SOM Toolbox | Online documentation | http://www.cis.hut.fi/projects/somtoolbox/ |
% SOM Toolbox
Version 2.0beta, Dec 21 2001 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 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 kmeans k-means algorithm kmeans_clusters try and evaluate several k-means clusterings neural_gas neural gas vector quantization algorithm som_linkage hierarchical clustering algorithms 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 Auxiliary functions som_bmus calculates BMUs for given data vectors som_eucdist2 pairwise squared euclidian 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_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 nanstats mean, std and median which ignore NaNs som_modify_dataset add, remove, or extract samples and components 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 network 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 Auxiliary functions for visualization 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 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