function varargout = ICAcleanerGUI(varargin)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Performs ICA decomposition and component removal. %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

% 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 31-Jul-2014 15:45:56

% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name',       mfilename, ...
                   'gui_Singleton',  gui_Singleton, ...
                   'gui_OpeningFcn', @ICAcleanerGUI_OpeningFcn, ...
                   'gui_OutputFcn',  @ICAcleanerGUI_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 ICAcleanerGUI is made visible. ---%
%-----------------------------------------------------%
function ICAcleanerGUI_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 ICAcleanerGUI (see VARARGIN)

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


% Make sure toolbox paths are added:
[PipelineDir, ~, ~] = fileparts(which('ICAcleanerGUI.m'));
handles.PipelineDir = PipelineDir;

addpath(genpath(PipelineDir));
rmpath([PipelineDir,'/DEFAULT_SETTINGS']);  % Make sure its calling from DataID
rmpath([PipelineDir,'/TEMPORARY_FIXES']);   % Make sure its calling from FT toolbox

CheckToolboxPaths(PipelineDir);

if exist('ErrorLog_ICAcleaner.txt', 'file')
    system('rm ErrorLog_ICAcleaner.txt');
end


% Initializes variables being displayed:
handles.paths.Rootpath = [];
handles.paths.DataID   = [];
handles.name.DataID    = [];

handles.name.GroupID = [];
handles.name.SubjID  = [];
handles.name.CondID  = [];

handles.paths.InputPreprocMEG = [];
handles.paths.ICAunmixing     = [];
handles.paths.ICAcomponents   = [];
handles.paths.ICAcleanData    = [];

handles.gui.InpOutStatus  = [];
handles.gui.RmvCompStatus = [];
handles.gui.SelectComps   = [];

handles.FTcfg = [];

% Save handles:
guidata(hObject, handles);


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


%--- Outputs from this function are returned to the command line. ---%
%--------------------------------------------------------------------%
function varargout = ICAcleanerGUI_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 SELECTING ROOTPATH: %
%===================================%

%--- Executes on button press in ButtonSetRootpath. ---%
%------------------------------------------------------%
function ButtonSetRootpath_Callback(hObject, eventdata, handles)
if ~isempty(handles.name.DataID)
	prompt = {'WARNING:'; '';
		'Changing root directory will clear all current settings!'; '';
		'Do you wish to continue?'};
    
	ChangeDir = questdlg(prompt, 'WARNING:', 'YES', 'NO', 'NO');
	if strcmp(ChangeDir, 'NO')
		return;
	end
end

% Select and set Rootpath:
SelectedPath = uigetdir;
if SelectedPath == 0
	return  % If user cancels
end

handles.paths.Rootpath = SelectedPath;
set(handles.TextboxRootpath, 'String', handles.paths.Rootpath);

% Start Waitbox:
WaitBox = StartWaitBox('SETTING ROOT DIRECTORY:');

% Reset DataID:
handles.name.DataID  = [];
handles.paths.DataID = [];
set(handles.TextboxDataID, 'String', 'Not Selected.');

% Reset settings & GUI panels:
handles = ResetGroupIDSettings (handles);
handles = ResetSubjIDSettings  (handles);
handles = ResetCondIDSettings  (handles);
handles = ResetStatusSettings  (handles);

handles.paths.InputPreprocMEG = [];
handles.paths.ICAcomponents   = [];
handles.paths.ICAunmixing     = [];
handles.paths.ICAcleanData    = [];
handles.gui.SelectComps		  = [];

% Update settings & GUI panels (to enable/disable):
% Note: Don't redetect or compile paths yet since no DataID yet.
handles = UpdateGroupIDSettings (handles);
handles = UpdateSubjIDSettings  (handles);
handles = UpdateCondIDSettings  (handles);
handles = UpdateStatusSettings  (handles);

% Save handles:
guidata(hObject, handles);
close(WaitBox);


%--- Textbox to display selected Rootpath: ---%
%---------------------------------------------%
function TextboxRootpath_Callback(hObject, eventdata, handles)
EnteredText = get(handles.TextboxRootpath, 'String');

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




%=========================================%
% FUNCTIONS FOR READING & LOADING DATAID: %
%=========================================%

%--- Textbox to display current DataID: ---%
%------------------------------------------%
function TextboxDataID_Callback(hObject, eventdata, handles)
EnteredText = get(handles.TextboxDataID, 'String');

if ~isequal(EnteredText, handles.name.DataID)
	set(handles.TextboxDataID, 'String', handles.name.DataID);
	msgbox('Note: Use button to change DataID.')
end


%--- Executes on button press in ButtonLoadDataID. ---%
%-----------------------------------------------------%
function ButtonLoadDataID_Callback(hObject, eventdata, handles)
if isempty(handles.paths.Rootpath)
	msgbox('Warning: Select target directory first.', 'Warning:');
	return;
end

% Get DataID folders in current rootpath:
DetectedFolders = dir([handles.paths.Rootpath,'/DataID_*']);

RemoveIndex = [];
for d = 1:length(DetectedFolders)
	if DetectedFolders(d).isdir ~= 1
		RemoveIndex = [RemoveIndex, d];  % Get unwanted indices
	end
end

DetectedFolders(RemoveIndex) = [];
if isempty(DetectedFolders)
    msgbox('Error: No DataID folders detected inside target directory.', 'Error:');
    return;
end

% List DataID folders for selection: 
DetectedFolders = {DetectedFolders.name};
SelectedIndex = listdlg('PromptString', 'Select DataID to load:',...
    'ListSize', [300, 300], 'SelectionMode', 'single', 'ListString', DetectedFolders);			
if isempty(SelectedIndex)  % If user cancels.
	return;
end

SelectedDataID		= DetectedFolders{SelectedIndex};
SelectedDataID(1:7) = [];  % Remove "DataID_" prefix to get DataID tag.
FullpathDataID		= [handles.paths.Rootpath,'/DataID_',SelectedDataID];

% Check or create settings .m file for ICA:
if ~exist([FullpathDataID,'/SETTINGS'], 'dir')
    success = mkdir([FullpathDataID,'/SETTINGS']);
    
    if success == 0
        message = {'ERROR:'; '';
            'Failed to create SETTINGS folder in selected DataID.';
            'Ensure you have proper folder and file permissions.'};
        msgbox(message, 'ERROR:')
        return;
    end
end

DefaultSettingsFile = [handles.PipelineDir,'/DEFAULT_SETTINGS/Settings_ICA.m'];
NewSettingsFile     = [FullpathDataID,'/SETTINGS/Settings_ICA.m'];

if ~exist(NewSettingsFile, 'file')
    status = copyfile(DefaultSettingsFile, NewSettingsFile, 'f');
    
    if status == 0
        message = {'ERROR:'; '';
            'Failed to create ICA advanced settings .m file for selected DataID.';
            'Could not copy file from [MEG]PLS "DEFAULT_SETTINGS" directory.';
            'Check for proper folder and file permissions.'};
        msgbox(message, 'ERROR:')
        return;
    end
end

% Set as current DataID:
handles.name.DataID  = SelectedDataID;
handles.paths.DataID = FullpathDataID;

% Reset settings & GUI panels:
handles = ResetGroupIDSettings (handles);
handles = ResetSubjIDSettings  (handles);
handles = ResetCondIDSettings  (handles);
handles = ResetStatusSettings  (handles);

handles.paths.InputPreprocMEG = [];
handles.paths.ICAcomponents   = [];
handles.paths.ICAunmixing     = [];
handles.paths.ICAcleanData    = [];
handles.gui.SelectComps		  = [];

% Compile Group, Subj, and CondIDs for DataID:
% Note: Also initializes Group, Subj, CondIDs.
handles = DetectGroupSubjCond(handles);

if isempty(handles.name.GroupID)
    msgbox('ERROR: No GroupID folders detected for selected DataID.')
    return;
end

% Compile paths & initialize other variables:
for g = 1:length(handles.name.GroupID)
	for s = 1:length(handles.name.SubjID{g})
		for c = 1:length(handles.name.CondID)
			
			handles = CompilePaths(handles, g, s, c);
			
			try
				handles.gui.SelectComps{g}{s,c};
				handles.gui.InpOutStatus{g}{s,c};   % Didn't check initialize in UpdateStatus.
				handles.gui.RmvCompStatus{g}{s,c};  % - More efficient for case-by-case basis.
			catch
				handles.gui.SelectComps{g}{s,c}   = [];
				handles.gui.InpOutStatus{g}{s,c}  = [];
				handles.gui.RmvCompStatus{g}{s,c} = [];
			end
			
		end
	end
end

% Update settings & GUI panels:
handles = UpdateGroupIDSettings (handles);
handles = UpdateSubjIDSettings  (handles);
handles = UpdateCondIDSettings  (handles);

% Detect & update status:
for g = 1:length(handles.name.GroupID)
    StatusWaitbar = waitbar(0, ['Please wait. Scanning status for: ', ...
        handles.name.GroupID{g}], 'Windowstyle', 'modal');
    
    for s = 1:length(handles.name.SubjID{g})
        waitbar(s/length(handles.name.SubjID{g}), StatusWaitbar);
        
        for c = 1:length(handles.name.CondID)
            handles = DetectStatus(handles, g, s, c);
        end
    end
    delete(StatusWaitbar)
end

handles = UpdateStatusSettings(handles);

% Save handles:
set(handles.TextboxDataID, 'String', handles.name.DataID);
guidata(hObject, handles);

% Remove ErrorLog if empty:
if exist([pwd,'/ErrorLog_ICAcleaner.txt'], 'file')
	LogCheck = dir('ErrorLog_ICAcleaner.txt');
	if LogCheck.bytes == 0
		delete('ErrorLog_ICAcleaner.txt');
	end
end


%--- Executes on button press in ButtonRedetectInputIDs. --%
%----------------------------------------------------------%
function ButtonRedetectInputIDs_Callback(hObject, eventdata, handles)

% Reset settings & GUI panels:
handles = ResetGroupIDSettings (handles);
handles = ResetSubjIDSettings  (handles);
handles = ResetCondIDSettings  (handles);
handles = ResetStatusSettings  (handles);

handles.paths.InputPreprocMEG = [];
handles.paths.ICAcomponents   = [];
handles.paths.ICAunmixing     = [];
handles.paths.ICAcleanData    = [];
handles.gui.SelectComps		  = [];

% Compile Group, Subj, and CondIDs for DataID:
% Note: Also initializes Group, Subj, CondIDs.
handles = DetectGroupSubjCond(handles);

if isempty(handles.name.GroupID)
    msgbox('ERROR: No GroupID folders detected for selected DataID.')
    return;
end

% Compile paths & initialize other variables:
for g = 1:length(handles.name.GroupID)
	for s = 1:length(handles.name.SubjID{g})
		for c = 1:length(handles.name.CondID)
			
			handles = CompilePaths(handles, g, s, c);
			
			try
				handles.gui.SelectComps{g}{s,c};
				handles.gui.InpOutStatus{g}{s,c};   % Didn't check initialize in UpdateStatus.
				handles.gui.RmvCompStatus{g}{s,c};  % - More efficient for case-by-case basis.
			catch
				handles.gui.SelectComps{g}{s,c}   = [];
				handles.gui.InpOutStatus{g}{s,c}  = [];
				handles.gui.RmvCompStatus{g}{s,c} = [];
			end
			
		end
	end
end

% Update settings & GUI panels:
handles = UpdateGroupIDSettings (handles);
handles = UpdateSubjIDSettings  (handles);
handles = UpdateCondIDSettings  (handles);

% Detect & update status:
for g = 1:length(handles.name.GroupID)
    StatusWaitbar = waitbar(0, ['Please wait. Scanning status for: ', ...
        handles.name.GroupID{g}], 'Windowstyle', 'modal');
    
    for s = 1:length(handles.name.SubjID{g})
        waitbar(s/length(handles.name.SubjID{g}), StatusWaitbar);
        
        for c = 1:length(handles.name.CondID)
            handles = DetectStatus(handles, g, s, c);
        end
    end
    delete(StatusWaitbar)
end

handles = UpdateStatusSettings(handles);

% Save handles:
guidata(hObject, handles);

% Remove ErrorLog if empty:
if exist([pwd,'/ErrorLog_ICAcleaner.txt'], 'file')
	LogCheck = dir('ErrorLog_ICAcleaner.txt');
	if LogCheck.bytes == 0
		delete('ErrorLog_ICAcleaner.txt');
	end
end


%--- Detect Group, Subj, and CondID's from DataID: ---%
%-----------------------------------------------------%
function OutputHandles = DetectGroupSubjCond(InputHandles)
handles = InputHandles;

% Reset params:
handles.name.GroupID = [];
handles.name.SubjID  = [];
handles.name.CondID  = [];

handles.paths.InputPreprocMEG = [];
handles.paths.ICAcomponents   = [];
handles.paths.ICAunmixing     = [];
handles.paths.ICAcleanData    = [];

% Acquire GroupID folders within DataID:
DetectedGroups = dir([handles.paths.DataID,'/GroupID_*']);

RemoveIndex = [];
for g = 1:length(DetectedGroups)
    DetectedGroups(g).name(1:8) = [];    % Remove "GroupID_" prefix
    
    if DetectedGroups(g).isdir ~= 1
        RemoveIndex = [RemoveIndex, g];  % Get unwanted indices
    end
end
DetectedGroups(RemoveIndex) = [];

if isempty(DetectedGroups)
    handles.name.GroupID = [];
else
    handles.name.GroupID = {DetectedGroups.name};
end

% Scan PreprocInput .mat files for SubjID's and CondID's:
CondIDs = [];

for g = 1:length(handles.name.GroupID)
    GroupPath = [handles.paths.DataID,'/GroupID_',handles.name.GroupID{g}];
    InputMats = dir([GroupPath,'/PreprocInputMEG_*.mat']);  % Find InputMats for group
    InputMats = {InputMats.name};
    
    SubjIDs = [];
    
    if ~isempty(InputMats)
        for m = 1:length(InputMats)
            LoadMat = load([GroupPath,'/',InputMats{m}]);
            SubjIDs = [SubjIDs; LoadMat.name.SubjID];
            CondIDs = [CondIDs; cellstr(LoadMat.name.CurrentCondID)];
        end
    else
        message = {['ERROR: PreprocInputMEG .mat file(s) missing for GroupID: ',...
            handles.name.GroupID{g}]; ''; ['As a result, some Subject & Condition IDs ' ...
            'for the selected DataID may not be detected.']};
        msgbox(message);
    end
    
    handles.name.SubjID{g} = unique(SubjIDs);
end

handles.name.CondID = unique(CondIDs);
    
% Set output handles:
OutputHandles = handles;


%--- Compiles paths for selected indices: ---%
%--------------------------------------------%
function OutputHandles = CompilePaths(InputHandles, g, s, c)
handles = InputHandles;

handles.paths.InputPreprocMEG{g}{s,c} = ...
    [handles.paths.DataID,'/GroupID_',handles.name.GroupID{g},'/', ...
    handles.name.CondID{c},'/',handles.name.SubjID{g}{s},'_PreprocMEG.mat'];

handles.paths.ICAunmixing{g}{s,c} = ...
	[handles.paths.DataID,'/GroupID_',handles.name.GroupID{g},'/', ...
	handles.name.CondID{c},'/',handles.name.SubjID{g}{s},'_ICAunmixing.mat'];

handles.paths.ICAcomponents{g}{s,c} = ...
    [handles.paths.DataID,'/ICAcomps/GroupID_',handles.name.GroupID{g},'/', ...
    handles.name.CondID{c},'/',handles.name.SubjID{g}{s},'_ICAcomponents.mat'];

handles.paths.ICAcleanData{g}{s,c} = ...
	[handles.paths.Rootpath,'/DataID-ICAclean_',handles.name.DataID, ...
	'/GroupID_',handles.name.GroupID{g},'/',handles.name.CondID{c},'/', ...
	handles.name.SubjID{g}{s},'_PreprocMEG.mat'];

% Set output handles:
OutputHandles = handles;




%==========================================%
% FUNCTIONS FOR ADDING OR REMOVING GROUPS: %
%==========================================%

%--- Executes on selection change in ListboxGroupID. ---%
%-------------------------------------------------------%
function ListboxGroupID_Callback(hObject, eventdata, handles)
if isempty(handles.name.GroupID)
    return;
end

handles = UpdateSubjIDSettings (handles);
handles = UpdateStatusSettings (handles);
guidata(hObject, handles);


%--- Executes on button press in ButtonRmvGroupID. ---%
%-----------------------------------------------------%
function ButtonRmvGroupID_Callback(hObject, eventdata, handles)
if isempty(handles.name.GroupID)
    return;
end
if length(handles.name.GroupID) <= 1
    msgbox('Note: Must have at least 1 GroupID.', 'Error:');
    return;
end

SelectedIndex = get(handles.ListboxGroupID, 'Value');
handles.name.GroupID(SelectedIndex) = [];

if ~isempty(handles.name.SubjID)
    handles.name.SubjID(SelectedIndex) = [];
end

if ~isempty(handles.paths.InputPreprocMEG)
    handles.paths.InputPreprocMEG (SelectedIndex) = [];
	handles.paths.ICAunmixing     (SelectedIndex) = [];
    handles.paths.ICAcomponents   (SelectedIndex) = [];
    handles.paths.ICAcleanData    (SelectedIndex) = [];
end

if ~isempty(handles.gui.SelectComps)
    handles.gui.SelectComps(SelectedIndex) = [];
end
    
if ~isempty(handles.gui.InpOutStatus)
    handles.gui.InpOutStatus(SelectedIndex) = [];
end
if ~isempty(handles.gui.RmvCompStatus)
    handles.gui.RmvCompStatus(SelectedIndex) = [];
end

% Update settings & GUI:
handles = UpdateGroupIDSettings (handles);
handles = UpdateSubjIDSettings  (handles);
handles = UpdateStatusSettings  (handles);

% Save handles:
guidata(hObject, handles);


%--- Update GroupID settings & GUI panel: ---%
%--------------------------------------------%
function OutputHandles = UpdateGroupIDSettings(InputHandles)
handles = InputHandles;

% Update listbox:
set(handles.ListboxGroupID, 'String', handles.name.GroupID);

CurrentIndex  = get(handles.ListboxGroupID, 'Value');
MaxGroupIndex = length(handles.name.GroupID);

if isempty(CurrentIndex) || CurrentIndex == 0 || CurrentIndex > MaxGroupIndex
	set(handles.ListboxGroupID, 'Value', MaxGroupIndex);
end

% Set output handles:
OutputHandles = handles;


%--- Reset GroupID settings & GUI panel: ---%
%-------------------------------------------%
function OutputHandles = ResetGroupIDSettings(InputHandles)
handles = InputHandles;

handles.name.GroupID = [];
set(handles.ListboxGroupID, 'String', []);
set(handles.ListboxGroupID, 'Value',  1);

% Set output handles:
OutputHandles = handles;




%============================================%
% FUNCTIONS FOR ADDING OR REMOVING SUBJECTS: %
%============================================%

%--- Executes on selection change in ListboxSubjID. ---%
%------------------------------------------------------%
function ListboxSubjID_Callback(hObject, eventdata, handles)
if isempty(handles.name.SubjID)
    return;
end

GroupIndex = get(handles.ListboxGroupID, 'Value');
if isempty(handles.name.SubjID{GroupIndex})
    return;
end

SubjIndex = get(handles.ListboxSubjID, 'Value');
set(handles.ListboxInpOutStatus,  'Value', SubjIndex);
set(handles.ListboxRmvCompStatus, 'Value', SubjIndex);


%--- User enters subject to add into this textbox. ---%
%-----------------------------------------------------%
function TextboxSubjID_Callback(hObject, eventdata, handles)
keypress = get(gcf,'CurrentCharacter');
if isequal(keypress, char(13))
    ButtonAddSubjID_Callback(hObject, eventdata, handles);
end


%--- Executes on button press in ButtonAddSubjID. ---%
%----------------------------------------------------%
function ButtonAddSubjID_Callback(hObject, eventdata, handles)
if isempty(handles.name.DataID)
    msgbox('Warning: Load DataID first.', 'Warning:');
    return;
end
if isempty(handles.name.GroupID)
    msgbox('Error: No GroupIDs specified.', 'Error:');
    return;
end

% Read entered SubjID:
InputSubjID = get(handles.TextboxSubjID, 'String');
InputSubjID = deblank(InputSubjID);
InputSubjID = regexprep(InputSubjID, '\s+', '_');
InputSubjID = cellstr(InputSubjID);
if isempty(InputSubjID{1})
	return;
end

GroupIndex = get(handles.ListboxGroupID, 'Value');
if ismember(InputSubjID{1}, handles.name.SubjID{GroupIndex})
	return;  % If SubjID already added
end

% Add SubjID for group & initialize:
handles.name.SubjID{GroupIndex} = [handles.name.SubjID{GroupIndex}; InputSubjID];
NewSubjIndex = length(handles.name.SubjID{GroupIndex});

for c = 1:length(handles.name.CondID)
    handles.gui.SelectComps{GroupIndex}{NewSubjIndex,c} = [];
    handles = CompilePaths(handles, GroupIndex, NewSubjIndex, c);
	handles = DetectStatus(handles, GroupIndex, NewSubjIndex, c);
end

% Update settings & GUI:
handles = UpdateSubjIDSettings (handles);
handles = UpdateStatusSettings (handles);

% Save handles:
set(handles.ListboxSubjID, 'Value', NewSubjIndex);
if ~isempty(handles.gui.InpOutStatus)
    set(handles.ListboxInpOutStatus,  'Value', NewSubjIndex);
end
if ~isempty(handles.gui.RmvCompStatus)
    set(handles.ListboxRmvCompStatus, 'Value', NewSubjIndex);
end
guidata(hObject, handles);


%--- Executes on button press in ButtonRmvSubjID. ---%
%----------------------------------------------------%
function ButtonRmvSubjID_Callback(hObject, eventdata, handles)
if isempty(handles.name.SubjID)
    return;
end

GroupIndex = get(handles.ListboxGroupID, 'Value');
SubjIndex  = get(handles.ListboxSubjID,  'Value');
if isempty(handles.name.SubjID{GroupIndex})
    return;
end

handles.name.SubjID{GroupIndex}(SubjIndex) = [];

if ~isempty(handles.paths.InputPreprocMEG)
    handles.paths.InputPreprocMEG {GroupIndex}(SubjIndex,:) = [];
	handles.paths.ICAunmixing     {GroupIndex}(SubjIndex,:) = [];
    handles.paths.ICAcomponents   {GroupIndex}(SubjIndex,:) = [];
    handles.paths.ICAcleanData    {GroupIndex}(SubjIndex,:) = [];
end

if ~isempty(handles.gui.SelectComps)
    handles.gui.SelectComps{GroupIndex}(SubjIndex,:) = [];
end

if ~isempty(handles.gui.InpOutStatus)
    handles.gui.InpOutStatus{GroupIndex}(SubjIndex,:) = [];
end
if ~isempty(handles.gui.RmvCompStatus)
    handles.gui.RmvCompStatus{GroupIndex}(SubjIndex,:) = [];
end

% Update settings & GUI:
handles = UpdateSubjIDSettings (handles);
handles = UpdateStatusSettings (handles);

% Save handles:
guidata(hObject, handles);


%--- Update SubjID settings & GUI panel: ---%
%-------------------------------------------%
function OutputHandles = UpdateSubjIDSettings(InputHandles)
handles = InputHandles;

% Update listbox:
GroupIndex = get(handles.ListboxGroupID, 'Value');
if isempty(handles.name.SubjID)
    set(handles.ListboxSubjID, 'String', []);
    MaxSubjIndex = 0;
else
    set(handles.ListboxSubjID, 'String', handles.name.SubjID{GroupIndex});
    MaxSubjIndex = length(handles.name.SubjID{GroupIndex});
end

SubjIndex = get(handles.ListboxSubjID, 'Value');
if isempty(SubjIndex) || SubjIndex == 0 || SubjIndex > MaxSubjIndex
	set(handles.ListboxSubjID, 'Value', MaxSubjIndex);
	
	if ~isempty(handles.gui.InpOutStatus)
		set(handles.ListboxInpOutStatus, 'Value', MaxSubjIndex);
	end
	if ~isempty(handles.gui.RmvCompStatus)
		set(handles.ListboxRmvCompStatus, 'Value', MaxSubjIndex);
	end
end

% Set output handles:
OutputHandles = handles;


%--- Reset SubjID settings & GUI panel: ---%
%------------------------------------------%
function OutputHandles = ResetSubjIDSettings(InputHandles)
handles = InputHandles;

handles.name.SubjID = [];
set(handles.ListboxSubjID, 'String', []);
set(handles.ListboxSubjID, 'Value',  1);

% Set output handles:
OutputHandles = handles;




%==============================================%
% FUNCTIONS FOR ADDING OR REMOVING CONDITIONS: %
%==============================================%

%--- Executes on selection change in ListboxCondID. ---%
%------------------------------------------------------%
function ListboxCondID_Callback(hObject, eventdata, handles)
if isempty(handles.name.CondID)
    return;
end

handles = UpdateStatusSettings(handles);
guidata(hObject, handles);


%--- User enters condition to add into this textbox. ---%
%-------------------------------------------------------%
function TextboxCondID_Callback(hObject, eventdata, handles)
keypress = get(gcf,'CurrentCharacter');
if isequal(keypress, char(13))
    ButtonAddCondID_Callback(hObject, eventdata, handles);
end


%--- Executes on button press in ButtonAddCondID. ---%
%----------------------------------------------------%
function ButtonAddCondID_Callback(hObject, eventdata, handles)
if isempty(handles.name.DataID)
    msgbox('Warning: Load DataID first.', 'Warning:');
    return;
end
if isempty(handles.name.GroupID)
    msgbox('Error: No GroupIDs specified.', 'Error:');
    return;
end

% Read entered CondID:
InputCondID = get(handles.TextboxCondID, 'String');
InputCondID = deblank(InputCondID);
InputCondID = regexprep(InputCondID, '\s+', '_');
InputCondID = cellstr(InputCondID);
if isempty(InputCondID{1})
	return;
end

if ismember(InputCondID{1}, handles.name.CondID)
	return;  % If CondID already added
end

% Add CondID and initialize:
handles.name.CondID = [handles.name.CondID; InputCondID];
NewCondIndex = length(handles.name.CondID);

for g = 1:length(handles.name.GroupID)
    if isempty(handles.name.SubjID)
        continue;
    end
    
    for s = 1:length(handles.name.SubjID{g})
        handles.gui.SelectComps{g}{s, NewCondIndex} = [];
        handles = CompilePaths(handles, g, s, NewCondIndex);
		handles = DetectStatus(handles, g, s, NewCondIndex);
    end
end

set(handles.ListboxCondID, 'Value', NewCondIndex);

% Update settings & GUI:
handles = UpdateCondIDSettings (handles);
handles = UpdateStatusSettings (handles);

% Save handles:
guidata(hObject, handles);


%--- Executes on button press in ButtonRmvCondID. ---%
%----------------------------------------------------%
function ButtonRmvCondID_Callback(hObject, eventdata, handles)
if isempty(handles.name.CondID)
    return;
end

SelectedIndex = get(handles.ListboxCondID, 'Value');
handles.name.CondID(SelectedIndex) = [];

for g = 1:length(handles.name.GroupID)
    if ~isempty(handles.paths.InputPreprocMEG)
        handles.paths.InputPreprocMEG {g}(:,SelectedIndex) = [];
		handles.paths.ICAunmixing     {g}(:,SelectedIndex) = [];
        handles.paths.ICAcomponents   {g}(:,SelectedIndex) = [];
        handles.paths.ICAcleanData    {g}(:,SelectedIndex) = [];
    end
    
    if ~isempty(handles.gui.SelectComps)
        handles.gui.SelectComps{g}(:,SelectedIndex) = [];
    end
    
    if ~isempty(handles.gui.InpOutStatus)
        handles.gui.InpOutStatus{g}(:,SelectedIndex) = [];
    end
    if ~isempty(handles.gui.RmvCompStatus)
        handles.gui.RmvCompStatus{g}(:,SelectedIndex) = [];
    end
end

% Update settings & GUI:
handles = UpdateCondIDSettings (handles);
handles = UpdateStatusSettings (handles);

% Save handles:
guidata(hObject, handles);


%--- Updates CondID settings & GUI panel: ---%
%--------------------------------------------%
function OutputHandles = UpdateCondIDSettings(InputHandles)
handles = InputHandles;

% Update listbox:
set(handles.ListboxCondID, 'String', handles.name.CondID);

CurrentIndex = get(handles.ListboxCondID, 'Value');
MaxCondIndex = length(handles.name.CondID);

if isempty(CurrentIndex) || CurrentIndex == 0 || CurrentIndex > MaxCondIndex
	set(handles.ListboxCondID, 'Value', MaxCondIndex);
end

% Set output handles:
OutputHandles = handles;


%--- Reset CondID settings & GUI panel: ---%
%------------------------------------------%
function OutputHandles = ResetCondIDSettings(InputHandles)
handles = InputHandles;

handles.name.CondID = [];
set(handles.ListboxCondID, 'String', []);
set(handles.ListboxCondID, 'Value',  1);

% Set output handles:
OutputHandles = handles;




%===============================%
% FUNCTIONS FOR STATUS UPDATES: %
%===============================%

%--- Executes on selection change in ListboxInpOutStatus. ---%
%------------------------------------------------------------%
function ListboxInpOutStatus_Callback(hObject, eventdata, handles)
if isempty(handles.gui.InpOutStatus)
    return;
end
if ~isempty(handles.name.GroupID)  % In case where SubjID exist but CondID missing
    GroupIndex = get(handles.ListboxGroupID, 'Value');
    if isempty(handles.gui.InpOutStatus{GroupIndex})
        return;
    end
end

SelectedIndex = get(handles.ListboxInpOutStatus, 'Value');
set(handles.ListboxSubjID,        'Value', SelectedIndex);
set(handles.ListboxRmvCompStatus, 'Value', SelectedIndex);


%--- Executes on selection change in ListboxRmvCompStatus. ---%
%-------------------------------------------------------------%
function ListboxRmvCompStatus_Callback(hObject, eventdata, handles)
if isempty(handles.gui.RmvCompStatus)
    return;
end
if ~isempty(handles.name.GroupID)
    GroupIndex = get(handles.ListboxGroupID, 'Value');
    if isempty(handles.gui.RmvCompStatus{GroupIndex})
        return;
    end
end

SelectedIndex = get(handles.ListboxRmvCompStatus, 'Value');
set(handles.ListboxSubjID,       'Value', SelectedIndex);
set(handles.ListboxInpOutStatus, 'Value', SelectedIndex);


%--- Executes on button press in ButtonRefreshStatus. ---%
%--------------------------------------------------------%
function ButtonRefreshStatus_Callback(hObject, eventdata, handles)

% Detect & update status:
for g = 1:length(handles.name.GroupID)
    StatusWaitbar = waitbar(0, ['Please wait. Scanning status for: ', ...
        handles.name.GroupID{g}], 'Windowstyle', 'modal');
    
    for s = 1:length(handles.name.SubjID{g})
        waitbar(s/length(handles.name.SubjID{g}), StatusWaitbar);
        
        for c = 1:length(handles.name.CondID)
            handles = DetectStatus(handles, g, s, c);
        end
    end
    delete(StatusWaitbar)
end

handles = UpdateStatusSettings(handles);

% Save handles:
guidata(hObject, handles);


%--- Executes on button press in CheckboxShowOutputStatus. ---%
%-------------------------------------------------------------%
function CheckboxShowOutputStatus_Callback(hObject, eventdata, handles)

% Detect & update status:
for g = 1:length(handles.name.GroupID)
    StatusWaitbar = waitbar(0, ['Please wait. Scanning status for: ', ...
        handles.name.GroupID{g}], 'Windowstyle', 'modal');
    
    for s = 1:length(handles.name.SubjID{g})
        waitbar(s/length(handles.name.SubjID{g}), StatusWaitbar);
        
        for c = 1:length(handles.name.CondID)
            handles = DetectStatus(handles, g, s, c);
        end
    end
    delete(StatusWaitbar)
end

handles = UpdateStatusSettings(handles);

% Save handles:
guidata(hObject, handles);

    
%--- Detect input file status: ---%
%---------------------------------%
function OutputHandles = DetectStatus(InputHandles, g, s, c)
handles = InputHandles;

InputPreprocMEG = handles.paths.InputPreprocMEG{g}{s,c};
ICAunmixing     = handles.paths.ICAunmixing{g}{s,c};
ICAcomponents   = handles.paths.ICAcomponents{g}{s,c};
ICAcleanData    = handles.paths.ICAcleanData{g}{s,c};

% Get input or output file status:
if ~exist(ICAcleanData, 'file') || get(handles.CheckboxShowOutputStatus, 'Value') == 0
    if exist(InputPreprocMEG, 'file')
        if exist(ICAcomponents, 'file')
            StatusMsg = 'Input PreprocMEG found  (ICA components found).';
        elseif exist(ICAunmixing, 'file')
            StatusMsg = 'Input PreprocMEG found  (Unmixing data found;  Run ICA to apply).';
        else
            StatusMsg = 'Input PreprocMEG found  (Ready for ICA).';
        end
    else
        StatusMsg = 'Error: Input PreprocMEG file missing.';
    end
    
else
    LoadCleanData = LoadFTmat(ICAcleanData, 'ICAcleaner');
    
    if isempty(LoadCleanData)
        StatusMsg = 'Error: Output file contains errors. See ErrorLog.'; 
    else
        if isfield(LoadCleanData, 'ICAcompRemoved')
            if isempty(LoadCleanData.ICAcompRemoved)
                StatusMsg = 'ICA cleaned file found: No components removed.';
            else
                NumCompRmv = num2str(length(LoadCleanData.ICAcompRemoved));
                StrCompRmv = regexprep(num2str(LoadCleanData.ICAcompRemoved), '\s+', ', ');
                
                StatusMsg = ['ICA cleaned file found: ', ...
                    NumCompRmv,' comp. removed (',StrCompRmv,')'];
            end
        else
            StatusMsg = 'Error: Output file is missing ICAcompRemoved field.';
        end
    end
end

handles.gui.InpOutStatus{g}{s,c} = StatusMsg;

% Get ICA component status:
if ~exist(ICAunmixing, 'file')
    RmvCompStatus = 'Missing ICA decomposition files  (Run ICA).';
else
    if isempty(handles.gui.SelectComps{g}{s,c})
        RmvCompStatus = 'Select unwanted components.';
    else
        StrCompRmv = regexprep(num2str(handles.gui.SelectComps{g}{s,c}), '\s+', ', ');
        RmvCompStatus = ['Rejecting components:  [',StrCompRmv,']'];
    end
end

handles.gui.RmvCompStatus{g}{s,c} = RmvCompStatus;

% Set output handles:
OutputHandles = handles;


%--- Update status settings & GUI panel: ---%
%-------------------------------------------%
function OutputHandles = UpdateStatusSettings(InputHandles)
handles = InputHandles;

% Make sure cells initialized:
for g = 1:length(handles.name.GroupID)
	for s = 1:length(handles.name.SubjID{g})
		for c = 1:length(handles.name.CondID)
			
			try
				handles.gui.SelectComps{g}{s,c};
				handles.gui.InpOutStatus{g}{s,c};   % Check just in case.
				handles.gui.RmvCompStatus{g}{s,c};  % - ** If too much delay, can rmv.
			catch
				handles.gui.SelectComps{g}{s,c}   = [];
				handles.gui.InpOutStatus{g}{s,c}  = [];
				handles.gui.RmvCompStatus{g}{s,c} = [];
			end
			
		end
	end
end

% Update listbox:
GroupIndex = get(handles.ListboxGroupID, 'Value');
SubjIndex  = get(handles.ListboxSubjID,  'Value');
CondIndex  = get(handles.ListboxCondID,  'Value');

if isempty(handles.gui.InpOutStatus) || isempty(handles.gui.InpOutStatus{GroupIndex})
    set(handles.ListboxInpOutStatus, 'String', []);
    set(handles.ListboxInpOutStatus, 'Value',  1);
else
    set(handles.ListboxInpOutStatus, 'String', ...
        handles.gui.InpOutStatus{GroupIndex}(:,CondIndex));
    
    if get(handles.ListboxInpOutStatus, 'Value') ~= SubjIndex
        set(handles.ListboxInpOutStatus, 'Value', SubjIndex);
    end
end

if isempty(handles.gui.RmvCompStatus) || isempty(handles.gui.RmvCompStatus{GroupIndex})
    set(handles.ListboxRmvCompStatus, 'String', []);
    set(handles.ListboxRmvCompStatus, 'Value',  1);
else
    set(handles.ListboxRmvCompStatus, 'String', ...
        handles.gui.RmvCompStatus{GroupIndex}(:,CondIndex));
    
    if get(handles.ListboxRmvCompStatus, 'Value') ~= SubjIndex
        set(handles.ListboxRmvCompStatus, 'Value', SubjIndex)
    end
end

% Set output handles:
OutputHandles = handles;


%--- Reset status settings & GUI panel: ---%
%------------------------------------------%
function OutputHandles = ResetStatusSettings(InputHandles)
handles = InputHandles;

% Reset:
handles.gui.InpOutStatus  = [];
handles.gui.RmvCompStatus = [];

% Reinitialize:
for g = 1:length(handles.name.GroupID)
    for s = 1:length(handles.name.SubjID{g})
        for c = 1:length(handles.name.CondID)
            
            handles.gui.InpOutStatus{g}{s,c}  = [];
            handles.gui.RmvCompStatus{g}{s,c} = [];
            
        end
    end
end

% Reset GUI listboxes:
set(handles.ListboxInpOutStatus,  'String', []);
set(handles.ListboxRmvCompStatus, 'String', []);
set(handles.ListboxInpOutStatus,  'Value',  1);
set(handles.ListboxRmvCompStatus, 'Value',  1);

% Set output handles:
OutputHandles = handles;




%=======================%
% FUNCTIONS TO RUN ICA: %
%=======================%

%--- Executes on button press in ButtonShowInstructions. ---%
%-----------------------------------------------------------%
function ButtonShowInstructions_Callback(hObject, eventdata, handles)

Instructions = {'-------------'; 'INSTRUCTIONS:'; '-------------'; '';
    'LOADING INPUT DATA:';
    ' 1) Load the DataID that you wish to apply ICA cleaning to.';
    ' 2) The DataID will be scanned for Group, Subject & Condition IDs.';
    ' 3) Use the "-" keys to exclude datasets from the ICA analysis.';
    ' 4) Use the "+" keys to add missing Subject or Condition IDs.';
    '';
    ' NOTE: To restore the full list of Group, Subject, and Condition IDs';
    ' found within the DataID, push the "Redetect Input" button.';
    ''; '';
    'RUN ICA DECOMPOSITION:';
    ' 1) Change ICA settings as needed using the "ICA Adv. Settings" button.';
    ' 2) Once desired data is selected (see above), push "Run ICA" button.';
    ''; '';
    'VIEWING ICA COMPONENT RESULTS:';
    ' - Select the Group, Subj & Cond ID you wish to view from the lists.';
    ' - Push the "View Components" button to open the component browser.';
    '   This browser displays topoplots & time-courses for each component.';
    '   Note: Time-courses display concatenated trial data for components.'; '';
    ' - Using the Data Browser:';
    '    a) To change components viewed, use the ">" & "<" keys for "Channels".';
    '    b) To scroll across time-course, use the ">" & "<" keys for "Segment".';
    '    c) To change amp. scaling, use the ">" & "<" keys under "Vertical".';
    '    d) To change time scaling, use the ">" & "<" keys under "Horizontal".';
    ''; '';
    'REJECTING COMPONENTS:';
    ' 1) Select the Group, Subj & Cond ID you wish to view from the lists.';
    ' 2) Identify artifact components for the selected dataset (see above).';
    ' 3) Push the "Select Components" button and select artifact components.';
    ' 4) Repeat Steps 1-3 for each dataset.';
    ' 5) When ready, push the "Rmv Comp. & Clean Data" button.'; ''; ''};

msgbox(Instructions, 'INSTRUCTIONS:')


%--- Executes on button press in ButtonAdvSettings. ---%
%------------------------------------------------------%
function ButtonAdvSettings_Callback(hObject, eventdata, handles)
if isempty(handles.paths.Rootpath)
	msgbox('Warning: Select target directory first.', 'Warning:');
	return;
end
if isempty(handles.name.DataID)
    msgbox('Warning: Load DataID first.', 'Warning:');
    return;
end
open([handles.paths.DataID,'/SETTINGS/Settings_ICA.m']);


%--- Executes on button press in ButtonRunICA. ---%
%-------------------------------------------------%
function ButtonRunICA_Callback(hObject, eventdata, handles)
if isempty(handles.name.DataID)
    msgbox('Warning: Load DataID first.', 'Warning:');
    return;
end
if isempty(handles.name.GroupID)
    msgbox('Error: No GroupIDs specified.', 'Error:');
    return;
end
if isempty(handles.name.SubjID)
    msgbox('Error: No SubjIDs specified.', 'Error:');
    return;
else
    for g = 1:length(handles.name.GroupID)
        if isempty(handles.name.SubjID{g})
            msgbox('Error: Not all Groups have SubjIDs added.', 'Error:')
            return;
        end
    end
end
if isempty(handles.name.CondID)
    msgbox('Error: No CondIDs specified.', 'Error:');
    return;
end

% Load required parameters:
InputParams.name                  = handles.name;
InputParams.paths.InputPreprocMEG = handles.paths.InputPreprocMEG;
InputParams.paths.ICAunmixing     = handles.paths.ICAunmixing;
InputParams.paths.ICAcomponents   = handles.paths.ICAcomponents;

FTcfg.ResampleICA = [];
FTcfg.ICA         = [];

CurrentDir = pwd;
cd([handles.paths.DataID,'/SETTINGS/']);
[FTcfg.ResampleICA, FTcfg.ICA] = Settings_ICA;
cd(CurrentDir);

% Check for previously computed unmixing matrices:
ExistingFiles = 0;

for g = 1:length(handles.name.GroupID)
    for s = 1:length(handles.name.SubjID{g})
        for c = 1:length(handles.name.CondID)
            
            if exist(handles.paths.ICAunmixing{g}{s,c}, 'file')
                ExistingFiles = 1;
            end
            
        end
    end
end

if ExistingFiles == 1
	prompt = {'CONFIRM: ICA unmixing matrices from previous ICA runs detected.'; '';
		'To APPLY existing unmixing data to their respective datasets, push APPLY.';
		'Note: Choose this option to save time if ICA settings have NOT changed.'; '';
		'To REDO & OVERWRITE the ICA decomposition for each dataset, push REDO.';
		'Note: Choose this option if you wish to re-run ICA with new settings.'};
	
    RunChoice = questdlg(prompt, 'NOTE:', 'APPLY', 'REDO', 'Cancel', 'Cancel');
else
	RunChoice = 'REDO';
end

if strcmp(RunChoice, 'Cancel')
    return;
end

CheckOpenPCT

% Run ICA decomposition:
disp('PERFORMING ICA DECOMPOSITION:')
MEGpipeline_RunICA(FTcfg, InputParams, RunChoice);

% Detect & update status:
for g = 1:length(handles.name.GroupID)
    StatusWaitbar = waitbar(0, ['Please wait. Scanning status for: ', ...
        handles.name.GroupID{g}], 'Windowstyle', 'modal');
    
    for s = 1:length(handles.name.SubjID{g})
        waitbar(s/length(handles.name.SubjID{g}), StatusWaitbar);
        
        for c = 1:length(handles.name.CondID)
            handles = DetectStatus(handles, g, s, c);
        end
    end
    delete(StatusWaitbar);
end

handles = UpdateStatusSettings(handles);

% Save handles:
guidata(hObject, handles);

% Remove ErrorLog if empty:
if exist([pwd,'/ErrorLog_ICAcleaner.txt'], 'file')
	LogCheck = dir('ErrorLog_ICAcleaner.txt');
	if LogCheck.bytes == 0
		delete('ErrorLog_ICAcleaner.txt');
	end
end




%========================================%
% FUNCTIONS TO VIEW & REJECT COMPONENTS: %
%========================================%

%--- Executes on button press in ButtonViewComponents. ---%
%---------------------------------------------------------%
function ButtonViewComponents_Callback(hObject, eventdata, handles)
if isempty(handles.name.DataID)
    msgbox('Warning: Load DataID first.', 'Warning:');
    return;
end
if isempty(handles.name.GroupID)
    msgbox('Error: No GroupIDs specified.', 'Error:');
    return;
end
if isempty(handles.name.SubjID)
    msgbox('Error: No SubjIDs specified.', 'Error:');
    return;
else
    g = get(handles.ListboxGroupID, 'Value');
    if isempty(handles.name.SubjID{g})
        msgbox('Error: No SubjIDs added for selected Group.', 'Error:')
        return;
    end
end
if isempty(handles.name.CondID)
    msgbox('Error: No CondIDs specified.', 'Error:');
    return;
end

% Load component file for dataset:
% Note: Didn't read from disk (need sensor layout).
g = get(handles.ListboxGroupID, 'Value');
s = get(handles.ListboxSubjID,  'Value');
c = get(handles.ListboxCondID,  'Value');

if ~exist(handles.paths.ICAcomponents{g}{s,c}, 'file')
	msgbox('Error: ICA component file missing for selected dataset.')
	return;
end

LoadComp = LoadFTmat(handles.paths.ICAcomponents{g}{s,c}, 'ICAcleaner');
if isempty(LoadComp)
	msgbox('Error: ICA component file found, but contains errors. See ErrorLog.')
	return;
end

% Open databrowser:
cfgview.viewmode   = 'component';
cfgview.channel    = [1:10];		% View 10 components at a time.
cfgview.compscale  = 'local';		% Keep this local for proper scaling.
cfgview.zlim       = 'maxmin';
cfgview.ylim       = 'maxmin';
cfgview.continuous = 'yes';         % Concatenate trials for viewing.
cfgview.blocksize  = 20;

ft_databrowser(cfgview, LoadComp);

% Also open topoplots for first 30 components:  ** Removed for now, takes too long
% figure;  % Open new figure.
% cfgtopo.component = [1:20];
% cfgtopo.comment   = 'no';
% ft_topoplotIC(cfgtopo, LoadComp);

% Save handles:
guidata(hObject, handles);


%--- Executes on button press in ButtonSelectComponents. ---%
%------------------------------------------------------------
function ButtonSelectComponents_Callback(hObject, eventdata, handles)
if isempty(handles.name.DataID)
    msgbox('Warning: Load DataID first.', 'Warning:');
    return;
end
if isempty(handles.name.GroupID)
    msgbox('Error: No GroupIDs specified.', 'Error:');
    return;
end
if isempty(handles.name.SubjID)
    msgbox('Error: No SubjIDs specified.', 'Error:');
    return;
else
    g = get(handles.ListboxGroupID, 'Value');
    if isempty(handles.name.SubjID{g})
        msgbox('Error: No SubjIDs added for selected Group.', 'Error:')
        return;
    end
end
if isempty(handles.name.CondID)
    msgbox('Error: No CondIDs specified.', 'Error:');
    return;
end

% Load unmixing info for dataset:
% Note: Only need unmixing info for component rejection.
% Allows user to apply previous ICA cleaning to a dataset.
g = get(handles.ListboxGroupID, 'Value');
s = get(handles.ListboxSubjID,  'Value');
c = get(handles.ListboxCondID,  'Value');

if ~exist(handles.paths.ICAunmixing{g}{s,c}, 'file')
	message = {'ERROR:';
		'ICA unmixing info is missing for the selected dataset.';
		'Run ICA for the dataset to generate required files.'};
	msgbox(message);
	return;
end

LoadUnmix = LoadFTmat(handles.paths.ICAunmixing{g}{s,c}, 'ICAcleaner');
if isempty(LoadUnmix)
	msgbox('Error: ICA unmixing file contains errors. See ErrorLog.')
	return;
end

% Open selection list for available components:
SelectedComps = listdlg('PromptString', 'Select ICA components to REJECT:', ...
	'ListSize', [300, 300], 'SelectionMode', 'multiple', 'ListString', LoadUnmix.label);

handles.gui.SelectComps{g}{s,c} = SelectedComps;

% Detect & update status:
handles = DetectStatus(handles, g, s, c);
handles = UpdateStatusSettings(handles);

% Save handles:
guidata(hObject, handles);


%--- Executes on button press in ButtonRmvCompCleanData. ---%
%-----------------------------------------------------------%
function ButtonRmvCompCleanData_Callback(hObject, eventdata, handles)
if isempty(handles.name.DataID)
    msgbox('Warning: Load DataID first.', 'Warning:');
    return;
end
if isempty(handles.name.GroupID)
    msgbox('Error: No GroupIDs specified.', 'Error:');
    return;
end
if isempty(handles.name.SubjID)
    msgbox('Error: No SubjIDs specified.', 'Error:');
    return;
else
    for g = 1:length(handles.name.GroupID)
        if isempty(handles.name.SubjID{g})
            msgbox('Error: Not all Groups have SubjIDs added.', 'Error:')
            return;
        end
    end
end
if isempty(handles.name.CondID)
    msgbox('Error: No CondIDs specified.', 'Error:');
    return;
end

% Load required parameters:
InputParams.name                  = handles.name;
InputParams.paths.InputPreprocMEG = handles.paths.InputPreprocMEG;
InputParams.paths.ICAunmixing     = handles.paths.ICAunmixing;
InputParams.paths.ICAcleanData    = handles.paths.ICAcleanData;
InputParams.RejectComps           = handles.gui.SelectComps;

% Check if unmixing info generated for each dataset:
% Check if components selected for each dataset:
MissingUnmixing  = 0;
MissingSelection = 0;

for g = 1:length(handles.name.GroupID)
	for s = 1:length(handles.name.SubjID{g})
		for c = 1:length(handles.name.CondID)
			
			if ~exist(handles.paths.ICAunmixing{g}{s,c}, 'file')
				MissingUnmixing = 1;
			end
			if isempty(handles.gui.SelectComps{g}{s,c})
				MissingSelection = 1;
			end
			
		end
	end
end

if MissingUnmixing == 1
	message = {'ERROR:'; '';
		'ICA unmixing info is missing for some of the selected datasets.';
		'Run ICA to generate the required files for these datasets.'};
	msgbox(message, 'ERROR:')
	return;
end

if MissingSelection == 1
	prompt = {'WARNING:'; '';
		'Some of the input datasets do NOT have components selected for removal.';
		'Are you sure you wish to leave these datasets UNALTERED?'; '';
		'IMPORTANT: If you continue, components will NOT be removed from';
		'the datasets in question. They will simply be copied into the output';
		'DataID-ICAclean folder.'};
	
	ContChoice = questdlg(prompt, 'WARNING:', 'CONTINUE', 'CANCEL', 'CANCEL');
	if strcmp(ContChoice, 'CANCEL')
		return;
	end
end

CheckOpenPCT

% Reject components and reconstruct data:
disp('REJECTING COMPONENTS & RECONSTRUCTING DATA:')
MEGpipeline_RemoveICAcomps(InputParams);

% Detect & update status:
for g = 1:length(handles.name.GroupID)
    StatusWaitbar = waitbar(0, ['Please wait. Scanning status for: ', ...
        handles.name.GroupID{g}], 'Windowstyle', 'modal');
    
    for s = 1:length(handles.name.SubjID{g})
        waitbar(s/length(handles.name.SubjID{g}), StatusWaitbar);
        
        for c = 1:length(handles.name.CondID)
            handles = DetectStatus(handles, g, s, c);
        end
    end
    delete(StatusWaitbar)
end

handles = UpdateStatusSettings(handles);

% Make copy of PreprocSettings .mat in new DataID folder:
PathOrigDataID  = handles.paths.DataID;
PathCleanDataID = [handles.paths.Rootpath,'/DataID-ICAclean_',handles.name.DataID];

OldSettingsFile = [PathOrigDataID,'/PreprocSettings.mat'];
NewSettingsFile = [PathCleanDataID,'/PreprocSettings.mat'];

if exist(OldSettingsFile, 'file')
	if exist(NewSettingsFile, 'file')
        delete(NewSettingsFile);
	end
	
	CopyStatus = copyfile(OldSettingsFile, NewSettingsFile, 'f');
	if CopyStatus == 0
		msgbox('Warning: Failed to copy PreprocSettings.mat to new DataID-ICAclean folder.')
	end
end

% Make copy of PreprocInputMEG .mat files in new DataID folder:
CopyFailed = 0;

for g = 1:length(handles.name.GroupID)
	GroupPath = [handles.paths.DataID,'/GroupID_',handles.name.GroupID{g}];
    InputMats = dir([GroupPath,'/PreprocInputMEG_*.mat']);  % Find InputMats for group
    InputMats = {InputMats.name};
	
	for m = 1:length(InputMats)
		OldMatFile = [PathOrigDataID,'/GroupID_',handles.name.GroupID{g},'/',InputMats{m}];
		NewMatFile = [PathCleanDataID,'/GroupID_',handles.name.GroupID{g},'/',InputMats{m}];
		
		if exist(NewMatFile, 'file')
            delete(NewMatFile);
		end
		
		CopyStatus = copyfile(OldMatFile, NewMatFile, 'f');
		if CopyStatus == 0
			CopyFailed = 1;
		end
	end
end

if CopyFailed == 1
	msgbox('Warning: Failed to copy PreprocInputMEG .mat(s) to new DataID-ICAclean folder.')
end

% Ask user if they wish to remove component files:
ButtonDeleteCompFiles_Callback(hObject, eventdata, handles);

% Save handles:
guidata(hObject, handles);

% Remove ErrorLog if empty:
if exist([pwd,'/ErrorLog_ICAcleaner.txt'], 'file')
	LogCheck = dir('ErrorLog_ICAcleaner.txt');
	if LogCheck.bytes == 0
		delete('ErrorLog_ICAcleaner.txt');
	end
end



%--- Executes on button press in ButtonDeleteCompFiles. ---%
%----------------------------------------------------------%
function ButtonDeleteCompFiles_Callback(hObject, eventdata, handles)
if isempty(handles.name.DataID)
    msgbox('Warning: Load DataID first.', 'Warning:');
    return;
end
if isempty(handles.name.GroupID)
    msgbox('Error: No GroupIDs specified.', 'Error:');
    return;
end
if isempty(handles.name.SubjID)
    msgbox('Error: No SubjIDs specified.', 'Error:');
    return;
else
    for g = 1:length(handles.name.GroupID)
        if isempty(handles.name.SubjID{g})
            msgbox('Error: Not all Groups have SubjIDs added.', 'Error:')
            return;
        end
    end
end
if isempty(handles.name.CondID)
    msgbox('Error: No CondIDs specified.', 'Error:');
    return;
end

% Confirm removal:
prompt = {'RECOMMENDED:'; '';
	'To save space, ICA component files can be removed after ICA cleaning.';
	'Do you wish to remove these large component files?'; '';
	'NOTE: Unmixing info from the ICA decompositions will be kept.';
	'These will allow you to quickly create component files again if needed.'};

RmvCompFiles = questdlg(prompt, 'RECOMMENDED:', 'YES', 'NO', 'YES');
if strcmp(RmvCompFiles, 'NO')
	return;
end

% Check if ICAcleanData exists for all datasets:
UnfinishedCleaning = 0;

for g = 1:length(handles.name.GroupID)
	for s = 1:length(handles.name.SubjID{g})
		for c = 1:length(handles.name.CondID)
            
            ICAcomponents = handles.paths.ICAcomponents{g}{s,c};
            ICAcleanData  = handles.paths.ICAcleanData{g}{s,c};
			
			if exist(ICAcomponents, 'file') && ~exist(ICAcleanData, 'file')
				UnfinishedCleaning = 1;
			end
			
		end
	end
end

if UnfinishedCleaning == 1
	prompt = {'WARNING:'; '';
		'Some of the selected datasets have NOT been ICA cleaned yet.';
		'Are you sure you wish to remove component files?'};
	
	ContinueRmv = questdlg(prompt, 'WARNING:', 'YES', 'NO', 'NO');
	if strcmp(ContinueRmv, 'NO')
		return;
	end
end

% Remove component files:
for g = 1:length(handles.name.GroupID)
    for s = 1:length(handles.name.SubjID{g})
        for c = 1:length(handles.name.CondID)
            
            if exist(handles.paths.ICAcomponents{g}{s,c}, 'file')
                delete(handles.paths.ICAcomponents{g}{s,c});
            end
            
        end
    end
end




%=================================%
% FUNCTION TO OPEN MODAL WAITBOX: %
%=================================%
function WaitBox = StartWaitBox(TextString)

WaitBox = dialog('Units', 'pixels', 'Position', [500 500 300 40],...
    'Windowstyle', 'modal', 'NextPlot', 'new', 'Name', 'Please Wait:');

uicontrol('Parent', WaitBox, 'Units', 'pixels', 'Position', [20 10 250 20],...
    'Style', 'text', 'String', TextString, 'FontWeight', 'bold');

movegui(WaitBox, 'center');




%============================%
% GUIDE CREATEFCN FUNCTIONS: %
%============================%

% --- Executes during object creation, after setting all properties.
function TextboxRootpath_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 TextboxDataID_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 ListboxGroupID_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 ListboxSubjID_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 TextboxSubjID_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 ListboxCondID_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 TextboxCondID_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 ListboxInpOutStatus_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 ListboxRmvCompStatus_CreateFcn(hObject, eventdata, handles)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor','white');
end