somtoolbox 工具箱函数说明

原文链接地址：http://www.cis.hut.fi/somtoolbox/package/docs2/somtoolbox.html

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

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_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_kmeans	k-means algorithm
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