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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN"><HTML><head><title>SOM Toolbox </title></head><body><BODY BGCOLOR="#FFFFFF"><A NAME="begin"><center><H1>Help SOM Toolbox -- Initialization & Training GUI</H1></center></A><H3> Purpose </H3>A graphical user interface for initialization and trainingof Self-Organizing Maps.<H3> Syntax </H3><UL><PRE>  som_gui([sD])</PRE></UL><H3> Optional input arguments </H3><PRE>  sD          Training data.     (struct) data struct     (matrix) data matrix, size [dlen dim]</PRE><H3>Help Topics</H3><DL><DT><A HREF="#intro">Introduction</A></DT><DD>     What is <B>SOM Toolbox -- Initialization & Training GUI</B> ? </DD>  <DT><A HREF="#load">Load data</A></DT><DD>  Load data.  <BR>  From workspace  <BR>  From file</DD><DT><A HREF="#pre">Preprocess data</A></DT><DD>  Preprocess  <BR></DD><DT><A HREF="#init">Initialize map</A></DT><DD>  Change default values  <BR>  Initialize</DD>     <DT><A HREF="#train">Train map</A></DT><DD>  Change default values  <BR>  Train</DD><DT><A HREF="#save">Save trained map</A></DT><DD>  Save map</DD><DT><A HREF="#vis">Visualize map</A></DT><DD>  Visualize map</DD><DT><A HREF="#restart">Restart from the beginning </A></DT><DD>  Restart </DD><DT><A HREF="#close">Close </A></DT><DD>  Close</DD>     <DT><A HREF="#main">Main window </A></DT><DD>  Main window</DD><DT><A HREF="#releted">Help </A></DT><DD>  GUI help.<BR>		  More information about SOM and SOM Toolbox.</DD>    </DL>     <HR><A NAME="intro"><H3>Introduction</H3><B>SOM Toolbox -- Initialization & Training GUI</B> is Graphigal User Interfacefor initializating and training SOM. It is based on matlab functions inSomtoolbox vs.2. <A NAME="load"><H3>Loading the data set</H3></A>You can load the data set from <A HREF="#mainwin"> main window </A> by pushingthe button <B>LOAD DATA</B> in upper left corner of window or by selecting<B>Load Data</B> from menu <B>Load/Save</B>. When the button is pushed or menu is selected, then the <B>Load GUI</B> is activated, see figure below. Data can be loaded  from workspace or from the file. Select the radiobutton <B>Workspace</B> if you want to load data from workspace or select radiobutton<B>File</B> if you want to load data from file. If you selected <B>File</B> then select the appropriate file type from popupmenu, you can choose either <B>dat file</B> (SOMPAK format) or<B>mat file</B>, which is ordinary matlab <B>.mat file</B>. Write the name ofdata in upper editfield if you have chosen <B>workspace</B> or write the filename in another editfield below that. You can also push button <B>Browse</B> and then you see all the choises that you have in <A HREF="browsewin.jpg">browse window</A> or in <A HREF="wspace.jpg">workspace window.</A> After that press button <B>Load</B> and selected data will be loaded and Load GUI disapear and controlreturn back to Main GUI. Note that there is also one checkbox called <B>Missing value char</B> and one empty field related to that. If you select <B>File</B> and after that file type <B>dat file</B> you can redefine char, which is ignored in case of <B>dat file</B>, default value is tab<P><CENTER><IMG SRC="loadgui.jpg" ALT="Load GUI"><BR><B>Figure 1. Load GUI</B></CENTER></P><A NAME="pre"><H3>Preprocessing the data</H3></A>After you have loaded the data then you can preprocess it. Select themenu called <B>Tools</B> from the menubar and from there select<B>Preprocess Data</B> and <A HREF="preprocess.html"> preprocessingGUI</A> will be activated.  After you have preprocessed data save itto the workspace and close the Preprocessin GUI after that you seelittle <A HREF="reload.gif"> question dialog box</A>, which askes thename saved data, default value is the name of data beforepreprocessing. After that the data is preprocessed and new defaultvalues are shown in main window.<A NAME="init"><H3>Map initialization</H3></A>In <A HREF="#mainwin">main window</A> the static fields show default initialization parameters for the training data. if you press button <B>INITIALIZE</B> and map will be initialized according to these parameters. You can also change these parameters by pressing button <B>Change values</B>.After that Initialization GUI, see figure below, will be activated and you canchange initialization parameters from there. Possible options are:<DL>  <DT> <B>Type:</B>  <DD> Type of initilailzation, either <B>random</B> or <B>linear</B>	  <DT> <B>Lattice:</B>  <DD> Form of map, either <B>rectancular</B> or <B>hexagonal</B>	  <DT> <B>Shape:</B>  <DD> Shape of map, <B>sheet</B>, <B>cylinder</B> or <B>toroid</B>  <DT> <B>Map size:</B>  <DD> Size of map in form vertical*horizontal map units  <DT> <B>Munits:</B>  <DD> Total number of map units, so that the proportio  of horizontal and vertical map units is same as in default map size.		</DL>Press <B>OK</B> when you are changesd the parameters and the new parameters are set and the initialization gui will disapper and control returns to Main GUI. Press button  <B>INITIALIZE</B> and map will be initilized according to new parameters.<P><CENTER><IMG SRC="initgui.jpg" ALT="Change Initialization GUI" ><BR><B>Figure 2. Initialization GUI</B></CENTER></P>	<A NAME="train"><H3>Map training</H3></A>After initialization you can train the map. Training have two phases,rough training and finetune phase. You can see default parameter for trainingin static fields of <A HREF="#mainwin">main window</A>. General values are common both for the rough and finetune phase and varying values show spesific values for both two phases. You can train the map with these values by pushing<B>TRAIN</B> button. It is also possible do only the finetune phase, bypushing <B>Only Finetune</B> radiobutton down. You can also change thesedefault values by pressing <B>Change values</B> button in botom of trainingpart. After that you can choose training algorithm, either sequential orbatch training, from the <A HREF="questdlg.jpg">question box</A>. After choosing the appropriate algorithm you can select parameters from parameter window, see below. The values you see first are the default values. Possible options are:<DL>  <DT> <B>Mask:</B>  <DD> BMU search mask, size dim*1  <DT> <B>Neigh:</B>  <DD> Neighborhood function, <B>gaussian</B>, <B>cutgauss</B>, <B>ep</B> or <B>bubble</B>,  <DT> <B>Tracking:</B>  <DD> Tracking level value between 0-3  <DT> <B>Length type:</B>  <DD> Training length type, either <B>samples</B> or <B>epochs</B>  <DT> <B>Order:</B>  <DD> Sample order, either <B>ordered</B> or <B>random</B>  <DT> <B>Learning func:</B>  <DD> Learning rate function, <B>inv</B>, <B>linear</B> or <B>power</B>  <DT> <B>Radius initial:</B>  <DD> Initial training radius  <DT> <B>Radius final:</B>  <DD> Final training radius  <DT> <B>Alpha initial:</B>  <DD> Initial learning rate  <DT> <B>Training length:</B>  <DD> Training length</DL><B>NOTE</B>, however that all of these values are not used in batch trainingand so you can not see or change these values. For example length typeis allways epochs in batch training so this value is hidden from you andyou cannot change it. You approve you choises by pressing button<B>Set parameters</B>. After that parameter window will disapper andcontrol returns back to main window. Then you can press <B>TRAIN</B>button map will be trained.<P><CENTER><IMG SRC="paragui.jpg" ALT="Change Parameters GUI"><BR><B>Figure 3. Change training parameters GUI</B></CENTER></P><A NAME="save"><H3>Save trained map</H3></A>After training you can save the trained map. Choose manu <B>Load/Save</B> fromthe menubar and there <B>Save map</B> and either <B>Save in workspace</B> or<B>Write cod-file</B>. If you choose <B>Save in workspace</B>, then<A HREF="savemap.gif">question box</A>asks the map name in workspace and the map is saved in that name.If you choose <B>Save map</B>, then <A HREF="browse.gif">browse window</A>asks the name of file where the map is saved. The Map is written to <B>.cod file</B>, which is SOMPAK format.<A NAME="vis"><H3>Visualize trained map</H3></A>You can visualize trained map by selecting <B>Tools</B> from menubar andthen selecting <B>Visualize map</B>. After that Visualization GUI is activatedand you can visualize map.<A NAME="restart"><H3>Start from beginning</H3></A>If you want to start from the beginning, this might be handy if you make somemistake or you want to train another map, then the best way to do it isby selectin <B>Tools</B> from the menu bar and <B>Clear all</B> from there.<A NAME="close"><H3>Close the program</H3></A>You can close the program when ever you wish by pressing <B>CLOSE</B> buttonin main window or by selecting <B>Tools</B> from menubar and <B>Close Figure</B>from there. <A NAME="main"><H3>Main window</H3></A>The main window has three separate parts, which are <B>Information</B>,<B>Initialization</B> and <B>Training</B>. <B>Information</B> part include useful information about map, data and actions which have been carried out.The Status field contain information about the last action which havebeen carried out. The map field contains the name of map and the datafield contain the name of training data.<P><B>Initialization</B> part contain all the information and actions neededto initialization of map. The static fields show the default initializationvalues for the particular data set. It is possible to change thesevalues by pushing the button <B>Change values</B> in bottom of initializationpart.<P><B>Training</B> part contains all the information and actions needed to trainthe map. Also in this case, static fields show default training values.<I>Genenral values</I> are common for both rough and finetune training.<I>Varying values</I> are separate for these two phases. It is possiblechange these values by pushing the button <B>Change values</B>  in bottomof training part. There is also radiobutton <B>only finetune</B>, whenthis button is activated the <B>Rough</B> values change inactive and only<B>finetune</B> is carried out.<A NAME="mainwin"><P><CENTER><IMG SRC="mwindow.jpg" ALT="GUI window"><BR><B>Figure 4. Main GUI</B>	</CENTER><P></A><A NAME="releted"><P><H3>Help</H3>There is menu called <B>Help/Info</B> in main window where you can find help. <B>WWW Help</B> shows this page and <B>Help window</B> shows this page in ascii format.<B>About GUI</B> shows some general information about this GUI in help window. If you didn't find answer to your problemthen you can try to look your answer in following web pages.<BR><A HREF="#begin">Back to begining</A><P></A></body></HTML>
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