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<!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML//EN"><html><head><title>SOM Toolbox</title></head><body bgcolor=#f0f0f0><table border=0 width="100%" cellpadding=0 cellspacing=0><tr><td valign=baseline><font size=+2>SOM Toolbox</font></td><td valign=baseline align=right><a href="http://www.cis.hut.fi/projects/somtoolbox/" target="_top">http://www.cis.hut.fi/projects/somtoolbox/</a></td></tr></table><p><center>[ <a href="#byfunc">Grouped by function</a> | <a href="#bysort">Alphabetical order</a> ]</center><p><b>NOTE:</b> The same help can be found from the functions themselves (in most cases).<BR>Try command <tt>'help <function_name>'</tt> or <tt>'type <function_name>'</tt> in Matlab prompt.<a name="byfunc"><H2> Grouped by function </H2></a><DL><P><DT><B>Demos</B></DT><P><DD><TT><a href="som_demo1.html">som_demo1</a></TT>: SOM Toolbox demo 1: basic properties<DD><TT><a href="som_demo2.html">som_demo2</a></TT>: SOM Toolbox demo 2: basic usage<DD><TT><a href="som_demo3.html">som_demo3</a></TT>: SOM Toolbox demo 3: visualization<DD><TT><a href="som_demo4.html">som_demo4</a></TT>: SOM Toolbox demo 4: data analysis<P><DT><B>Creation of structs</B></DT><P><DD><TT><a href="som_set.html">som_set</a></TT>: create & set (& check) values to structs<DD><TT><a href="som_info.html">som_info</a></TT>: print out information on a given struct <DD><TT><a href="som_data_struct.html">som_data_struct</a></TT>: create & initialize a data struct <DD><TT><a href="som_map_struct.html">som_map_struct</a></TT>: create & initialize a map struct <DD><TT><a href="som_topol_struct.html">som_topol_struct</a></TT>: create & initialize a topology struct <DD><TT><a href="som_train_struct.html">som_train_struct</a></TT>: create & initialize a train struct <DD><TT><a href="som_clstruct.html">som_clstruct</a></TT>: create a cluster struct<DD><TT><a href="som_clset.html">som_clset</a></TT>: set properties in a cluster struct<DD><TT><a href="som_clget.html">som_clget</a></TT>: get stuff from a cluster struct<P><DT><B>Struct conversion and file I/O</B></DT><P><DD><TT><a href="som_vs1to2.html">som_vs1to2</a></TT>: converts a version 1.0 struct to version 2.0 struct<DD><TT><a href="som_vs2to1.html">som_vs2to1</a></TT>: converts a version 2.0 struct to version 1.0 struct<DD><TT><a href="som_read_data.html">som_read_data</a></TT>: reads a (SOM_PAK format) ASCII data file<DD><TT><a href="som_write_data.html">som_write_data</a></TT>: writes a SOM_PAK format codebook file<DD><TT><a href="som_write_cod.html">som_write_cod</a></TT>: writes a SOM_PAK format data file<DD><TT><a href="som_read_cod.html">som_read_cod</a></TT>: reads a SOM_PAK format codebook file<P><DT><B>Data preprocessing</B></DT><P><DD><TT><a href="som_normalize.html">som_normalize</a></TT>: normalize data set<DD><TT><a href="som_denormalize.html">som_denormalize</a></TT>: denormalize data set <DD><TT><a href="som_norm_variable.html">som_norm_variable</a></TT>: (de)normalize one variable<DD><TT><a href="preprocess.html">preprocess</a></TT>: preprocessing GUI<P><DT><B>Initialization and training functions</B></DT><P><DD><TT><a href="som_make.html">som_make</a></TT>: create, initialize and train a SOM<DD><TT><a href="som_randinit.html">som_randinit</a></TT>: random initialization algorithm<DD><TT><a href="som_lininit.html">som_lininit</a></TT>: linear initialization algorithm<DD><TT><a href="som_seqtrain.html">som_seqtrain</a></TT>: sequential training algorithm<DD><TT><a href="som_batchtrain.html">som_batchtrain</a></TT>: batch training algorithm<DD><TT><a href="som_gui.html">som_gui</a></TT>: SOM initialization and training GUI<DD><TT><a href="som_prototrain.html">som_prototrain</a></TT>: a simple version of sequential training: easy to modify<P><DT><B>Clustering algorithms</B></DT><P><DD><TT><a href="som_kmeans.html">som_kmeans</a></TT>: k-means algorithm<DD><TT><a href="kmeans_clusters.html">kmeans_clusters</a></TT>: try and evaluate several k-means clusterings<DD><TT><a href="neural_gas.html">neural_gas</a></TT>: neural gas vector quantization algorithm<DD><TT><a href="som_linkage.html">som_linkage</a></TT>: hierarchical clustering algorithms<DD><TT><a href="som_cllinkage.html">som_cllinkage</a></TT>: hierarchical clustering of SOM<DD><TT><a href="som_dmatminima.html">som_dmatminima</a></TT>: local minima from distance (or U-) matrix<DD><TT><a href="som_dmatclusters.html">som_dmatclusters</a></TT>: distance (or U-) matrix based clustering<DD><TT><a href="som_clspread.html">som_clspread</a></TT>: spreads clusters to unassinged map units<DD><TT><a href="som_cldist.html">som_cldist</a></TT>: calculate distances between clusters<DD><TT><a href="som_gapindex.html">som_gapindex</a></TT>: gap validity index of clustering<DD><TT><a href="db_index.html">db_index</a></TT>: Davies-Bouldin validity index of clustering <P><DT><B>Supervised/classification algorithms</B></DT><P><DD><TT><a href="som_supervised.html">som_supervised</a></TT>: supervised SOM algorithm<DD><TT><a href="lvq1.html">lvq1</a></TT>: LVQ1 algorithm<DD><TT><a href="lvq3.html">lvq3</a></TT>: LVQ3 algorithm<DD><TT><a href="knn.html">knn</a></TT>: k-NN classification algorithm <DD><TT><a href="knn_old.html">knn_old</a></TT>: k-NN classification algorithm (old version)<P><DT><B>SOM error measures</B></DT><P><DD><TT><a href="som_quality.html">som_quality</a></TT>: quantization and topographic error of SOM<DD><TT><a href="som_distortion.html">som_distortion</a></TT>: SOM distortion measure<DD><TT><a href="som_distortion3.html">som_distortion3</a></TT>: elements of the SOM distortion measure<P><DT><B>Auxiliary functions</B></DT><P><DD><TT><a href="som_bmus.html">som_bmus</a></TT>: calculates BMUs for given data vectors<DD><TT><a href="som_eucdist2.html">som_eucdist2</a></TT>: pairwise squared euclidian distances between vectors<DD><TT><a href="som_mdist.html">som_mdist</a></TT>: calculates pairwise distances between vectors <DD><TT><a href="som_divide.html">som_divide</a></TT>: extract subsets of data based on map<DD><TT><a href="som_label.html">som_label</a></TT>: give labels to map units<DD><TT><a href="som_label2num.html">som_label2num</a></TT>: rcodes string data labels to interger class labels <DD><TT><a href="som_autolabel.html">som_autolabel</a></TT>: automatically labels the SOM based on given data<DD><TT><a href="som_unit_coords.html">som_unit_coords</a></TT>: calculates coordinates in output space for map units<DD><TT><a href="som_unit_dists.html">som_unit_dists</a></TT>: distances in output space between map units<DD><TT><a href="som_unit_neighs.html">som_unit_neighs</a></TT>: units in 1-neighborhood for each map unit<DD><TT><a href="som_neighborhood.html">som_neighborhood</a></TT>: calculates neighborhood matrix for the given map<DD><TT><a href="som_neighbors.html">som_neighbors</a></TT>: calculates different kinds of neighborhoods <DD><TT><a href="som_neighf.html">som_neighf</a></TT>: calculates neighborhood function values<DD><TT><a href="som_select.html">som_select</a></TT>: GUI for manual selection of map units<DD><TT><a href="som_estimate_gmm.html">som_estimate_gmm</a></TT>: create Gaussian mixture model on top of SOM<DD><TT><a href="som_probability_gmm.html">som_probability_gmm</a></TT>: evaluate Gaussian mixture model<DD><TT><a href="som_ind2sub.html">som_ind2sub</a></TT>: from linear index to subscript index <DD><TT><a href="som_sub2ind.html">som_sub2ind</a></TT>: from subscript index to linear index<DD><TT><a href="som_ind2cod.html">som_ind2cod</a></TT>: from linear index to SOM_PAK linear index <DD><TT><a href="som_cod2ind.html">som_cod2ind</a></TT>: from SOM_linear index to SOM_PAK linear index <DD><TT><a href="nanstats.html">nanstats</a></TT>: mean, std and median which ignore NaNs<DD><TT><a href="som_modify_dataset.html">som_modify_dataset</a></TT>: add, remove, or extract samples and components<DD><TT><a href="som_fillnans.html">som_fillnans</a></TT>: fill NaNs in a data set based on given SOM<DD><TT><a href="som_stats.html">som_stats</a></TT>: statistics of a data set<DD><TT><a href="som_drmake.html">som_drmake</a></TT>: calculate descriptive rules for a cluster<DD><TT><a href="som_dreval.html">som_dreval</a></TT>: evaluate descriptive rules for a cluster<DD><TT><a href="som_drsignif.html">som_drsignif</a></TT>: rule significance measures<P><DT><B>Using SOM_PAK from Matlab</B></DT><P><DD><TT><a href="som_sompaktrain.html">som_sompaktrain</a></TT>: uses SOM_PAK to train a map<DD><TT><a href="sompak_gui.html">sompak_gui</a></TT>: GUI for using SOM_PAK from Matlab<DD><TT><a href="sompak_init.html">sompak_init</a></TT>: call SOM_PAK's initialization programs from Matlab<DD><TT><a href="sompak_init_gui.html">sompak_init_gui</a></TT>: GUI for using SOM_PAK's initialization from Matlab<DD><TT><a href="sompak_rb_control.html">sompak_rb_control</a></TT>: an auxiliary function for sompak_*_gui functions.<DD><TT><a href="sompak_sammon.html">sompak_sammon</a></TT>: call SOM_PAK's Sammon program from Matlab<DD><TT><a href="sompak_sammon_gui.html">sompak_sammon_gui</a></TT>: GUI for using SOM_PAK's Sammon program from Matlab<DD><TT><a href="sompak_train.html">sompak_train</a></TT>: call SOM_PAK's training program from Matlab<DD><TT><a href="sompak_train_gui.html">sompak_train_gui</a></TT>: GUI for using SOM_PAK's training program from Matlab <P><DT><B>Visualization</B></DT><P><DD><TT><a href="som_show.html">som_show</a></TT>: basic visualization<DD><TT><a href="som_show_add.html">som_show_add</a></TT>: add labels, hits and trajectories<DD><TT><a href="som_show_clear.html">som_show_clear</a></TT>: remove extra markers<DD><TT><a href="som_recolorbar.html">som_recolorbar</a></TT>: refresh/reconfigure colorbars<DD><TT><a href="som_show_gui.html">som_show_gui</a></TT>: GUI for using som_show and associated functions<DD><TT><a href="som_grid.html">som_grid</a></TT>: visualization of SOM grid<DD><TT><a href="som_cplane.html">som_cplane</a></TT>: component planes and U-matrices<DD><TT><a href="som_barplane.html">som_barplane</a></TT>: bar chart visualization of map<DD><TT><a href="som_pieplane.html">som_pieplane</a></TT>: pie chart visualization of map<DD><TT><a href="som_plotplane.html">som_plotplane</a></TT>: plot chart visualization of map<DD><TT><a href="som_trajectory.html">som_trajectory</a></TT>: launches a GUI for presenting comet-trajectories <DD><TT><a href="som_dendrogram.html">som_dendrogram</a></TT>: visualization of clustering tree<DD><TT><a href="som_plotmatrix.html">som_plotmatrix</a></TT>: pairwise scatter plots and histograms<DD><TT><a href="som_order_cplanes.html">som_order_cplanes</a></TT>: order and visualize the component planes<DD><TT><a href="som_clplot.html">som_clplot</a></TT>: plots of clusters (based on cluster struct)<DD><TT><a href="som_projections_plot.html">som_projections_plot</a></TT>: projections plots (see som_projections)<DD><TT><a href="som_stats_plot.html">som_stats_plot</a></TT>: plots of statistics (see som_stats)<P><DT><B>Auxiliary functions for visualization</B></DT><P><DD><TT><a href="hits.html">hits</a></TT>: calculates hits, or sum of values for each map unit<DD><TT><a href="som_hits.html">som_hits</a></TT>: calculates the response of data on the map<DD><TT><a href="som_umat.html">som_umat</a></TT>: calculates the U-matrix<DD><TT><a href="cca.html">cca</a></TT>: curvilinear component analysis projection algorithm<DD><TT><a href="pcaproj.html">pcaproj</a></TT>: principal component projection algorithm<DD><TT><a href="sammon.html">sammon</a></TT>: Sammon's mapping projection algorithm<DD><TT><a href="som_connection.html">som_connection</a></TT>: connection matrix for map <DD><TT><a href="som_vis_coords.html">som_vis_coords</a></TT>: map unit coordinates used in visualizations<DD><TT><a href="som_colorcode.html">som_colorcode</a></TT>: create color coding for map/2D data<DD><TT><a href="som_bmucolor.html">som_bmucolor</a></TT>: colors of the BMUs from a given map color code<DD><TT><a href="som_normcolor.html">som_normcolor</a></TT>: simulate indexed colormap<DD><TT><a href="som_clustercolor.html">som_clustercolor</a></TT>: color coding which depends on clustering structure<DD><TT><a href="som_kmeanscolor.html">som_kmeanscolor</a></TT>: color coding according to k-means clustering<DD><TT><a href="som_kmeanscolor2.html">som_kmeanscolor2</a></TT>: a newer version of the som_kmeanscolor function<DD><TT><a href="som_fuzzycolor.html">som_fuzzycolor</a></TT>: a fuzzy color coding <DD><TT><a href="som_coloring.html">som_coloring</a></TT>: a SOM-based color coding <DD><TT><a href="som_projections.html">som_projections</a></TT>: calculates a default set of projections<P><DT><B>Report generation stuff</B></DT><P><DD><TT><a href="som_table_struct.html">som_table_struct</a></TT>: creates a table struct<DD><TT><a href="som_table_modify.html">som_table_modify</a></TT>: modifies a table struct<DD><TT><a href="som_table_print.html">som_table_print</a></TT>: print a table in various formats<DD><TT><a href="rep_utils.html">rep_utils</a></TT>: various utilities for printing report elements<DD><TT><a href="som_stats_table.html">som_stats_table</a></TT>: a table of data set statistics<DD><TT><a href="som_stats_report.html">som_stats_report</a></TT>: report on data set statistics<P><DT><B>Low level routines used by visualization functions</B></DT><P><DD><TT><a href="vis_patch.html">vis_patch</a></TT>: defines hexagonal and rectangular patches<DD><TT><a href="vis_som_show_data.html">vis_som_show_data</a></TT>: returns UserData and subplot handles stored by som_show.m<DD><TT><a href="vis_valuetype.html">vis_valuetype</a></TT>: used for type checks <DD><TT><a href="vis_footnote.html">vis_footnote</a></TT>: adds a movable text to the current figure <DD><TT><a href="vis_trajgui.html">vis_trajgui</a></TT>: the actual GUI started by som_trajectory.m <DD><TT><a href="vis_PlaneAxisProperties.html">vis_PlaneAxisProperties</a></TT>: set axis properties in visualization functions<DD><TT><a href="vis_footnoteButtonDownFcn.html">vis_footnoteButtonDownFcn</a></TT>: callback function for vis_footnote.m<DD><TT><a href="vis_planeGetArgs.html">vis_planeGetArgs</a></TT>: converts topol struct to lattice, msize argument pair⌨️ 快捷键说明
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