SOM Toolbox | Help Desk |

**NOTE:** Some of the files have no helpdisk help file.
For them, the only available documentation is in the function file itself.
Try command `'help <function_name>'` in Matlab prompt.

**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**`som_kmeans`: k-means algorithm`kmeans_clusters`: try and evaluate several k-means clusterings`neural_gas`: neural gas vector quantization algorithm**Supervised/classification algorithms**`som_supervised`: supervised SOM algorithm`lvq1`: LVQ1 algorithm`lvq3`: LVQ3 algorithm`knn`: k-NN classification algorithm**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_divide`: extract subsets of data based on map`som_label`: give labels to map units`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**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_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**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**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**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

Contents | Overview of SOM Toolbox functions |

Copyright.txt | Copyright notice |

License.txt | GNU General Public License |

cca | curvilinear component analysis projection algorithm |

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 |

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 |

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_clustercolor | color coding which depends on clustering structure |

som_colorcode | create color coding for map/2D data |

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_denormalize | denormalize data set |

som_distortion | SOM distortion measure |

som_divide | extract subsets of data based on map |

som_estimate_gmm | create Gaussian mixture model on top of SOM |

som_grid | visualization of SOM network |

som_gui | SOM initialization and training GUI |

som_hits | calculates the response of data on the map |

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_label | give labels to map units |

som_lininit | linear initialization algorithm |

som_make | create, initialize and train a SOM |

som_map_struct | create & initialize a map struct |

som_neighborhood | calculates neighborhood matrix for the given map |

som_norm_variable | (de)normalize one variable |

som_normalize | normalize data set |

som_normcolor | simulate indexed colormap |

som_pieplane | pie chart visualization of map |

som_plotplane | plot chart visualization of map |

som_probability_gmm | evaluate Gaussian mixture model |

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_sompaktrain | uses SOM_PAK to train a map |

som_sub2ind | from subscript index to linear index |

som_supervised | supervised SOM algorithm |

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_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 |