SOM Toolbox

http://www.cis.hut.fi/projects/somtoolbox/

[ Grouped by function | Alphabetical order ]

NOTE: The same help can be found from the functions themselves (in most cases).
Try command 'help <function_name>' or 'type <function_name>' in Matlab prompt.

Grouped by function

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

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

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
Contents: Overview of SOM Toolbox functions


Alphabetical order

Contents Overview of SOM Toolbox functions
Copyright.txt Copyright notice
License.txt GNU General Public License
cca curvilinear component analysis projection algorithm
db_index Davies-Bouldin validity index of clustering
hits calculates hits, or sum of values for each map unit
iris.data IRIS data set (used in demos)
kmeans k-means algorithm
kmeans_clusters try and evaluate several k-means clusterings
knn k-NN classification algorithm
knn_old k-NN classification algorithm (old version)
lvq1 LVQ1 algorithm
lvq3 LVQ3 algorithm
nanstats mean, std and median which ignore NaNs
neural_gas neural gas vector quantization algorithm
pcaproj principal component projection algorithm
preprocess preprocessing GUI
rep_utils various utilities for printing report elements
sammon Sammon's mapping projection algorithm
som_autolabel automatically labels the SOM based on given data
som_barplane bar chart visualization of map
som_batchtrain batch training algorithm
som_bmucolor colors of the BMUs from a given map color code
som_bmus calculates BMUs for given data vectors
som_cldist calculate distances between clusters
som_clget get stuff from a cluster struct
som_cllinkage hierarchical clustering of SOM
som_clplot plots of clusters (based on cluster struct)
som_clset set properties in a cluster struct
som_clspread spreads clusters to unassinged map units
som_clstruct create a cluster struct
som_clustercolor color coding which depends on clustering structure
som_cod2ind from SOM_linear index to SOM_PAK linear index
som_colorcode create color coding for map/2D data
som_coloring a SOM-based color coding
som_connection connection matrix for map
som_cplane component planes and U-matrices
som_data_struct create & initialize a data struct
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
som_dendrogram visualization of clustering tree
som_denormalize denormalize data set
som_distortion SOM distortion measure
som_distortion3 elements of the SOM distortion measure
som_divide extract subsets of data based on map
som_dmatclusters distance (or U-) matrix based clustering
som_dmatminima local minima from distance (or U-) matrix
som_dreval evaluate descriptive rules for a cluster
som_drmake calculate descriptive rules for a cluster
som_drsignif rule significance measures
som_estimate_gmm create Gaussian mixture model on top of SOM
som_eucdist2 pairwise squared euclidian distances between vectors
som_fillnans fill NaNs in a data set based on given SOM
som_fuzzycolor a fuzzy color coding
som_gapindex gap validity index of clustering
som_grid visualization of SOM grid
som_gui SOM initialization and training GUI
som_hits calculates the response of data on the map
som_ind2cod from linear index to SOM_PAK linear index
som_ind2sub from linear index to subscript index
som_info print out information on a given struct
som_kmeanscolor color coding according to k-means clustering
som_kmeanscolor2 a newer version of the som_kmeanscolor function
som_label give labels to map units
som_label2num rcodes string data labels to interger class labels
som_lininit linear initialization algorithm
som_linkage hierarchical clustering algorithms
som_make create, initialize and train a SOM
som_map_struct create & initialize a map struct
som_mdist calculates pairwise distances between vectors
som_modify_dataset add, remove, or extract samples and components
som_neighborhood calculates neighborhood matrix for the given map
som_neighbors calculates different kinds of neighborhoods
som_neighf calculates neighborhood function values
som_norm_variable (de)normalize one variable
som_normalize normalize data set
som_normcolor simulate indexed colormap
som_order_cplanes order and visualize the component planes
som_pieplane pie chart visualization of map
som_plotmatrix pairwise scatter plots and histograms
som_plotplane plot chart visualization of map
som_probability_gmm evaluate Gaussian mixture model
som_projections calculates a default set of projections
som_projections_plot projections plots (see som_projections)
som_prototrain a simple version of sequential training: easy to modify
som_quality quantization and topographic error of SOM
som_randinit random initialization algorithm
som_read_cod reads a SOM_PAK format codebook file
som_read_data reads a (SOM_PAK format) ASCII data file
som_recolorbar refresh/reconfigure colorbars
som_select GUI for manual selection of map units
som_seqtrain sequential training algorithm
som_set create & set (& check) values to structs
som_show basic visualization
som_show_add add labels, hits and trajectories
som_show_clear remove extra markers
som_show_gui GUI for using som_show and associated functions
som_sompaktrain uses SOM_PAK to train a map
som_stats statistics of a data set
som_stats_plot plots of statistics (see som_stats)
som_stats_report report on data set statistics
som_stats_table a table of data set statistics
som_sub2ind from subscript index to linear index
som_supervised supervised SOM algorithm
som_table_modify modifies a table struct
som_table_print print a table in various formats
som_table_struct creates a table struct
som_topol_struct create & initialize a topology struct
som_train_struct create & initialize a train struct
som_trajectory launches a GUI for presenting comet-trajectories
som_umat calculates the U-matrix
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_vis_coords map unit coordinates used in visualizations
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_write_cod writes a SOM_PAK format data file
som_write_data writes a SOM_PAK format codebook file
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
somtoolbox this file
vis_PlaneAxisProperties set axis properties in visualization functions
vis_footnote adds a movable text to the current figure
vis_footnoteButtonDownFcn callback function for vis_footnote.m
vis_patch defines hexagonal and rectangular patches
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
vis_som_show_data returns UserData and subplot handles stored by som_show.m
vis_trajgui the actual GUI started by som_trajectory.m
vis_valuetype used for type checks