SOM Toolbox Online documentation


% 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.
            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
      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 
             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
           somtoolbox   this file
     IRIS data set (used in demos)
          License.txt   GNU General Public License 
        Copyright.txt   Copyright notice

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