brainstorm.m

function varargout = brainstorm( varargin )
% BRAINSTORM Brainstorm startup function.
%
% USAGE: brainstorm               : Start Brainstorm
%        brainstorm start         : Start Brainstorm
%        brainstorm nogui         : Start Brainstorm without interface
%        brainstorm server        : Start Brainstorm on a Matlab server (keeps the environment alive at the end of the execution)
%        brainstorm ... local     : Start Brainstorm with a local database (in .brainstorm folder)
%        brainstorm stop          : Quit Brainstorm
%        brainstorm reset         : Re-inialize Brainstorm (delete preferences and database)
%        brainstorm digitize      : Digitize points using a Polhemus system
%        brainstorm update        : Download and install latest Brainstorm update
%        brainstorm autopilot ... : Call bst_autopilot with the following arguments
%        brainstorm setpath       : Add Brainstorm subdirectories to current path
%        brainstorm startjava     : Add Brainstorm Java classes to dynamic classpath
%        brainstorm info          : Open Brainstorm website
%        brainstorm license       : Displays license agreement window
%        brainstorm tutorial name : Run the validation script attached to a tutorial (ctf, neuromag, raw, resting, yokogawa
%        brainstorm tutorial all  : Run all the validation scripts
%        brainstorm test          : Run a coverage test
%        brainstorm deploy        : Create a zip file for distribution (see bst_deploy for options)
%        brainstorm deploy 1      : Compile the current version of Brainstorm with Matlab mcc compiler
%  res = brainstorm('status')     : Return brainstorm status (1=running, 0=stopped)

% @=============================================================================
% This function is part of the Brainstorm software:
% http://neuroimage.usc.edu/brainstorm
% 
% Copyright (c)2000-2017 University of Southern California & McGill University
% This software is distributed under the terms of the GNU General Public License
% as published by the Free Software Foundation. Further details on the GPLv3
% license can be found at http://www.gnu.org/copyleft/gpl.html.
% 
% FOR RESEARCH PURPOSES ONLY. THE SOFTWARE IS PROVIDED "AS IS," AND THE
% UNIVERSITY OF SOUTHERN CALIFORNIA AND ITS COLLABORATORS DO NOT MAKE ANY
% WARRANTY, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO WARRANTIES OF
% MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE, NOR DO THEY ASSUME ANY
% LIABILITY OR RESPONSIBILITY FOR THE USE OF THIS SOFTWARE.
%
% For more information type "brainstorm license" at command prompt.
% =============================================================================@
%
% Authors: Francois Tadel, 2008-2017

% Make sure that "more" is off
more off

% Compiled version
if exist('isdeployed', 'builtin') && isdeployed
    BrainstormHomeDir = fileparts(fileparts(which(mfilename)));
    %disp(['Running from: ' BrainstormHomeDir]);
else
    % Assume we are in the Brainstorm folder
    BrainstormHomeDir = fileparts(which(mfilename));
    % Add path to the core subfolders, used in this function
    corePath = fullfile(BrainstormHomeDir, 'toolbox', 'core');
    if ~exist(corePath, 'dir')
        error(['Unable to find ' corePath ' directory.']);
    end
    % Test if the folders are already in the path first
    p = path();
    if isempty(strfind(p, corePath))
        addpath(corePath, '-BEGIN');
        addpath(fullfile(BrainstormHomeDir, 'toolbox', 'io'), '-BEGIN');
        addpath(fullfile(BrainstormHomeDir, 'toolbox', 'misc'), '-BEGIN');
    end
end

% Get JOGL version
% If JOGL1 is available
if exist('javax.media.opengl.GLCanvas', 'class') && exist('com.sun.opengl.util.j2d.TextRenderer', 'class')
    JOGLVersion = 1;
% If JOGL2 is available
elseif exist('javax.media.opengl.awt.GLCanvas', 'class')
    JOGLVersion = 2;
% If JOGL2.3 is available
elseif exist('com.jogamp.opengl.awt.GLCanvas', 'class')
    JOGLVersion = 2.3;
% No JOGL available
else
    JOGLVersion = 0;
end
% Define jar file to remove from the Java classpath
switch (JOGLVersion)
    case 0,    jarfile = '';  disp('ERROR: JOGL not supported');
    case 1,    jarfile = 'brainstorm_jogl1.jar'; 
    case 2,    jarfile = 'brainstorm_jogl2.jar';
    case 2.3,  jarfile = 'brainstorm_jogl2.3.jar';
end
    
% Set dynamic JAVA CLASS PATH
if ~exist('org.brainstorm.tree.BstNode', 'class')
    % Add Brainstorm JARs to classpath
    javaaddpath([BrainstormHomeDir '/java/RiverLayout.jar']);
    javaaddpath([BrainstormHomeDir '/java/brainstorm.jar']);
    javaaddpath([BrainstormHomeDir '/java/vecmath.jar']);
    % Add JOGL package
    if ~isempty(jarfile)
        javaaddpath([BrainstormHomeDir '/java/' jarfile]);
    end
end
% Deployed: Remove one of the two JOGL packages from the Java classpath
if exist('isdeployed', 'builtin') && isdeployed
    % Find the entry in the classpath
    if ~isempty(jarfile)
        jarfileRemove = setdiff({'brainstorm_jogl1.jar', 'brainstorm_jogl2.jar', 'brainstorm_jogl2.3.jar'}, jarfile);
        for i = 1:length(jarfileRemove)
            dynamicPath = javaclasspath('-dynamic');
            iClass = find(~cellfun(@(c)isempty(strfind(c,jarfileRemove{i})), dynamicPath));
            if ~isempty(iClass)
                javarmpath(dynamicPath{iClass(1)});
            end
        end
    end
end

% Default action : start
if (nargin == 0)
    action = 'start';
    BrainstormDbDir = [];
else
    action = lower(varargin{1});
    % Local start
    if ismember(action, {'start', 'nogui', 'server'}) && (nargin == 2) && strcmpi(varargin{2}, 'local')
        BrainstormDbDir = 'local';
    else
        BrainstormDbDir = [];
    end
end

res = 1;
switch action
    case 'start'
        bst_set_path(BrainstormHomeDir);
        bst_startup(BrainstormHomeDir, 1, BrainstormDbDir);
    case 'nogui'
        bst_set_path(BrainstormHomeDir);
        bst_startup(BrainstormHomeDir, 0, BrainstormDbDir);
    case 'server'
        bst_set_path(BrainstormHomeDir);
        bst_startup(BrainstormHomeDir, -1, BrainstormDbDir);
    case 'autopilot'
        if ~isappdata(0, 'BrainstormRunning')
            bst_set_path(BrainstormHomeDir);
            bst_startup(BrainstormHomeDir, 2, BrainstormDbDir);
        end
        res = bst_autopilot(varargin{2:end});
    case 'digitize'
        brainstorm nogui
        panel_digitize('Start');
    case {'status', 'isstarted', 'isrunning'}
        res = isappdata(0, 'BrainstormRunning');
    case {'exit', 'stop', 'quit'}
        bst_exit();
    case 'reset'
        bst_reset();
    case 'setpath'
        disp('Adding all Brainstorm directories to local path...');
        bst_set_path(BrainstormHomeDir);
    case 'startjava'
        disp('Starting Java...');
    case {'info', 'website'}
        web('http://neuroimage.usc.edu/brainstorm/', '-browser');
    case 'forum'
        web('http://neuroimage.usc.edu/forums/', '-browser');
    case 'license'
        bst_set_path(BrainstormHomeDir);
        bst_set('BrainstormHomeDir', BrainstormHomeDir);
        bst_license();
    case 'update'
        % Add path to java_dialog function
        addpath(fullfile(BrainstormHomeDir, 'toolbox', 'gui'));
        % Update
        bst_update(0);
    case 'tutorial'
        bst_set_path(BrainstormHomeDir);
        tutonames = varargin{2};
        % Tutorial folder
        if (nargin < 3)
            tutorial_dir = 'C:\Work\RawData\Tutorials';
        else
            tutorial_dir = varargin{3};
        end
        % Run all the tutorial scripts
        if isequal(tutonames, 'all')
            tutonames = {'ctf', 'raw', 'epilepsy', 'resting', 'neuromag', 'yokogawa', 'auditory'};
        elseif ischar(tutonames)
            tutonames = {tutonames};
        elseif ~iscell(tutonames)
            error('Invalid call.');
        end
        % Run all the requested validation scripts
        for i = 1:length(tutonames)
            disp([10 '===== TUTORIAL: ' upper(tutonames{i}) ' =====']);
            startTime = tic;
            eval(['tutorial_' lower(tutonames{i}) '(''' tutorial_dir ''');']);
            % Done
            stopTime = toc(startTime);
            if (stopTime > 60)
                disp(sprintf('BST> Done in %dmin\n', round(stopTime/60)));
            else
                disp(sprintf('BST> Done in %ds\n', round(stopTime)));
            end
            % Close report viewer if it is not the last tutorial to run
            if (i < length(tutonames))
                bst_report('Close');
            end
        end
    case 'test'
        bst_set_path(BrainstormHomeDir);
        if (nargin < 2)
            error(['You must specify an empty test folder.' 10 'Usage: brainstorm test test_dir']);
        end
        test_dir = varargin{2};
        test_all(test_dir);
    case 'deploy'
        % Close Brainstorm
        if isappdata(0, 'BrainstormRunning')
            bst_exit();
        end
        % Initialize path
        bst_set_path(BrainstormHomeDir);
        % Get Matlab version
        ReleaseName = bst_get('MatlabReleaseName');
        % Add path to java_dialog function
        deployPath = fullfile(BrainstormHomeDir, 'deploy');
        addpath(deployPath);
        bst_set('BrainstormHomeDir', BrainstormHomeDir);
        % Remove .brainstorm from the path
        rmpath(bst_get('UserMexDir'));
        rmpath(bst_get('UserProcessDir'));
        % Build the name of the deployment function
        bst_deploy_java = str2func(['bst_deploy_java_' ReleaseName(2:end)]);
        % Update
        if (nargin > 1)
            bst_deploy_java(varargin{2:end});
        else
            bst_deploy_java();
        end
    case 'packagebin'
        bst_set_path(BrainstormHomeDir);
        deployPath = fullfile(BrainstormHomeDir, 'deploy');
        addpath(deployPath);
        bst_set('BrainstormHomeDir', BrainstormHomeDir);
        bst_package_bin(varargin{2:end});
    otherwise
        disp(' ');
        disp('Usage : brainstorm start         : Start Brainstorm');
        disp('        brainstorm nogui         : Start Brainstorm without interface (for scripts)');
        disp('        brainstorm stop          : Stop Brainstorm');
        disp('        brainstorm server        : Start Brainstorm on a Matlab server');
        disp('        brainstorm update        : Download and install latest Brainstorm update (see bst_update)');
        disp('        brainstorm reset         : Re-initialize Brainstorm database and preferences');
        disp('        brainstorm digitize      : Digitize electrodes positions and head shape using a Polhemus system');
        disp('        brainstorm setpath       : Add Brainstorm subdirectories to current path');
        disp('        brainstorm startjava     : Add Brainstorm Java classes to dynamic classpath');
        disp('        brainstorm info          : Open Brainstorm website');
        disp('        brainstorm forum         : Open Brainstorm forum');
        disp('        brainstorm license       : Display license');
        disp('        brainstorm tutorial name : Run the validation script attached to a tutorial (ctf, neuromag, raw, resting, yokogawa)');
        disp('        brainstorm tutorial all  : Run all the validation scripts');
        disp('        brainstorm deploy        : Create a zip file for distribution (see bst_deploy)');
        disp('        brainstorm deploy 1      : Deploy + compile the current version of Brainstorm with Matlab mcc compiler');
        disp('        brainstorm packagebin    : Create separate zip files for all the currently available binary distributions');
        disp(' ');
end

% Return value
if (nargout >= 1)
    varargout{1} = res;
end

end


%% ===== SET PATH =====
function bst_set_path(BrainstormHomeDir)
    % Cancel add path in case of deployed application
    if exist('isdeployed', 'builtin') && isdeployed
        return
    end
    % Brainstorm folder itself
    addpath(BrainstormHomeDir, '-BEGIN'); % make sure the main brainstorm folder is in the path
    % List of folders to add
    NEXTDIR = {'external','toolbox'}; % in reverse order of priority
    for i = 1:length(NEXTDIR)
        nextdir = fullfile(BrainstormHomeDir,NEXTDIR{i});
        % Reset the last warning to blank
        lastwarn('');
        % Check that directory exist
        if ~isdir(nextdir)
            error(['Directory "' NEXTDIR{i} '" does not exist in Brainstorm path.' 10 ...
                   'Please re-install Brainstorm.']);
        end
        % Recursive search for subfolders in each main folder
        P = genpath(nextdir);
        % Add directory and subdirectories
        addpath(P, '-BEGIN');
    end
    % Adding user's mex path
    userMexDir = bst_get('UserMexDir');
    addpath(userMexDir, '-BEGIN');
    % Adding user's custom process path
    userProcessDir = bst_get('UserProcessDir');
    addpath(userProcessDir, '-BEGIN');
end