eegmp_analysis/tools/[MEG]PLS/MEGPLS_PIPELINE_v2.02b/InstallationGUI.m

function varargout = InstallationGUI(varargin)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Configures toolbox paths for pipeline and installs fixes. %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

% Copyright (C) 2013-2014, Michael J. Cheung
%
% This file is a part of the MEG & PLS Pipeline (MEGPLS). For more 
% details, see the documentation included with the software package.
%
% MEGPLS is free software: you can redistribute it and/or modify it under
% the terms of the GNU General Public License version 2 as published by 
% the Free Software Foundation. This program is distributed in the hope 
% that it will be useful, but WITHOUT ANY WARRANTY; without even the 
% implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. 
% See the GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License along
% with this program. If not, you can download the license here: 
% <http://www.gnu.org/licenses/old-licenses/gpl-2.0>.


% Last Modified by GUIDE v2.5 26-Feb-2014 21:48:15

% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name',       mfilename, ...
                   'gui_Singleton',  gui_Singleton, ...
                   'gui_OpeningFcn', @InstallationGUI_OpeningFcn, ...
                   'gui_OutputFcn',  @InstallationGUI_OutputFcn, ...
                   'gui_LayoutFcn',  [] , ...
                   'gui_Callback',   []);
if nargin && ischar(varargin{1})
    gui_State.gui_Callback = str2func(varargin{1});
end

if nargout
    [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
else
    gui_mainfcn(gui_State, varargin{:});
end
% End initialization code - DO NOT EDIT


%--- Executes just before InstallationGUI is made visible. ---%
%---------------------------------------------------------%
function InstallationGUI_OpeningFcn(hObject, eventdata, handles, varargin)
% This function has no output args, see OutputFcn.
% hObject    handle to figure
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
% varargin   command line arguments to InstallationGUI (see VARARGIN)

% Choose default command line output for InstallationGUI
handles.output = hObject;

% Update handles structure
guidata(hObject, handles);


% Get pipeline run directory:
[PipelineDir, ~, ~] = fileparts(which('InstallationGUI.m'));
handles.PipelineDir = PipelineDir;

% Initialize variables:
if exist([PipelineDir,'/ToolboxPaths.mat'], 'file')
	ToolboxPaths = load([PipelineDir,'/ToolboxPaths.mat']);
	
	handles.paths.Fieldtrip   = ToolboxPaths.paths.Fieldtrip;
	handles.paths.SPM         = ToolboxPaths.paths.SPM;
	handles.paths.AFNIMatlab  = ToolboxPaths.paths.AFNIMatlab;
    
    set(handles.TextboxFieldtripPath,  'String', handles.paths.Fieldtrip);
    set(handles.TextboxSPMPath,        'String', handles.paths.SPM);
    set(handles.TextboxAFNIMatlabPath, 'String', handles.paths.AFNIMatlab);
	
else
	handles.paths.Fieldtrip   = [];
	handles.paths.SPM		  = [];
	handles.paths.AFNIMatlab  = [];
	
end

% Save handles:
guidata(hObject, handles);


% UIWAIT makes InstallationGUI wait for user response (see UIRESUME)
% uiwait(handles.figure1);


%--- Outputs from this function are returned to the command line. ---%
%--------------------------------------------------------------------%
function varargout = InstallationGUI_OutputFcn(hObject, eventdata, handles) 
% varargout  cell array for returning output args (see VARARGOUT);
% hObject    handle to figure
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Get default command line output from handles structure
varargout{1} = handles.output;




%======================================%
% FUNCTIONS FOR SETTING TOOLBOX PATHS: %
%======================================%

%--- Executes on button press in ButtonFieldtripPath. ---%
%--------------------------------------------------------%
function ButtonFieldtripPath_Callback(hObject, eventdata, handles)
SelectedPath = uigetdir(pwd, 'Specify Fieldtrip toolbox directory:');
if SelectedPath == 0
	return;  % If user cancels
end

% Check if selected path is Fieldtrip toolbox:
if ~exist([SelectedPath,'/ft_defaults.m'], 'file')
    ErrMsg = {'ERROR:';
        'Selected directory does not seem to be Fieldtrip toolbox.';
        'Cannot find "ft_defaults.m" function in target location.'};
	msgbox(ErrMsg, 'Error:');
	return;
end

% Import required fieldtrip private functions:
ImportFcnDir = [handles.PipelineDir,'/MEGPLS_COMPONENTS/FieldtripPrivate'];
if ~exist(ImportFcnDir, 'dir')
	status = mkdir(ImportFcnDir);
	
	if status == 0
		msgbox('Error: Failed to create folder in pipeline directory.')
		return;
	end
end

if exist([ImportFcnDir,'/parameterselection.m'], 'file');
    delete([ImportFcnDir,'/parameterselection.m']);
end
if exist([ImportFcnDir,'/align_ijk2xyz.m'], 'file');
    delete([ImportFcnDir,'/align_ijk2xyz.m']);
end

status1 = copyfile([SelectedPath,'/private/parameterselection.m'], [ImportFcnDir,'/'], 'f');
status2 = copyfile([SelectedPath,'/private/align_ijk2xyz.m'],      [ImportFcnDir,'/'], 'f');

if status1 == 0 || status2 == 0
	msgbox('Error: Failed to import Fieldtrip private functions.')
	return;
end

% Set fieldtrip path:
handles.paths.Fieldtrip = SelectedPath;
set(handles.TextboxFieldtripPath, 'String', handles.paths.Fieldtrip);

% Save handles:
guidata(hObject, handles);


%--- Textbox to display selected Fieldtrip path: ---%
%---------------------------------------------------%
function TextboxFieldtripPath_Callback(hObject, eventdata, handles)
EnteredText = get(handles.TextboxFieldtripPath, 'String');

if ~isequal(EnteredText, handles.paths.Fieldtrip);
	set(handles.TextboxFieldtripPath, 'String', handles.paths.Fieldtrip);
	msgbox('Note: Use button to change Fieldtrip path.')
end


%--- Executes on button press in ButtonSPMPath. ---%
%--------------------------------------------------%
function ButtonSPMPath_Callback(hObject, eventdata, handles)
SelectedPath = uigetdir(pwd, 'Specify SPM8 toolbox directory:');
if SelectedPath == 0
	return;  % If user cancels
end

% Check if selected path is SPM toolbox:
if ~exist([SelectedPath,'/spm_get_defaults.m'], 'file')
    ErrMsg = {'ERROR:';
        'Selected directory does not seem to be SPM8 toolbox.';
        'Cannot find "spm_get_defaults.m" function in target location.'};
	msgbox(ErrMsg, 'Error:');
	return;
end

% Set SPM path:
handles.paths.SPM = SelectedPath;
set(handles.TextboxSPMPath, 'String', handles.paths.SPM);

% Save handles:
guidata(hObject, handles);


%--- Textbox to display selected SPM path: ---%
%---------------------------------------------%
function TextboxSPMPath_Callback(hObject, eventdata, handles)
EnteredText = get(handles.TextboxSPMPath, 'String');

if ~isequal(EnteredText, handles.paths.SPM);
	set(handles.TextboxSPMPath, 'String', handles.paths.SPM);
	msgbox('Note: Use button to change SPM path.')
end


%--- Executes on button press in ButtonAFNIMatlabPath. ---%
%---------------------------------------------------------%
function ButtonAFNIMatlabPath_Callback(hObject, eventdata, handles)
SelectedPath = uigetdir(pwd, 'Specify AFNI-Matlab toolbox directory:');
if SelectedPath == 0
	return;  % If user cancels
end

% Check if selected path is AFNI-Matlab toolbox:
if ~exist([SelectedPath,'/BrikLoad.m'], 'file')
    ErrMsg = {'ERROR:';
        'Selected directory does not seem to be AFNI-Matlab toolbox.';
        'Cannot find "BrikLoad.m" function in target location.'};
	msgbox(ErrMsg, 'Error:');
	return;
end

% Set AFNI-Matlab path:
handles.paths.AFNIMatlab = SelectedPath;
set(handles.TextboxAFNIMatlabPath, 'String', handles.paths.AFNIMatlab);

% Save handles:
guidata(hObject, handles);


%--- Textbox to display selected AFNI-Matlab path: ---%
%-----------------------------------------------------%
function TextboxAFNIMatlabPath_Callback(hObject, eventdata, handles)
EnteredText = get(handles.TextboxAFNIMatlabPath, 'String');

if ~isequal(EnteredText, handles.paths.AFNIMatlab);
	set(handles.TextboxAFNIMatlabPath, 'String', handles.paths.AFNIMatlab);
	msgbox('Note: Use button to change AFNI-Matlab path.')
end


%--- Executes on button press in ButtonSaveSettings. ---%
%-------------------------------------------------------%
function ButtonSaveSettings_Callback(hObject, eventdata, handles)
if isempty(handles.paths.Fieldtrip)
	msgbox('Warning: Fieldtrip path has not been set.', 'Warning:');
	return;
end
if isempty(handles.paths.SPM)
	msgbox('Warning: SPM path has not been set.', 'Warning:');
	return;
end
if isempty(handles.paths.AFNIMatlab)
	msgbox('Warning: AFNI-Matlab path has not been set.', 'Warning:');
	return;
end

% Install fixes:
Success = MEGPLS_Install_Fixes(handles);
if Success == 0
    return;
end

% Remove existing .mat:
if exist([handles.PipelineDir,'/ToolboxPaths.mat'], 'file')
    delete([handles.PipelineDir,'/ToolboxPaths.mat']);
    
    if exist([handles.PipelineDir,'/ToolboxPaths.mat'], 'file')
        msgbox('Error: Failed to remove previous ToolboxPaths.mat for overwrite.', 'Error:')
        return;
    end
end

% Save paths to .mat:
paths = handles.paths;
save([handles.PipelineDir,'/ToolboxPaths.mat'], 'paths');

% Addpaths:
addpath(genpath(handles.PipelineDir));
rmpath([handles.PipelineDir,'/DEFAULT_SETTINGS']);  % Only want to call the ones in AnalysisID
rmpath([handles.PipelineDir,'/TEMPORARY_FIXES']);   % Want to call from Fieldtrip toolbox

addpath([paths.Fieldtrip,'/']);
ft_defaults;

addpath([paths.SPM,'/']);
addpath([paths.AFNIMatlab,'/']);

% Feedback:
if exist([handles.PipelineDir,'/ToolboxPaths.mat'], 'file')
    msgbox('Toolbox paths successfully saved.');
end


%--- Executes on button press in ButtonUninstallFixes. ---%
%---------------------------------------------------------%
function ButtonUninstallFixes_Callback(hObject, eventdata, handles)
Success = MEGPLS_Uninstall_Fixes(handles);
if Success == 0
    return;
else
    msgbox('MEGPLS compatibility fixes successfully uninstalled.');
end




%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% FUNCTIONS FOR MEGPLS COMPATIBILITY FIXES: %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%--- Installs compatibility fixes: ---%
%-------------------------------------%
function Success = MEGPLS_Install_Fixes(InputHandles)
handles = InputHandles;
paths   = handles.paths;

InstallErrMsg = {'Error:'; '';
    'Failed to apply FieldTrip compatibility patch for [MEG]PLS pipeline.';
    'Ensure you have read/write permissions to Fieldtrip and [MEG]PLS folders.';
    'For more details, see README file in "TEMPORARY_FIXES" folder.'};

FixBackupFolder = [paths.Fieldtrip,'/MEGPLS_INSTALL_BACKUP'];
if ~exist(FixBackupFolder, 'dir')
    Status = mkdir(FixBackupFolder);
    
    if Status == 0
        msgbox(InstallErrMsg, 'Error:');
        Success = 0;
        return;
    end
end


% Apply temporary "warning_once" fix (See readme in "TEMPORARY_FIXES" folder):
% Bug in newer version of FT "warning_once.m" that occurs when calling from MATLAB GUIDE.
% Link: http://mailman.science.ru.nl/pipermail/fieldtrip/2013-August/006889.html

% Backup original file:
if ~exist([FixBackupFolder,'/warning_once.m'], 'file')
    TargetFile = [paths.Fieldtrip,'/private/warning_once.m'];
    
    if ~exist(TargetFile, 'file')
        msgbox('Error: Failed to find original "warning_once.m" file.', 'Error:')
        msgbox(InstallErrMsg, 'Error:')
        Success = 0;
        return;
    end
    
    MakeBackup = copyfile(TargetFile, [FixBackupFolder,'/'], 'f');
    
    if MakeBackup == 0
        msgbox('Error: Failed to create backup of original "warning_once.m" file.', 'Error:')
        msgbox(InstallErrMsg, 'Error:')
        Success = 0;
        return;
    end
end

% Apply fixed files (overwrite if needed):
FixedFile = [handles.PipelineDir,'/TEMPORARY_FIXES/warning_once_20130211.m'];

if exist([paths.Fieldtrip,'/private/warning_once.m'], 'file')
    delete([paths.Fieldtrip,'/private/warning_once.m']);
    
    if exist([paths.Fieldtrip,'/private/warning_once.m'], 'file')
        msgbox('Error: Failed to remove previous "warning_once.m" files for overwrite.', 'Error:')
        msgbox(InstallErrMsg, 'Error:')
        Success = 0;
        return;
    end
    
    Copy1 = copyfile(FixedFile, [paths.Fieldtrip,'/private/warning_once.m'], 'f');
else
    Copy1 = 1;
end

if exist([paths.Fieldtrip,'/utilities/private/warning_once.m'], 'file')
    delete([paths.Fieldtrip,'/utilities/private/warning_once.m']);
    
    if exist([paths.Fieldtrip,'/utilities/private/warning_once.m'], 'file')
        msgbox('Error: Failed to remove previous "warning_once.m" files for overwrite.', 'Error:')
        msgbox(InstallErrMsg, 'Error:')
        Success = 0;
        return;
    end
    
    Copy2 = copyfile(FixedFile, [paths.Fieldtrip,'/utilities/private/warning_once.m'], 'f');
else
    Copy2 = 1;
end

if exist([paths.Fieldtrip,'/specest/private/warning_once.m'], 'file')
    delete([paths.Fieldtrip,'/specest/private/warning_once.m']);
    
    if exist([paths.Fieldtrip,'/specest/private/warning_once.m'], 'file')
        msgbox('Error: Failed to remove previous "warning_once.m" files for overwrite.', 'Error:')
        msgbox(InstallErrMsg, 'Error:')
        Success = 0;
        return;
    end
    
    Copy3 = copyfile(FixedFile, [paths.Fieldtrip,'/specest/private/warning_once.m'], 'f');
else
    Copy3 = 1;
end

if Copy1 == 0 || Copy2 == 0 || Copy3 == 0
    msgbox(InstallErrMsg, 'Error:');
    Success = 0;
    return;
end


% Apply temporary "ft_postamble_history" fix (See readme in "TEMPORARY_FIXES" folder):
% Bug in newer version of FT "warning_once.m" that occurs when calling from MATLAB GUIDE.
% Link: http://mailman.science.ru.nl/pipermail/fieldtrip/2013-August/006889.html

% Backup original file:
if ~exist([FixBackupFolder,'/ft_postamble_history.m'], 'file')
    TargetFile = [paths.Fieldtrip,'/utilities/private/ft_postamble_history.m'];
    
    if ~exist(TargetFile, 'file')
        msgbox('Error: Failed to find original "ft_postamble_history.m" file.', 'Error:')
        msgbox(InstallErrMsg, 'Error:')
        Success = 0;
        return;
    end
    
    MakeBackup = copyfile(TargetFile, [FixBackupFolder,'/'], 'f');
    
    if MakeBackup == 0
        msgbox(InstallErrMsg, 'Error:')
        Success = 0;
        return;
    end
end

% Apply fixed files (overwrite if needed):
FixedFile = [handles.PipelineDir,'/TEMPORARY_FIXES/ft_postamble_history_20130211.m'];

if exist([paths.Fieldtrip,'/utilities/private/ft_postamble_history.m'], 'file')
    delete([paths.Fieldtrip,'/utilities/private/ft_postamble_history.m']);
    
    if exist([paths.Fieldtrip,'/utilities/private/ft_postamble_history.m'], 'file')
        msgbox('Error: Failed to remove previous "ft_postamble_history.m" for overwrite.', 'Error:')
        msgbox(InstallErrMsg, 'Error:')
        Success = 0;
        return;
    end
end

Copy = copyfile(FixedFile, ...
    [paths.Fieldtrip,'/utilities/private/ft_postamble_history.m'], 'f');

if Copy == 0
    msgbox(InstallErrMsg, 'Error:');
    Success = 0;
    return;
end


% Add legend functionality to "ft_singleplotER" function.
% (So children of interactive multiplot have legends applied).
if ~exist([FixBackupFolder,'/ft_singleplotER.m'], 'file')
    TargetFile = [paths.Fieldtrip,'/ft_singleplotER.m'];
    
    if ~exist(TargetFile, 'file')
        msgbox('Error: Failed to find original "ft_singleplotER.m" file.', 'Error:')
        msgbox(InstallErrMsg, 'Error:')
        Success = 0;
        return;
    end
    
    MakeBackup = copyfile(TargetFile, [FixBackupFolder,'/'], 'f');
    
    if MakeBackup == 0
        msgbox(InstallErrMsg, 'Error:')
        Success = 0;
        return;
    end
    
    % Add fix to file once:
    TempPathFT = strrep(paths.Fieldtrip, ' ', '\ ');  % Replace spaces with "\ " for unix.
    
    system(['sed -i "/ft_postamble previous/ a\ \n'...
    'if isfield(cfg, ''legend'')\n'...
    '    if numel(cfg.legend) ~= Ndata\n'...
    '        disp(''Warning: # legend inputs does not match # datasets.'')\n'...
    '    end\n'...
    '    clickableLegend(cfg.legend, ''interpreter'', ''none'');\n'...
    'end\n\n" ',TempPathFT,'/ft_singleplotER.m'])

    % SED function to add text after match:
    % Format: sed -i '/regexp-string-to-match/ a\ string-to-append' filename
    % Note:   a\ option is used to append text after line of address match.
end

Success = 1;


%--- Uninstalls compatibility fixes: ---%
%---------------------------------------%
function Success = MEGPLS_Uninstall_Fixes(InputHandles)
handles = InputHandles;
paths   = handles.paths;

UninstallErrMsg = {'Error:'; '';
    'Failed to uninstall compatibility fixes for MEGPLS pipeline.';
    'Check permissions on Fieldtrip and MEGPLS pipeline folders.';
    'See README file in "TEMPORARY_FIXES" folder.'};

FixBackupFolder = [paths.Fieldtrip,'/MEGPLS_INSTALL_BACKUP'];


% Uninstall "warning_once.m" fix:
BackupFile = [FixBackupFolder,'/warning_once.m'];

if exist(BackupFile, 'file')
    if exist([paths.Fieldtrip,'/private/warning_once.m'], 'file')
        delete([paths.Fieldtrip,'/private/warning_once.m']);
        
        if exist([paths.Fieldtrip,'/private/warning_once.m'], 'file')
            msgbox('Error: Failed to remove "warning_once.m" files for uninstall.', 'Error:')
            msgbox(UninstallErrMsg, 'Error:')
            Success = 0;
            return;
        end
        
        Restore1 = copyfile(BackupFile, [paths.Fieldtrip,'/private/warning_once.m'], 'f');
    else
        Restore1 = 1;
    end
    
    if exist([paths.Fieldtrip,'/utilities/private/warning_once.m'], 'file')
        delete([paths.Fieldtrip,'/utilities/private/warning_once.m']);
        
        if exist([paths.Fieldtrip,'/utilities/private/warning_once.m'], 'file')
            msgbox('Error: Failed to remove "warning_once.m" files for uninstall.', 'Error:')
            msgbox(UninstallErrMsg, 'Error:')
            Success = 0;
            return;
        end
        
        Restore2 = copyfile(BackupFile, [paths.Fieldtrip,'/utilities/private/warning_once.m'], 'f');
    else
        Restore2 = 1;
    end
    
    if exist([paths.Fieldtrip,'/specest/private/warning_once.m'], 'file')
        delete([paths.Fieldtrip,'/specest/private/warning_once.m']);
        
        if exist([paths.Fieldtrip,'/specest/private/warning_once.m'], 'file')
            msgbox('Error: Failed to remove "warning_once.m" files for uninstall.', 'Error:')
            msgbox(UninstallErrMsg, 'Error:')
            Success = 0;
            return;
        end
        
        Restore3 = copyfile(BackupFile, [paths.Fieldtrip,'/specest/private/warning_once.m'], 'f');
    else
        Restore3 = 1;
    end
    
    if Restore1 == 0 || Restore2 == 0 || Restore3 == 0
        msgbox(UninstallErrMsg, 'Error:');
        Success = 0;
        return;
    end
end

% Uninstall "ft_postamble_history" fix:
BackupFile = [FixBackupFolder,'/ft_postamble_history.m'];

if exist(BackupFile, 'file')
    delete([paths.Fieldtrip,'/utilities/private/ft_postamble_history.m']);
    
    if exist([paths.Fieldtrip,'/utilities/private/ft_postamble_history.m'], 'file')
        msgbox('Error: Failed to remove "ft_postamble_history.m" files for uninstall.', 'Error')
        msgbox(UninstallErrMsg, 'Error:')
        Success = 0;
        return;
    end
    
    Restore = copyfile(BackupFile, ...
        [paths.Fieldtrip,'/utilities/private/ft_postamble_history.m'], 'f');
    
    if Restore == 0
        msgbox(UninstallErrMsg, 'Error:');
        Success = 0;
        return;
    end
end

% Uninstall "ft_singleplotER" legend modification:
BackupFile = [FixBackupFolder,'/ft_singleplotER.m'];

if exist(BackupFile, 'file')
    delete([paths.Fieldtrip,'/ft_singleplotER.m']);
    
    if exist([paths.Fieldtrip,'/ft_singleplotER.m'], 'file')
        msgbox('Error: Failed to remove "ft_singleplotER.m" file for uninstall.', 'Error:')
        msgbox(UninstallErrMsg, 'Error:')
        Success = 0;
        return;
    end
    
    Restore = copyfile(BackupFile, [paths.Fieldtrip,'/ft_singleplotER.m'], 'f');
    
    if Restore == 0
        msgbox(UninstallErrMsg, 'Error:');
        Success = 0;
        return;
    end
end

% Remove ToolboxPaths.mat file:
ToolboxPathsFile = [handles.PipelineDir,'/ToolboxPaths.mat'];

if exist(ToolboxPathsFile, 'file')
    delete(ToolboxPathsFile);
    
    if exist(ToolboxPathsFile, 'file')
        msgbox('Error: Failed to remove ToolboxPaths.mat file for uninstall.', 'Error:')
        return;
    end
end
if exist(FixBackupFolder, 'dir')
    rmdir(FixBackupFolder, 's');
end

Success = 1;




%============================%
% GUIDE CREATEGUI FUNCTIONS: %
%============================%

% --- Executes during object creation, after setting all properties.
function TextboxFieldtripPath_CreateFcn(hObject, eventdata, handles)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor','white');
end
% --- Executes during object creation, after setting all properties.
function TextboxSPMPath_CreateFcn(hObject, eventdata, handles)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor','white');
end
% --- Executes during object creation, after setting all properties.
function TextboxAFNIMatlabPath_CreateFcn(hObject, eventdata, handles)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor','white');
end