diff toolboxes/MIRtoolbox1.3.2/somtoolbox/somtoolbox.m @ 0:e9a9cd732c1e tip

first hg version after svn

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+++ b/toolboxes/MIRtoolbox1.3.2/somtoolbox/somtoolbox.m	Tue Feb 10 15:05:51 2015 +0000
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+% 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