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starting som prediction fine-tuned class-performance visualisation

git-svn-id: https://svn.discofish.de/MATLAB/spmtoolbox/SVMCrossVal@112 83ab2cfd-5345-466c-8aeb-2b2739fb922d

Christoph Budziszewski authored on21/01/2009 16:34:25
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+% SOM Toolbox
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+% Version 2.0beta, May 30 2002
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+% 
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+% Copyright 1997-2000 by
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+% Esa Alhoniemi, Johan Himberg, Juha Parhankangas and Juha Vesanto
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+% Contributed files may contain copyrights of their own.
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+% 
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+% SOM Toolbox comes with ABSOLUTELY NO WARRANTY; for details
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+% see License.txt in the program package. This is free software,
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+% and you are welcome to redistribute it under certain conditions;
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+% see License.txt for details.
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+% 
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+% 
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+% Demos
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+% 
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+%            som_demo1   SOM Toolbox demo 1: basic properties
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+%            som_demo2   SOM Toolbox demo 2: basic usage
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+%            som_demo3   SOM Toolbox demo 3: visualization
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+%            som_demo4   SOM Toolbox demo 4: data analysis
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+% 
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+% Creation of structs
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+% 
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+%              som_set   create & set (& check) values to structs
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+%             som_info   print out information on a given struct  
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+%      som_data_struct   create & initialize a data struct 
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+%       som_map_struct   create & initialize a map struct 
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+%     som_topol_struct   create & initialize a topology struct 
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+%     som_train_struct   create & initialize a train struct 
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+%         som_clstruct   create a cluster struct
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+%            som_clset   set properties in a cluster struct
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+%            som_clget   get stuff from a cluster struct
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+% 
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+% Struct conversion and file I/O
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+% 
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+%           som_vs1to2   converts a version 1.0 struct to version 2.0 struct
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+%           som_vs2to1   converts a version 2.0 struct to version 1.0 struct
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+%        som_read_data   reads a (SOM_PAK format) ASCII data file
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+%       som_write_data   writes a SOM_PAK format codebook file
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+%        som_write_cod   writes a SOM_PAK format data file
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+%         som_read_cod   reads a SOM_PAK format codebook file
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+% 
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+% Data preprocessing
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+% 
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+%        som_normalize   normalize data set
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+%      som_denormalize   denormalize data set 
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+%    som_norm_variable   (de)normalize one variable
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+%           preprocess   preprocessing GUI
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+% 
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+% Initialization and training functions
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+% 
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+%             som_make   create, initialize and train a SOM
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+%         som_randinit   random initialization algorithm
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+%          som_lininit   linear initialization algorithm
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+%         som_seqtrain   sequential training algorithm
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+%       som_batchtrain   batch training algorithm
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+%              som_gui   SOM initialization and training GUI
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+%       som_prototrain   a simple version of sequential training: easy to modify
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+% 
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+% Clustering algorithms
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+% 
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+%           som_kmeans   k-means algorithm (was earlier kmeans)
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+%      kmeans_clusters   try and evaluate several k-means clusterings
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+%           neural_gas   neural gas vector quantization algorithm
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+%          som_linkage   hierarchical clustering algorithms
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+%        som_cllinkage   hierarchical clustering of SOM
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+%       som_dmatminima   local minima from distance (or U-) matrix
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+%     som_dmatclusters   distance (or U-) matrix based clustering
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+%         som_clspread   spreads clusters to unassinged map units
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+%           som_cldist   calculate distances between clusters
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+%         som_gapindex   gap validity index of clustering
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+%             db_index   Davies-Bouldin validity index of clustering  
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+% 
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+% Supervised/classification algorithms
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+% 
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+%       som_supervised   supervised SOM algorithm
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+%                 lvq1   LVQ1 algorithm
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+%                 lvq3   LVQ3 algorithm
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+%                  knn   k-NN classification algorithm 
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+%              knn_old   k-NN classification algorithm (old version)
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+% 
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+% SOM error measures
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+% 
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+%          som_quality   quantization and topographic error of SOM
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+%       som_distortion   SOM distortion measure
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+%      som_distortion3   elements of the SOM distortion measure
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+% 
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+% Auxiliary functions
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+% 
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+%             som_bmus   calculates BMUs for given data vectors
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+%         som_eucdist2   pairwise squared euclidian distances between vectors
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+%            som_mdist   calculates pairwise distances between vectors 
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+%           som_divide   extract subsets of data based on map
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+%            som_label   give labels to map units
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+%        som_label2num   rcodes string data labels to interger class labels 
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+%        som_autolabel   automatically labels the SOM based on given data
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+%      som_unit_coords   calculates coordinates in output space for map units
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+%       som_unit_dists   distances in output space between map units
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+%      som_unit_neighs   units in 1-neighborhood for each map unit
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+%     som_neighborhood   calculates neighborhood matrix for the given map
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+%        som_neighbors   calculates different kinds of neighborhoods 
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+%           som_neighf   calculates neighborhood function values
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+%           som_select   GUI for manual selection of map units
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+%     som_estimate_gmm   create Gaussian mixture model on top of SOM
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+%  som_probability_gmm   evaluate Gaussian mixture model
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+%          som_ind2sub   from linear index to subscript index 
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+%          som_sub2ind   from subscript index to linear index
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+%          som_ind2cod   from linear index to SOM_PAK linear index 
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+%          som_cod2ind   from SOM_linear index to SOM_PAK linear index 
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+%             nanstats   mean, std and median which ignore NaNs
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+%   som_modify_dataset   add, remove, or extract samples and components
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+%         som_fillnans   fill NaNs in a data set based on given SOM
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+%            som_stats   statistics of a data set
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+%           som_drmake   calculate descriptive rules for a cluster
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+%           som_dreval   evaluate descriptive rules for a cluster
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+%         som_drsignif   rule significance measures
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+% 
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+% Using SOM_PAK from Matlab
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+% 
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+%      som_sompaktrain   uses SOM_PAK to train a map
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+%           sompak_gui   GUI for using SOM_PAK from Matlab
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+%          sompak_init   call SOM_PAK's initialization programs from Matlab
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+%      sompak_init_gui   GUI for using SOM_PAK's initialization from Matlab
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+%    sompak_rb_control   an auxiliary function for sompak_*_gui functions.
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+%        sompak_sammon   call SOM_PAK's Sammon program from Matlab
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+%    sompak_sammon_gui   GUI for using SOM_PAK's Sammon program from Matlab
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+%         sompak_train   call SOM_PAK's training program from Matlab
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+%     sompak_train_gui   GUI for using SOM_PAK's training program from Matlab 
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+% 
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+% Visualization
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+% 
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+%             som_show   basic visualization
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+%         som_show_add   add labels, hits and trajectories
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+%       som_show_clear   remove extra markers
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+%       som_recolorbar   refresh/reconfigure colorbars
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+%         som_show_gui   GUI for using som_show and associated functions
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+%             som_grid   visualization of SOM grid
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+%           som_cplane   component planes and U-matrices
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+%         som_barplane   bar chart visualization of map
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+%         som_pieplane   pie chart visualization of map
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+%        som_plotplane   plot chart visualization of map
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+%       som_trajectory   launches a GUI for presenting comet-trajectories 
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+%       som_dendrogram   visualization of clustering tree
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+%       som_plotmatrix   pairwise scatter plots and histograms
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+%    som_order_cplanes   order and visualize the component planes
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+%           som_clplot   plots of clusters (based on cluster struct)
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+% som_projections_plot   projections plots (see som_projections)
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+%       som_stats_plot   plots of statistics (see som_stats)
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+% 
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+% Auxiliary functions for visualization
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+% 
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+%                 hits   calculates hits, or sum of values for each map unit
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+%             som_hits   calculates the response of data on the map
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+%             som_umat   calculates the U-matrix
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+%                  cca   curvilinear component analysis projection algorithm
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+%              pcaproj   principal component projection algorithm
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+%               sammon   Sammon's mapping projection algorithm
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+%       som_connection   connection matrix for map 
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+%       som_vis_coords   map unit coordinates used in visualizations
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+%        som_colorcode   create color coding for map/2D data
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+%         som_bmucolor   colors of the BMUs from a given map color code
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+%        som_normcolor   simulate indexed colormap
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+%     som_clustercolor   color coding which depends on clustering structure
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+%      som_kmeanscolor   color coding according to k-means clustering
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+%     som_kmeanscolor2   a newer version of the som_kmeanscolor function
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+%       som_fuzzycolor   a fuzzy color coding 
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+%         som_coloring   a SOM-based color coding 
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+%      som_projections   calculates a default set of projections
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+% 
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+% Report generation stuff
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+% 
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+%     som_table_struct   creates a table struct
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+%     som_table_modify   modifies a table struct
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+%      som_table_print   print a table in various formats
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+%            rep_utils   various utilities for printing report elements
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+%      som_stats_table   a table of data set statistics
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+%     som_stats_report   report on data set statistics
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+% 
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+% Low level routines used by visualization functions
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+% 
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+%            vis_patch   defines hexagonal and rectangular patches
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+%    vis_som_show_data   returns UserData and subplot handles stored by som_show.m
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+%        vis_valuetype   used for type checks 
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+%         vis_footnote   adds a movable text to the current figure 
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+%          vis_trajgui   the actual GUI started by som_trajectory.m 
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+% vis_PlaneAxisProperties   set axis properties in visualization functions
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+% vis_footnoteButtonDownFcn   callback function for vis_footnote.m
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+%     vis_planeGetArgs   converts topol struct to lattice, msize argument pair
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+%    vis_show_gui_comp   internal function used by som_show_gui.m
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+%    vis_show_gui_tool   internal function used by som_show_gui.m
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+% 
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+% Other
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+% 
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+%           somtoolbox   this file
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+%            iris.data   IRIS data set (used in demos)
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+%          License.txt   GNU General Public License 
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+%        Copyright.txt   Copyright notice