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

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Alphabetical order

ContentsOverview of SOM Toolbox functionsCopyright.txtCopyright noticeLicense.txtGNU General Public Licenseccacurvilinear component analysis projection algorithmdb_indexDavies-Bouldin validity index of clusteringhitscalculates hits, or sum of values for each map unitiris.dataIRIS data set (used in demos)kmeans_clusterstry and evaluate several k-means clusteringsknnk-NN classification algorithmknn_oldk-NN classification algorithm (old version)lvq1LVQ1 algorithmlvq3LVQ3 algorithmnanstatsmean, std and median which ignore NaNsneural_gasneural gas vector quantization algorithmpcaprojprincipal component projection algorithmpreprocesspreprocessing GUIrep_utilsvarious utilities for printing report elementssammonSammon's mapping projection algorithmsom_autolabelautomatically labels the SOM based on given datasom_barplanebar chart visualization of mapsom_batchtrainbatch training algorithmsom_bmucolorcolors of the BMUs from a given map color codesom_bmuscalculates BMUs for given data vectorssom_cldistcalculate distances between clusterssom_clgetget stuff from a cluster structsom_cllinkagehierarchical clustering of SOMsom_clplotplots of clusters (based on cluster struct)som_clsetset properties in a cluster structsom_clspreadspreads clusters to unassinged map unitssom_clstructcreate a cluster structsom_clustercolorcolor coding which depends on clustering structuresom_cod2indfrom SOM_linear index to SOM_PAK linear indexsom_colorcodecreate color coding for map/2D datasom_coloringa SOM-based color codingsom_connectionconnection matrix for mapsom_cplanecomponent planes and U-matricessom_data_structcreate & initialize a data structsom_demo1SOM Toolbox demo 1: basic propertiessom_demo2SOM Toolbox demo 2: basic usagesom_demo3SOM Toolbox demo 3: visualizationsom_demo4SOM Toolbox demo 4: data analysissom_dendrogramvisualization of clustering treesom_denormalizedenormalize data setsom_distortionSOM distortion measuresom_distortion3elements of the SOM distortion measuresom_divideextract subsets of data based on mapsom_dmatclustersdistance (or U-) matrix based clusteringsom_dmatminimalocal minima from distance (or U-) matrixsom_drevalevaluate descriptive rules for a clustersom_drmakecalculate descriptive rules for a clustersom_drsignifrule significance measuressom_estimate_gmmcreate Gaussian mixture model on top of SOMsom_eucdist2pairwise squared euclidian distances between vectorssom_fillnansfill NaNs in a data set based on given SOMsom_fuzzycolora fuzzy color codingsom_gapindexgap validity index of clusteringsom_gridvisualization of SOM gridsom_guiSOM initialization and training GUIsom_hitscalculates the response of data on the mapsom_ind2codfrom linear index to SOM_PAK linear indexsom_ind2subfrom linear index to subscript indexsom_infoprint out information on a given structsom_kmeansk-means algorithmsom_kmeanscolorcolor coding according to k-means clusteringsom_kmeanscolor2a newer version of the som_kmeanscolor functionsom_labelgive labels to map unitssom_label2numrcodes string data labels to interger class labelssom_lininitlinear initialization algorithmsom_linkagehierarchical clustering algorithmssom_makecreate, initialize and train a SOMsom_map_structcreate & initialize a map structsom_mdistcalculates pairwise distances between vectorssom_modify_datasetadd, remove, or extract samples and componentssom_neighborhoodcalculates neighborhood matrix for the given mapsom_neighborscalculates different kinds of neighborhoodssom_neighfcalculates neighborhood function valuessom_norm_variable(de)normalize one variablesom_normalizenormalize data setsom_normcolorsimulate indexed colormapsom_order_cplanesorder and visualize the component planessom_pieplanepie chart visualization of mapsom_plotmatrixpairwise scatter plots and histogramssom_plotplaneplot chart visualization of mapsom_probability_gmmevaluate Gaussian mixture modelsom_projectionscalculates a default set of projectionssom_projections_plotprojections plots (see som_projections)som_prototraina simple version of sequential training: easy to modifysom_qualityquantization and topographic error of SOMsom_randinitrandom initialization algorithmsom_read_codreads a SOM_PAK format codebook filesom_read_datareads a (SOM_PAK format) ASCII data filesom_recolorbarrefresh/reconfigure colorbarssom_selectGUI for manual selection of map unitssom_seqtrainsequential training algorithmsom_setcreate & set (& check) values to structssom_showbasic visualizationsom_show_addadd labels, hits and trajectoriessom_show_clearremove extra markerssom_show_guiGUI for using som_show and associated functionssom_sompaktrainuses SOM_PAK to train a mapsom_statsstatistics of a data setsom_stats_plotplots of statistics (see som_stats)som_stats_reportreport on data set statisticssom_stats_tablea table of data set statisticssom_sub2indfrom subscript index to linear indexsom_supervisedsupervised SOM algorithmsom_table_modifymodifies a table structsom_table_printprint a table in various formatssom_table_structcreates a table structsom_topol_structcreate & initialize a topology structsom_train_structcreate & initialize a train structsom_trajectorylaunches a GUI for presenting comet-trajectoriessom_umatcalculates the U-matrixsom_unit_coordscalculates coordinates in output space for map unitssom_unit_distsdistances in output space between map unitssom_unit_neighsunits in 1-neighborhood for each map unitsom_vis_coordsmap unit coordinates used in visualizationssom_vs1to2converts a version 1.0 struct to version 2.0 structsom_vs2to1converts a version 2.0 struct to version 1.0 structsom_write_codwrites a SOM_PAK format data filesom_write_datawrites a SOM_PAK format codebook filesompak_guiGUI for using SOM_PAK from Matlabsompak_initcall SOM_PAK's initialization programs from Matlabsompak_init_guiGUI for using SOM_PAK's initialization from Matlabsompak_rb_controlan auxiliary function for sompak_*_gui functions.sompak_sammoncall SOM_PAK's Sammon program from Matlabsompak_sammon_guiGUI for using SOM_PAK's Sammon program from Matlabsompak_traincall SOM_PAK's training program from Matlabsompak_train_guiGUI for using SOM_PAK's training program from Matlabsomtoolboxthis filevis_PlaneAxisPropertiesset axis properties in visualization functionsvis_footnoteadds a movable text to the current figurevis_footnoteButtonDownFcncallback function for vis_footnote.mvis_patchdefines hexagonal and rectangular patchesvis_planeGetArgsconverts topol struct to lattice, msize argument pairvis_show_gui_compinternal function used by som_show_gui.mvis_show_gui_toolinternal function used by som_show_gui.mvis_som_show_datareturns UserData and subplot handles stored by som_show.mvis_trajguithe actual GUI started by som_trajectory.mvis_valuetypeused for type checks