matlab wolffd@0: % sompak_init_gui GUI for using SOM_PAK's initialization from Matlab wolffd@0: % sompak_rb_control an auxiliary function for sompak_*_gui functions. wolffd@0: % sompak_sammon call SOM_PAK's Sammon program from Matlab wolffd@0: % sompak_sammon_gui GUI for using SOM_PAK's Sammon program from Matlab wolffd@0: % sompak_train call SOM_PAK's training program from Matlab wolffd@0: % sompak_train_gui GUI for using SOM_PAK's training program from Matlab wolffd@0: % wolffd@0: % Visualization wolffd@0: % wolffd@0: % som_show basic visualization wolffd@0: % som_show_add add labels, hits and trajectories wolffd@0: % som_show_clear remove extra markers wolffd@0: % som_recolorbar refresh/reconfigure colorbars wolffd@0: % som_show_gui GUI for using som_show and associated functions wolffd@0: % som_grid visualization of SOM grid wolffd@0: % som_cplane component planes and U-matrices wolffd@0: % som_barplane bar chart visualization of map wolffd@0: % som_pieplane pie chart visualization of map wolffd@0: % som_plotplane plot chart visualization of map wolffd@0: % som_trajectory launches a GUI for presenting comet-trajectories wolffd@0: % som_dendrogram visualization of clustering tree wolffd@0: % som_plotmatrix pairwise scatter plots and histograms wolffd@0: % som_order_cplanes order and visualize the component planes wolffd@0: % som_clplot plots of clusters (based on cluster struct) wolffd@0: % som_projections_plot projections plots (see som_projections) wolffd@0: % som_stats_plot plots of statistics (see som_stats) wolffd@0: % wolffd@0: % Auxiliary functions for visualization wolffd@0: % wolffd@0: % hits calculates hits, or sum of values for each map unit wolffd@0: % som_hits calculates the response of data on the map wolffd@0: % som_umat calculates the U-matrix wolffd@0: % cca curvilinear component analysis projection algorithm wolffd@0: % pcaproj principal component projection algorithm wolffd@0: % sammon Sammon's mapping projection algorithm wolffd@0: % som_connection connection matrix for map wolffd@0: % som_vis_coords map unit coordinates used in visualizations wolffd@0: % som_colorcode create color coding for map/2D data wolffd@0: % som_bmucolor colors of the BMUs from a given map color code wolffd@0: % som_normcolor simulate indexed colormap wolffd@0: % som_clustercolor color coding which depends on clustering structure wolffd@0: % som_kmeanscolor color coding according to k-means clustering wolffd@0: % som_kmeanscolor2 a newer version of the som_kmeanscolor function wolffd@0: % som_fuzzycolor a fuzzy color coding wolffd@0: % som_coloring a SOM-based color coding wolffd@0: % som_projections calculates a default set of projections wolffd@0: % wolffd@0: % Report generation stuff wolffd@0: % wolffd@0: % som_table_struct creates a table struct wolffd@0: % som_table_modify modifies a table struct wolffd@0: % som_table_print print a table in various formats wolffd@0: % rep_utils various utilities for printing report elements wolffd@0: % som_stats_table a table of data set statistics wolffd@0: % som_stats_report report on data set statistics wolffd@0: % wolffd@0: % Low level routines used by visualization functions wolffd@0: % wolffd@0: % vis_patch defines hexagonal and rectangular patches wolffd@0: % vis_som_show_data returns UserData and subplot handles stored by som_show.m wolffd@0: % vis_valuetype used for type checks wolffd@0: % vis_footnote adds a movable text to the current figure wolffd@0: % vis_trajgui the actual GUI started by som_trajectory.m wolffd@0: % vis_PlaneAxisProperties set axis properties in visualization functions wolffd@0: % vis_footnoteButtonDownFcn callback function for vis_footnote.m wolffd@0: % vis_planeGetArgs converts topol struct to lattice, msize argument pair wolffd@0: % vis_show_gui_comp internal function used by som_show_gui.m wolffd@0: % vis_show_gui_tool internal function used by som_show_gui.m wolffd@0: % wolffd@0: % Other wolffd@0: % wolffd@0: % somtoolbox this file wolffd@0: % iris.data IRIS data set (used in demos) wolffd@0: % License.txt GNU General Public License wolffd@0: % Copyright.txt Copyright notice