function varargout = JOVE_GUI4(varargin)

gui_Singleton = 1;
gui_State = struct('gui_Name',       mfilename, ...
                   'gui_Singleton',  gui_Singleton, ...
                   'gui_OpeningFcn', @JOVE_GUI4_OpeningFcn, ...
                   'gui_OutputFcn',  @JOVE_GUI4_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_GUI4_OpeningFcn(hObject, eventdata, handles, varargin)

handles.output = hObject;

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

handles.NullType = 'Normal';

handles.IsISFCDataLoaded = 0;
handles.IsNullLoaded = 0;
handles.IsCodeBookLoaded = 0;
handles.W = realmax;
handles.TR = 1;
handles.IsTREntered = 0;
handles.IsWEntered = 0;
handles.ISFC_Data = {};
handles.Null_Data = {};
handles.Alpha = 0.01;
handles.NullThresh = {};
handles.SignMat = [];
handles.IDX= [];
handles.t_start = 0;
handles.t_end = realmax;
handles.range = [-1,1];
handles.SaveName = 'DefaultName';

guidata(hObject, handles);

function varargout = JOVE_GUI4_OutputFcn(hObject, eventdata, handles) 

varargout{1} = handles.output;


%% Loading the ISFC data to threshold
function DataButton_Callback(hObject, eventdata, handles)

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

% If the user has indeed entered files
if ~isequal(filename1,0) || ~isequal(pathname1,0)    
        if ~ischar(filename1)
    
            % The files are loaded sequentially: File{t} contains the path
            % towards the t-th frame
            for f = 1:length(filename1)   
                load((fullfile(pathname1, filename1{f})));
                assignin('base','ISFC_Final', ISFC_Final);
                handles.ISFC_Data = [handles.ISFC_Data,ISFC_Final];
            end
        
        else
            load((fullfile(pathname1, filename1)));
            assignin('base','ISFC_Final', ISFC_Final);
            handles.ISFC_Data = ISFC_Final;
        end
            
        handles.IsISFCDataLoaded = 1;
        
        % If we have entered all required fields, we prepare the slider to
        % lie within the t_start/t_end interval
        if handles.IsTREntered && handles.IsWEntered && handles.IsISFCDataLoaded
            handles.t_start = (handles.TR*handles.W)-1;
            handles.t_end = (size(handles.ISFC_Data{1},2)-1)*handles.TR + handles.t_start;

            set(handles.Slider,'Value',handles.t_start);
            set(handles.Slider,'Min',handles.t_start);
            set(handles.Slider,'Max',handles.t_end);
        end 
end

guidata(hObject,handles);


%% Loading of the null data
function NullButton_Callback(hObject, eventdata, handles)

% Selection of all the fMRI files
[filename2,pathname2]=uigetfile({'*.*','All Files'},...
  'Select null ISFC files...','MultiSelect','on');

% If the user has indeed entered files
if ~isequal(filename2,0) || ~isequal(pathname2,0)
    
    if ~ischar(filename2)
    
        % The files are loaded sequentially: File{t} contains the path
        % towards the t-th frame
        for f = 1:length(filename2)   
            load((fullfile(pathname2, filename2{f})));
            assignin('base','ISFC_Final', ISFC_Final);
            handles.Null_Data = [handles.Null_Data,ISFC_Final];
        end
    else
        load((fullfile(pathname2, filename2)));
        assignin('base','ISFC_Final', ISFC_Final);
        handles.Null_Data = ISFC_Final;
    end
        
        handles.IsNullLoaded = 1;
end

guidata(hObject,handles);




%% Entry of the percentile value at which to threshold
function PercentileText_Callback(hObject, eventdata, handles)

if (~isempty(str2double(get(hObject,'String')))) && ...
        (str2double(get(hObject,'String')) > 0) && ...
        (str2double(get(hObject,'String')) < 100)
    
    handles.Alpha = 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 PercentileText_CreateFcn(hObject, eventdata, handles)

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

guidata(hObject,handles);


function PercentileText_ButtonDownFcn(hObject, eventdata, handles)

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

guidata(hObject,handles);


%% Plotting button
function PlotButton_Callback(hObject, eventdata, handles)

if handles.IsISFCDataLoaded && handles.IsNullLoaded
    
    % Computes excursions (size conn x n_swtp x subj)
    [SignMat,NullThresh] = JOVE_FindExcursions(handles.ISFC_Data,handles.Null_Data,handles.Alpha,handles.NullType);
    
    handles.SignMat = SignMat;
    
    handles.NullThresh = NullThresh;
    
    % Sorts the time courses, so that we display first the ones with the
    % largest excursion values (absolute)
    [tmp,IDX] = sort(squeeze(sum(abs(mean(handles.SignMat,3)),2)),'descend');
    handles.IDX = IDX(~isnan(tmp));

    tmp = handles.ISFC_Data{1}(handles.IDX,:);
    tmp = tmp(:);
    handles.range = [-max(abs(tmp)),max(abs(tmp))];
    
    % Plots the ISFC data as well as the associated thresholds
    [handles.ISFCPlot] = JOVE_PlotAtlasTC(handles.ISFCPlot,handles.ISFC_Data{1},handles.IDX(1:3),'ISFC',handles.W,handles.Step,handles.TR);
    
    tmp_CM = cbrewer('qual','Set1',3);
    
    for i = 1:3
        plot([handles.t_start,handles.t_end],[handles.NullThresh{1}(handles.IDX(i),1),handles.NullThresh{1}(handles.IDX(i),1)],'Parent',handles.ISFCPlot,'Color',tmp_CM(i,:));
        plot([handles.t_start,handles.t_end],[handles.NullThresh{1}(handles.IDX(i),2),handles.NullThresh{1}(handles.IDX(i),2)],'Parent',handles.ISFCPlot,'Color',tmp_CM(i,:));
    end
    
    handles.Line1 = plot([handles.t_start handles.t_start],[-1 1],'color',[0 0 0],'Parent',handles.ISFCPlot);
    
    % Plots the excursion time courses
    for i = 1:3
        tmp_vec = zeros(size(handles.ISFC_Data{1},1),1);
        tmp_vec(handles.IDX(i)) = 1;
        tmp_mat = jVecToUpperTriMat(tmp_vec,(1+sqrt(1+4*2*size(handles.SignMat,1)))/2);
        
        JOVE_Plot_Conn_TimeCourse(handles.ExcPlot,handles.SignMat,find(sum(tmp_mat,2)==1),find(sum(tmp_mat,1)==1),handles.W,handles.TR,tmp_CM(i,:),tmp_CM(i,:));
    end
        
    handles.Line2 = plot([handles.t_start handles.t_start],[-1 1],'color',[0 0 0],'Parent',handles.ExcPlot);
    
    if handles.IsCodeBookLoaded == 1

        curtime = floor((get(handles.Slider,'Value')-handles.t_start)/(handles.Step*handles.TR)) + 1;

        Spatial_OI = mean(squeeze(handles.SignMat(:,curtime,:)),2);

        tmp_MAT = jVecToUpperTriMat(Spatial_OI,(1+sqrt(1+4*2*size(handles.SignMat,1)))/2)+jVecToUpperTriMat(Spatial_OI,(1+sqrt(1+4*2*size(handles.SignMat,1)))/2)';
        tmp_DEG = sum(abs(tmp_MAT),1)/2;

        Factor_plots = 2*max(tmp_DEG);
 
        PlotBrainGraph_Kmeans_withtitle(handles.BrainPlot,tmp_MAT,tmp_DEG,handles.CodeBook,0.2,...
                Factor_plots,Factor_plots,2,1,'hot','spring',1,0.5,[-1 1],...
                'W10_Alpha001','W10_Alpha001');
    end
end

guidata(hObject,handles);


%% Slider controls
function Slider_Callback(hObject, eventdata, handles)

handles.Line1.XData = [get(hObject,'Value'), get(hObject,'Value')];
handles.Line2.XData = [get(hObject,'Value'), get(hObject,'Value')];


if handles.IsCodeBookLoaded == 1
    
    curtime = floor((get(hObject,'Value')-handles.t_start)/(handles.Step*handles.TR)) + 1;
    
    Spatial_OI = mean(squeeze(handles.SignMat(:,curtime,:)),2);

    tmp_MAT = jVecToUpperTriMat(Spatial_OI,(1+sqrt(1+4*2*size(handles.SignMat,1)))/2)+jVecToUpperTriMat(Spatial_OI,(1+sqrt(1+4*2*size(handles.SignMat,1)))/2)';
    tmp_DEG = sum(abs(tmp_MAT),1)/2;

    Factor_plots = 2*max(tmp_DEG);

    cla(handles.BrainPlot);
    
    PlotBrainGraph_Kmeans_withtitle(handles.BrainPlot,tmp_MAT,tmp_DEG,handles.CodeBook,0.2,...
            Factor_plots,Factor_plots,2,1,'hot','spring',1,0.5,[-1 1],...
            'W10_Alpha001','W10_Alpha001');
    
end

guidata(hObject, handles);


function Slider_CreateFcn(hObject, eventdata, handles)


if isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor',[.9 .9 .9]);
end
guidata(hObject, handles); 


%% Save button
function SaveButton_Callback(hObject, eventdata, handles)

SM = handles.SignMat;
save(handles.SaveName,'SM');

guidata(hObject,handles);


%% Clear button
function ClearButton_Callback(hObject, eventdata, handles)

handles.NullType = 'Normal';

handles.IsISFCDataLoaded = 0;
handles.IsNullLoaded = 0;

handles.IsMovieLoaded = 0;

handles.W = realmax;
handles.TR = 1;

handles.IsTREntered = 0;
handles.IsWEntered = 0;

handles.ISFC_Data = {};
handles.Null_Data = {};
handles.Alpha = 0.05;

handles.NullThresh = {};
handles.SignMat = [];

handles.IDX= [];

handles.t_start = 0;
handles.t_end = realmax;

handles.range = [-1,1];

handles.SaveName = 'DefaultName';

cla(handles.ISFCPlot);
cla(handles.ExcPlot);
cla(handles.BrainPlot);

set(handles.Slider,'Value',0);
set(handles.Slider,'Min',0);
set(handles.Slider,'Max',1);

set(handles.WindowText,'Enable','off');
set(handles.WindowText,'BackgroundColor',240/255*[1 1 1]);
WindowText_CreateFcn(handles.WindowText, eventdata, handles);

set(handles.TRText,'Enable','off');
set(handles.TRText,'BackgroundColor',240/255*[1 1 1]);
TRText_CreateFcn(handles.TRText, eventdata, handles);

set(handles.StepText,'Enable','off');
set(handles.StepText,'BackgroundColor',240/255*[1 1 1]);
StepText_CreateFcn(handles.StepText, eventdata, handles);

set(handles.SaveText,'Enable','off');
set(handles.SaveText,'BackgroundColor',240/255*[1 1 1]);
SaveText_CreateFcn(handles.SaveText, eventdata, handles);

set(handles.PercentileText,'Enable','off');
set(handles.PercentileText,'BackgroundColor',240/255*[1 1 1]);
PercentileText_CreateFcn(handles.PercentileText, eventdata, handles);

guidata(hObject,handles);


%% Window text entry
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.ISFC_Data{1},2))
    
    handles.W = str2double(get(hObject,'String'));    
    set(hObject,'BackgroundColor', [0.4 0.6 0.4]);
    
    handles.IsWEntered = 1;
    
    if handles.IsTREntered && handles.IsWEntered && handles.IsISFCDataLoaded
        handles.t_start = (handles.TR*handles.W)-1;
        handles.t_end = (size(handles.ISFC_Data{1},2)-1)*handles.TR + handles.t_start;

        set(handles.Slider,'Value',handles.t_start);
        set(handles.Slider,'Min',handles.t_start);
        set(handles.Slider,'Max',handles.t_end);

    end
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');

guidata(hObject,handles);

function WindowText_ButtonDownFcn(hObject, eventdata, handles)

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


%% Loading of codebook
function MovieButton_Callback(hObject, eventdata, handles)

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

% If the user has indeed entered files
if ~isequal(filename3,0) || ~isequal(pathname3,0)

    load((fullfile(pathname3, filename3)));
    assignin('base','CodeBook', CodeBook);
    handles.CodeBook = CodeBook;
      
    handles.IsCodeBookLoaded = 1;
end

guidata(hObject,handles);


%% TR text entry
function TRText_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.TR = str2double(get(hObject,'String'));    
    set(hObject,'BackgroundColor', [0.4 0.6 0.4]);
    
    handles.IsTREntered = 1;
    
    if handles.IsTREntered && handles.IsWEntered && handles.IsISFCDataLoaded
        handles.t_start = (handles.TR*handles.W)-1;
        handles.t_end = (size(handles.ISFC_Data{1},2)-1)*handles.TR + handles.t_start;

        set(handles.Slider,'Value',handles.t_start);
        set(handles.Slider,'Min',handles.t_start);
        set(handles.Slider,'Max',handles.t_end);
    end
else 
    set(hObject,'BackgroundColor', [0.93 0.84 0.84]);
end

guidata(hObject,handles);


function TRText_CreateFcn(hObject, eventdata, handles)

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

guidata(hObject,handles);



function TRText_ButtonDownFcn(hObject, eventdata, handles)

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



%% Step text entry
function StepText_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)
    
    handles.Step = 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 StepText_CreateFcn(hObject, eventdata, handles)

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

guidata(hObject,handles);

function StepText_ButtonDownFcn(hObject,eventdata,handles)

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


%% Save text entry
function SaveText_Callback(hObject, eventdata, handles)

% If the high-pass takes a reasonable value, then we validate it
if (~isempty(get(hObject,'String')))
    
    handles.SaveName = 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 SaveText_CreateFcn(hObject, eventdata, handles)

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

guidata(hObject,handles);


function SaveText_ButtonDownFcn(hObject, eventdata, handles)

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