brainstorm.m

function varargout = brainstorm( varargin )
% BRAINSTORM Brainstorm startup function.
%
% USAGE: brainstorm                 : Start Brainstorm
%        brainstorm start           : Start Brainstorm
%        brainstorm nogui           : Start Brainstorm with hidden interface (for scripts)
%        brainstorm server          : Start Brainstorm on a distant server (completely headless)
%        brainstorm [script] [args] : Start Brainstorm in server mode and execute the input script
%        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
%        brainstorm deploy 2        : Compile including SPM and FieldTrip functions used by Brainstorm
%        brainstorm workshop        : Download OpenMEEG and the SPM atlases, and run some small tests
%  res = brainstorm('status')       : Return brainstorm status (1=running, 0=stopped)

% @=============================================================================
% This function is part of the Brainstorm software:
% https://neuroimage.usc.edu/brainstorm
% 
% Copyright (c)2000-2020 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
    
    % === INITIALIZE MFFMATLABIO LIBRARY ===
    [mffJarPath, mffJarExists] = bst_get('MffJarFile');
    mffDirTmp = bst_fullfile(bst_get('BrainstormUserDir'), 'mffmatlabioNew');
    if isdir(mffDirTmp)
        % A new library version is available, install it
        mffDir = fileparts(mffJarPath);
        if isdir(mffDir)
            rmdir(mffDir, 's');
        end
        mkdir(mffDir);
        libDir = bst_fullfile(mffDirTmp, 'mffmatlabio', '*');
        file_move(libDir, mffDir);
        rmdir(mffDirTmp, 's');
        mffJarExists = 1;
    end
    % Add MFF JAR file if present
    if mffJarExists
        javaaddpath(mffJarPath);
    end
    
    % === INITIALIZE NWB LIBRARY ===
    NWBDir = bst_fullfile(bst_get('BrainstormUserDir'), 'NWB');        
    initialization_flag_file = bst_fullfile(NWBDir,'NWB_initialized.mat');
    if exist(initialization_flag_file,'file') == 2
        load(initialization_flag_file);
        if ~NWB_initialized
            % The generateCore needs to run from a specific folder
            current_path = pwd;
            % Add NWB to Matlab path
            addpath(genpath(NWBDir));
            % Generate the NWB Schema (First time run)
            disp(['Installing NWB library: ' NWBDir '...']);
            cd(NWBDir);
            generateCore();
            % Update path with new folders
            addpath(genpath(NWBDir));
            % Update Initialization flag
            NWB_initialized = 1;
            save(bst_fullfile(NWBDir,'NWB_initialized.mat'), 'NWB_initialized');
            cd(current_path);
        end
    end
    
    % === INITIALIZE NWB-ECoG LIBRARY ===
    NWB_ECoGDir = bst_fullfile(bst_get('BrainstormUserDir'), 'NWB', 'ECoG');        
    initialization_flag_file = bst_fullfile(NWB_ECoGDir,'NWB_ECoGinitialized.mat');
    if exist(initialization_flag_file,'file') == 2
        load(initialization_flag_file);
        if ~NWB_ECoGinitialized
            disp('Installing NWB - ECoG library...');
            % The generateCore needs to run from a specific folder
            current_path = pwd;
            cd(NWB_ECoGDir);
            % Add NWB to Matlab path
            addpath(genpath(NWB_ECoGDir));
            % Generate the NWB Schema (First time run)
            generateCore(bst_fullfile('ecog.namespace.yaml'))
            % Update Initialization flag
            NWB_ECoGinitialized = 1;
            save(bst_fullfile(NWB_ECoGDir,'NWB_ECoGinitialized.mat'), 'NWB_ECoGinitialized');
            cd(current_path);
        end
    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('https://neuroimage.usc.edu/brainstorm/', '-browser');
    case 'forum'
        web('https://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;
            if (length(varargin) == 4)
                eval(['tutorial_' lower(tutonames{i}) '(''' tutorial_dir ''', ''' varargin{4} ''');']);
            else
                eval(['tutorial_' lower(tutonames{i}) '(''' tutorial_dir ''');']);
            end
            % 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 'workshop'
        % Runs Brainstorm normally (asks for brainstorm_db)
        if ~isappdata(0, 'BrainstormRunning')
            bst_set_path(BrainstormHomeDir);
            bst_startup(BrainstormHomeDir, 1, BrainstormDbDir);
        end
        % Message
        java_dialog('msgbox', 'Brainstorm will now download additional files needed for the workshop.', 'Workshop');
        % Downloads OpenMEEG
        bst_openmeeg('download');
        % Downloads the TMP.nii SPM atlas
        bst_normalize_mni('install');
        % Message
        java_dialog('msgbox', ['Brainstorm will now test your display and open a 3D figure:' 10 10 ... 
                               ' - You should see two surfaces: a brain surface and a transparent head.' 10 ...
                               ' - Make sure you can rotate the brain with your mouse, ' 10 ...
                               ' - Then close the figure.' 10 10], 'Workshop');
        % Creates an empty test protocol
        ProtocolName = 'TestWorkshop';
        gui_brainstorm('DeleteProtocol', ProtocolName);
        gui_brainstorm('CreateProtocol', ProtocolName, 0, 0);
        % Display the default anatomy cortex and head 
        hFig = view_surface('@default_subject/tess_cortex_pial_low.mat');
        hFig = view_surface('@default_subject/tess_head.mat', [], [], hFig);
        waitfor(hFig);
        % Delete test protocol
        gui_brainstorm('DeleteProtocol', ProtocolName);
        % Confirmation message
        java_dialog('msgbox', 'You computer is ready for the workshop.', 'Workshop');
        
    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
        % Check if trying to execute a script
        if file_exist(action)
            ScriptFile = action;
        elseif file_exist(fullfile(pwd, action))
            ScriptFile = fullfile(pwd, action);
        else
            ScriptFile = [];
        end
        % Execute script
        if ~isempty(ScriptFile)
            % Start brainstorm in server mode
            brainstorm server;
            % Execute script
            if (length(varargin) > 1)
                panel_command('ExecuteScript', ScriptFile, varargin{2:end});
            else
                panel_command('ExecuteScript', ScriptFile);
            end
            % Quit
            brainstorm stop;
            
        % Display usage
        else
            disp(' ');
            disp('Usage : brainstorm start           : Start Brainstorm');
            disp('        brainstorm nogui           : Start Brainstorm with hidden interface (for scripts)');
            disp('        brainstorm server          : Start Brainstorm on a distant server (completely headless)');
            disp('        brainstorm <script> <args> : Start Brainstorm in server mode, execute the input script and quit');
            disp('        brainstorm ... local       : Start Brainstorm with a local database (in .brainstorm folder)');
            disp('        brainstorm stop            : Quit Brainstorm');
            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 packagebin      : Create separate zip files for all the currently available binary distributions');
            disp('  res = brainstorm(''status'')     : Return brainstorm status (1=running, 0=stopped)');
            disp(' ');
        end
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