function varargout = JOVE_GUI2(varargin)

gui_Singleton = 1;
gui_State = struct('gui_Name',       mfilename, ...
                   'gui_Singleton',  gui_Singleton, ...
                   'gui_OpeningFcn', @JOVE_GUI2_OpeningFcn, ...
                   'gui_OutputFcn',  @JOVE_GUI2_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

function JOVE_GUI2_OpeningFcn(hObject, eventdata, handles, varargin)

handles.output = hObject;

addpath(genpath(fullfile(pwd,'Utilities')));

handles.Header = [];
handles.FuncFile = '';

handles.Data = [];

handles.Atlas = '';
handles.AtlasName = '';

handles.iy = [];

handles.GM = [];

handles.TC = [];
handles.TC2 = [];

handles.TR = realmax;

handles.W = realmax;

handles.ScrubT = realmax;

handles.IsFuncLoaded = 0;
handles.IsAtlasLoaded = 0;
handles.IsWarpLoaded = 0;
handles.IsMotLoaded = 0;
handles.IsHeaderLoaded = 0;

handles.SN = '';

handles.Mot = [];
handles.FD = [];

handles.CodeBook = [];

% Update handles structure
guidata(hObject, handles);


% --- Outputs from this function are returned to the command line.
function varargout = JOVE_GUI2_OutputFcn(hObject, eventdata, handles) 
varargout{1} = handles.output;




% --- Executes on button press in DataButton.
function DataButton_Callback(hObject, eventdata, handles)

% Selection of all the fMRI files
[filename1,pathname1]=uigetfile({'*.*','All Files'},...
  'Select fMRI files (NIFTI)...','MultiSelect','off');

% If the user has indeed entered files
if ~isequal(filename1,0) || ~isequal(pathname1,0)
    
        load((fullfile(pathname1, filename1)));
        assignin('base','ISFC_VX', ISFC_VX);
        handles.Data = ISFC_VX;

        handles.GM = zeros(size(handles.Data,1),1);
        handles.GM(~isnan(handles.Data(:,1))) = 1;
        handles.GM = logical(handles.GM);

        % Confirms that functional data has been loaded
        handles.IsFuncLoaded = 1;
end

if JOVE_IsAllLoaded(handles.IsFuncLoaded,handles.IsAtlasLoaded,handles.IsWarpLoaded,handles.IsMotLoaded,handles.IsHeaderLoaded)
    handles.TC = JOVE_AtlasData(handles.Data,handles.GM,handles.Atlas,handles.iy,handles.FuncFile);
end


guidata(hObject,handles);




% --- Executes on button press in AtlasButton.
function AtlasButton_Callback(hObject, eventdata, handles)

% Selection of the file
[filename2,pathname2]=uigetfile({'*.*','All Files'},...
  'Select structural files...','MultiSelect','off');

% If the user has indeed entered files
if ~isequal(filename2,0) || ~isequal(pathname2,0)
    
       % The atlas is warped at the right resolution
       handles.Atlas = fullfile(pathname2, filename2);
       handles.AtlasName = filename2;
       
       tmp = spm_read_vols(spm_vol(handles.Atlas));
       tmp = tmp(:);
       
       [handles.CodeBook] = CreateCodeBook(handles.Atlas,1:max(tmp),realmax);
        
       handles.IsAtlasLoaded = 1;
end

if JOVE_IsAllLoaded(handles.IsFuncLoaded,handles.IsAtlasLoaded,handles.IsWarpLoaded,handles.IsMotLoaded,handles.IsHeaderLoaded)
    handles.TC = JOVE_AtlasData(handles.Data,handles.GM,handles.Atlas,handles.iy,handles.FuncFile);
end

guidata(hObject,handles);


% --- Executes on button press in WarpButton.
function WarpButton_Callback(hObject, eventdata, handles)

% Selection of the file
[filename3,pathname3]=uigetfile({'*.*','All Files'},...
  'Select structural files...','MultiSelect','off');

% If the user has indeed entered files
if ~isequal(filename3,0) || ~isequal(pathname3,0)
    
        handles.iy = fullfile(pathname3,filename3);
        
        handles.IsWarpLoaded = 1;
end

if JOVE_IsAllLoaded(handles.IsFuncLoaded,handles.IsAtlasLoaded,handles.IsWarpLoaded,handles.IsMotLoaded,handles.IsHeaderLoaded)
    
    handles.TC = JOVE_AtlasData(handles.Data,handles.GM,handles.Atlas,handles.iy,handles.FuncFile);
end

guidata(hObject,handles);


function MotionButton_Callback(hObject, eventdata, handles)

% Selection of the file
[filename4,pathname4]=uigetfile({'*.*','All Files'},...
  'Select motion file...','MultiSelect','off');

if ~isequal(filename4,0) || ~isequal(pathname4,0)

    handles.Mot = textread(fullfile(pathname4,filename4));
    handles.Mot = handles.Mot(:,1:6);
    
    handles.IsMotLoaded = 1;
end

if JOVE_IsAllLoaded(handles.IsFuncLoaded,handles.IsAtlasLoaded,handles.IsWarpLoaded,handles.IsMotLoaded,handles.IsHeaderLoaded)
    handles.TC = JOVE_AtlasData(handles.Data,handles.GM,handles.Atlas,handles.iy,handles.FuncFile);
end

guidata(hObject,handles);



% --- Executes on button press in PlotButton.
function PlotButton_Callback(hObject, eventdata, handles)

if JOVE_IsAllLoaded(handles.IsFuncLoaded,handles.IsAtlasLoaded,handles.IsWarpLoaded,handles.IsMotLoaded,handles.IsHeaderLoaded)

    % Scrubbing
    % Converts the rotational components into [mm]
    handlesMot(:,4:6) = 50*handles.Mot(:,4:6);
        
    % Computes FD
    handles.FD = sum(abs([0 0 0 0 0 0; diff(handles.Mot)]),2);
    
    set(handles.ScrubTextPerc,'String',[num2str(100*sum(handles.FD > handles.ScrubT)/length(handles.FD)),' [%] scrubbed']);
    
    % Scrubbing according to chosen scheme
    switch get(handles.ScrubbingPopup,'Value');
        
        % No scrubbing at all
        case 1
            Scrub_mask_final = logical(zeros(size(handles.FD)));
            
        % Only the implicated frames are scrubbed
        case 2
            Scrub_mask_final = logical(handles.FD > handles.ScrubT);
            
        % also one frame afterwards scrubbed
        case 3
            Scrub_mask = logical(handles.FD > handles.ScrubT);
            
            tmp = circshift(Scrub_mask,[1 0]);
            tmp(1) = 0;
            
            Scrub_mask_final = Scrub_mask | tmp;
            
        case 4
            
            Scrub_mask = logical(handles.FD > handles.ScrubT);
            
            tmp = circshift(Scrub_mask,[1 0]);
            tmp(1) = 0;
            
            Scrub_mask_final = Scrub_mask | tmp;
            
            tmp = circshift(Scrub_mask,[-1 0]);
            tmp(end) = 0;
            
            Scrub_mask_final = Scrub_mask_final | tmp;
            
        case 5
            
            Scrub_mask = logical(handles.FD > handles.ScrubT);
            
            tmp = circshift(Scrub_mask,[1 0]);
            tmp(1) = 0;
            
            Scrub_mask_final = Scrub_mask | tmp;
            
            tmp = circshift(Scrub_mask,[-1 0]);
            tmp(end) = 0;
            
            Scrub_mask_final = Scrub_mask_final | tmp;
            
            tmp = circshift(Scrub_mask,[2 0]);
            tmp(1) = 0;
            tmp(2) = 0;
            
            Scrub_mask_final = Scrub_mask_final | tmp;
            
        case 6
            Scrub_mask = logical(handles.FD > handles.ScrubT);
            
            tmp = circshift(Scrub_mask,[1 0]);
            tmp(1) = 0;
            
            Scrub_mask_final = Scrub_mask | tmp;
            
            tmp = circshift(Scrub_mask,[-1 0]);
            tmp(end) = 0;
            
            Scrub_mask_final = Scrub_mask_final | tmp;
            
            tmp = circshift(Scrub_mask,[2 0]);
            tmp(1) = 0;
            tmp(2) = 0;
            
            Scrub_mask_final = Scrub_mask_final | tmp;
            
            tmp = circshift(Scrub_mask,[-2 0]);
            tmp(end) = 0;
            tmp(end-1) = 0;
            
            Scrub_mask_final = Scrub_mask_final | tmp;
            
        case 7
            Scrub_mask = logical(handles.FD > handles.ScrubT);
            
            tmp = circshift(Scrub_mask,[1 0]);
            tmp(1) = 0;
            
            Scrub_mask_final = Scrub_mask | tmp;
            
            tmp = circshift(Scrub_mask,[-1 0]);
            tmp(end) = 0;
            
            Scrub_mask_final = Scrub_mask_final | tmp;
            
            tmp = circshift(Scrub_mask,[2 0]);
            tmp(1) = 0;
            tmp(2) = 0;
            
            Scrub_mask_final = Scrub_mask_final | tmp;
            
            tmp = circshift(Scrub_mask,[-2 0]);
            tmp(end) = 0;
            tmp(end-1) = 0;
            
            Scrub_mask_final = Scrub_mask_final | tmp;
            
            
            tmp = circshift(Scrub_mask,[3 0]);
            tmp(1) = 0;
            tmp(2) = 0;
            tmp(3) = 0;
            
            Scrub_mask_final = Scrub_mask_final | tmp;
        otherwise
            
    end
   

    if sum(Scrub_mask_final) > 0
        % Finds the values at the time points that we know are not 
        % corrupted
        TCon = handles.TC(:,find(~Scrub_mask_final));
        TCon(isnan(TCon)) = 0;

        % tinter is all the time points
        tinter = 1:length(Scrub_mask_final);

        % torig is the time points that we know
        torig = tinter(find(~Scrub_mask_final));

        % We interpolate all time point values using the info that we
        % know (TCon at torig)
        handles.TC2 = interp1(torig,TCon',tinter,'spline')';

    end
    
       
    handles.TC2 = handles.TC;
    
    % We want to keep the 'NaN's that we had because they are used to
    % remove bad regional time courses later on
    handles.TC2(isnan(handles.TC)) = NaN;
    handles.TC2 = real(y_IdealFilter(handles.TC2', handles.TR, [1/(handles.W*handles.TR) 0]))';
        
    % Randomly picks 10 time courses for plotting
    n_ROI = size(handles.TC2,1);
    IDX = randperm(n_ROI);
    
    % Plots first graph
    handles.StartPlot = JOVE_PlotAtlasTC(handles.StartPlot,handles.TC-repmat(mean(handles.TC,2),1,size(handles.TC2,2)),IDX(1:6),'Atlas',handles.W,[],handles.TR);

    % Plots second graph
    handles.EndPlot = JOVE_PlotAtlasTC(handles.EndPlot,handles.TC2,IDX(1:6),'Atlas',handles.W,[],handles.TR);
    
end     

guidata(hObject,handles);


function TRText_Callback(hObject, eventdata, handles)

% If the TR takes a reasonable value, then we validate it
if (~isempty(str2double(get(hObject,'String')))) && ...
        (str2double(get(hObject,'String')) > 0)
    
    handles.TR = str2double(get(hObject,'String'));    
    set(hObject,'BackgroundColor', [0.4 0.6 0.4]);
else 
    set(hObject,'BackgroundColor', [0.93 0.84 0.84]);
end

guidata(hObject,handles);


% --- Executes during object creation, after setting all properties.
function TRText_CreateFcn(hObject, eventdata, handles)

set(hObject,'String','Enter TR...');
set(hObject,'FontAngle','italic');


function TRText_ButtonDownFcn(hObject,eventdata,handles)

set(hObject,'Enable','on');
set(hObject,'String','');
set(hObject,'FontAngle','normal');
uicontrol(hObject);
guidata(hObject, handles); 



% --- Executes on selection change in ScrubbingPopup.
function ScrubbingPopup_CreateFcn(hObject, eventdata, handles)

Scrubbing_Types = {'None','0|0','0|1','1|1','1|2','2|2','2|3'};

set(hObject,'String',Scrubbing_Types);

guidata(hObject,handles);



% --- Executes during object creation, after setting all properties.
function ScrubbingPopup_Callback(hObject, eventdata, handles)

guidata(hObject,handles);



function ScrubText_Callback(hObject, eventdata, handles)
   
% If the high-pass takes a reasonable value, then we validate it
if (~isempty(str2double(get(hObject,'String')))) && ...
        (str2double(get(hObject,'String')) > 0)
    
    handles.ScrubT = str2double(get(hObject,'String'));    
    set(hObject,'BackgroundColor', [0.4 0.6 0.4]);
else 
    set(hObject,'BackgroundColor', [0.93 0.84 0.84]);
end

guidata(hObject,handles);



function ScrubText_CreateFcn(hObject, eventdata, handles)

set(hObject,'String','Enter scrubbing threshold...');
set(hObject,'FontAngle','italic');


function ScrubText_ButtonDownFcn(hObject,eventdata,handles)

set(hObject,'Enable','on');
set(hObject,'String','');
set(hObject,'FontAngle','normal');
uicontrol(hObject);
guidata(hObject, handles); 



function WindowText_Callback(hObject, eventdata, handles)

% If the high-pass takes a reasonable value, then we validate it
if (~isempty(str2double(get(hObject,'String')))) && ...
        (str2double(get(hObject,'String')) > 1) && ...
        (str2double(get(hObject,'String')) < size(handles.Data,2))
    
    handles.W = str2double(get(hObject,'String'));    
    set(hObject,'BackgroundColor', [0.4 0.6 0.4]);
else 
    set(hObject,'BackgroundColor', [0.93 0.84 0.84]);
end

guidata(hObject,handles);


function WindowText_CreateFcn(hObject, eventdata, handles)

set(hObject,'String','Enter window size...');
set(hObject,'FontAngle','italic');


function WindowText_ButtonDownFcn(hObject,eventdata,handles)

set(hObject,'Enable','on');
set(hObject,'String','');
set(hObject,'FontAngle','normal');
uicontrol(hObject);
guidata(hObject,handles);



function SaveButton_Callback(hObject, eventdata, handles)

ToSave = handles.TC2;
CodeBook = handles.CodeBook;

save(handles.SN,'ToSave');

save('CodeBook','CodeBook');

guidata(hObject,handles);


function SaveText_Callback(hObject, eventdata, handles)

if (~isempty(get(hObject,'String')))  
    set(hObject,'BackgroundColor', [0.4 0.6 0.4]);
    handles.SN = get(hObject,'String');
else 
    set(hObject,'BackgroundColor', [0.93 0.84 0.84]);
end

guidata(hObject,handles);


function SaveText_CreateFcn(hObject, eventdata, handles)

set(hObject,'String','Enter save name...');
set(hObject,'FontAngle','italic');


function SaveText_ButtonDownFcn(hObject, eventdata, handles)

set(hObject,'Enable','on');
set(hObject,'String','');
set(hObject,'FontAngle','normal');
uicontrol(hObject);
guidata(hObject,handles);


function ClearButton_Callback(hObject, eventdata, handles)

handles.FuncFile = '';
handles.Header = [];

handles.Data = [];

handles.Atlas = '';
handles.AtlasName = '';

handles.iy = [];

handles.GM = [];

handles.TC = [];
handles.TC2 = [];

handles.TR = realmax;

handles.W = realmax;

handles.ScrubT = realmax;

handles.IsFuncLoaded = 0;
handles.IsAtlasLoaded = 0;
handles.IsWarpLoaded = 0;
handles.IsMotLoaded = 0;
handles.IsHeaderLoaded = 0;

handles.SN = '';

handles.Mot = [];
handles.FD = [];

cla(handles.StartPlot);
cla(handles.EndPlot);

SaveText_CreateFcn(handles.SaveText,eventdata,handles);
TRText_CreateFcn(handles.TRText,eventdata,handles);
ScrubText_CreateFcn(handles.ScrubText,eventdata,handles);
WindowText_CreateFcn(handles.WindowText,eventdata,handles);

set(handles.TRText,'Enable','off');
set(handles.ScrubText,'Enable','off');
set(handles.WindowText,'Enable','off');
set(handles.SaveText,'Enable','off');

set(handles.TRText,'BackgroundColor',240/255*[1 1 1]);
set(handles.ScrubText,'BackgroundColor',240/255*[1 1 1]);
set(handles.WindowText,'BackgroundColor',240/255*[1 1 1]);
set(handles.SaveText,'BackgroundColor',240/255*[1 1 1]);

set(handles.ScrubbingPopup,'Value',1);
set(handles.ScrubTextPerc,'String','- [%] scrubbed');


% Update handles structure
guidata(hObject, handles);


function HeaderButton_Callback(hObject, eventdata, handles)

% Selection of all the fMRI files
[filename0,pathname0]=uigetfile({'*.*','All Files'},...
  'Select fMRI files (NIFTI)...','MultiSelect','off');

% If the user has indeed entered files
if ~isequal(filename0,0) || ~isequal(pathname0,0)
    
        handles.FuncFile = fullfile(pathname0,filename0);
        handles.Header = spm_vol(handles.FuncFile);
    
        % Confirms that functional data has been loaded
        handles.IsHeaderLoaded = 1;
end

if JOVE_IsAllLoaded(handles.IsFuncLoaded,handles.IsAtlasLoaded,handles.IsWarpLoaded,handles.IsMotLoaded,handles.IsHeaderLoaded)
    handles.TC = JOVE_AtlasData(handles.Data,handles.GM,handles.Atlas,handles.iy,handles.FuncFile);
end

guidata(hObject,handles);