File: $CORTEX/README

Introduction:

The code in this archive (Cortex Version 3.0.3) has been tested in
Matlab Version 7.2 (R2006).  Version 3.0.3 depends on Kevin Murphy's
Bayes Net Toolbox (BNT).  BNT can be downloaded from SourceForge
http://bnt.sourceforge.net and is well worth looking into if you work
with Matlab and graphical models.  I have included a modified 2004
version of BNT with this archive.  The modifications were made to
support additional functionality required by the Cortex sortware.

Directory structure:

    $CORTEX/README                    % This introductory file.
            CHANGES                   % The Cortex version history.
            init.m                    % Modify to suit your system.
            synthetic/demo.m          % Demos using synthetic data 
            pictionary/demo.m         % and Dileep George's dataset.
    $CORTEX/../FullBNT/               % Version of Murphy's BNT (1).

    $CORTEX/variable/                 % Data and code for exploring
            variable/data/*.mat       % inertial priors for SFA (2). 
    $CORTEX/input/*.mat               % Previously computed models.
___________

 1. This is a modification of the version of Murphy's code last updated 
    on 9 June 2004.  BNT is distributed under the GNU Library GPL as is 
    all of the code in this archive - see ../FullBNT/BNT/license.gpl.txt.

 2. There are a number of tar files containing the Cortex software, plus
    demonstrations, precomputed models and experimental results available 
    at the URL: http://www.cs.brown.edu/~tld/projects/cortex/software.html
___________

Installation instructions:

Here is how the basic software archive was created:

% cd /u/tld/programming/matlab/projects/
% tar -cf cortex.tar ./cortex ../FullBNT
% gzip cortex.tar 

Here is one way to obtain and expand the software archive and related components:

% if ( ! -e projects ) mkdir projects
% cd projects
% curl -O http://www.cs.brown.edu/~tld/projects/cortex/archive/3.0.3/cortex.tar.gz
% gunzip cortex.tar.gz
% tar -xf cortex.tar
% mv FullBNT ..
% rm cortex.tar
% curl -O http://www.cs.brown.edu/~tld/projects/cortex/supplements/variable.tar.gz
% gunzip variable.tar.gz
% tar -xf variable.tar
% curl -O http://www.cs.brown.edu/~tld/projects/cortex/supplements/data.tar.gz
% gunzip data.tar.gz
% tar -xf data.tar
% vi cortex/init.tar

The last command assumes that you want to modify the file-system-specific 
directories specified in cortex/init.m using a using the Unix 'vi' editor.


Optional and required C libraries:

 BNT has optional C code that must be compiled to run on your machine
 architecture.  This code can speed up BNT operations considerably and
 is recommended.  Instalation instructions can be found on Murphy's 
 web site at http://www.cs.ubc.ca/~murphyk/Software/BNT/usage.html.

 The Cortex software also has C code.  This code is required if you are
 going to use variable-order models.  The source code is in ./bin/ and 
 can be compiled from within Matlab by running the following commands: 

>> cd cortex/bin 
>> compile