function varargout = JOVE_GUI1(varargin)

gui_Singleton = 1;
gui_State = struct('gui_Name',       mfilename, ...
                   'gui_Singleton',  gui_Singleton, ...
                   'gui_OpeningFcn', @JOVE_GUI1_OpeningFcn, ...
                   'gui_OutputFcn',  @JOVE_GUI1_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

% --- Executes just before JOVE_GUI1 is made visible.
function JOVE_GUI1_OpeningFcn(hObject, eventdata, handles, varargin)

handles.output = hObject;

warning('off');

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

handles.Data = [];
handles.FuncLink = '';
handles.FuncFolder = '';

handles.c1 = [];
handles.c2 = [];
handles.c3 = [];

handles.IsFuncLoaded = 0;
handles.IsMotLoaded = 0;
handles.IsStructLoaded = 0;
handles.AreAllDataLoaded = 0;

handles.TR = 1;

handles.Mot = [];

% Makes the plots as we want
set(handles.CSFWMPlot,'Box','off');
set(handles.TransPlot,'Box','off');
set(handles.RotPlot,'Box','off');

set(handles.CSFWMPlot,'XTick',[]);
set(handles.TransPlot,'XTick',[]);

xlabel(handles.RotPlot,'Time [s]');

ylabel(handles.CSFWMPlot,'CSF/WM [a.u.]');
ylabel(handles.TransPlot,'Trans. [mm]');
ylabel(handles.RotPlot,'Rot. [deg]');

ylabel(handles.GMPlot,'GM voxels');

% Update handles structure
guidata(hObject, handles);


function varargout = JOVE_GUI1_OutputFcn(hObject, eventdata, handles) 
varargout{1} = handles.output;


%% Data button: fMRI data
function DataButton_Callback(hObject, eventdata, handles)

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

% If the user has indeed entered files
if ~isequal(filename1,0) || ~isequal(pathname1,0)
    
        tmp_idx = 1;
    
        % The files are loaded sequentially: File{t} contains the path
        % towards the t-th frame
        for t = 1:length(filename1)
            
            File{t} = fullfile(pathname1, filename1{t});
            
            if strcmp(File{t}(end-2:end),'img')
            else
                % Reads the frame
                tmp_header = spm_vol(File{tmp_idx});
                tmp = spm_read_vols(tmp_header);

                handles.Data(:,tmp_idx) = tmp(:);
                tmp_idx = tmp_idx + 1;
            end
        end
        
        % Link towards one of the functional files
        handles.FuncLink = fullfile(pathname1, filename1{t});
        
        handles.FuncFolder = fullfile(pathname1);
        
        % Confirms that functional data has been loaded
        handles.IsFuncLoaded = 1;
end

guidata(hObject,handles);
           

%% Data button: probabilistic tissue maps
function DataButton2_Callback(hObject, eventdata, handles)

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

% If the user has indeed entered files
if ~isequal(filename2,0) || ~isequal(pathname2,0)
    if handles.IsFuncLoaded == 1
        
        % Probabilistic tissue maps are binarized to be able to compute WM
        % and CSF regressors, as well as global signal
        handles.c1 = mapVolumeToVolume(fullfile(pathname2, filename2{1}),handles.FuncLink);
        handles.c1(handles.c1 < 0.99) = 0; handles.c1(handles.c1 >= 0.99) = 1;
        handles.c1 = logical(handles.c1(:));
        handles.c2 = mapVolumeToVolume(fullfile(pathname2, filename2{2}),handles.FuncLink);
        handles.c2(handles.c2 < 0.99) = 0; handles.c2(handles.c2 >= 0.99) = 1;
        handles.c2 = logical(handles.c2(:));
        handles.c3 = mapVolumeToVolume(fullfile(pathname2, filename2{3}),handles.FuncLink);
        handles.c3(handles.c3 < 0.99) = 0; handles.c3(handles.c3 >= 0.99) = 1;
        handles.c3 = logical(handles.c3(:));
    else
        
        errordlg('Please load functional data first !');
    end
    
    handles.IsStructLoaded = 1;
end

% Computes the CSF and WM regressors
handles.CSF_regressor = mean(handles.Data(handles.c2,:),1);
handles.CSF_regressor = handles.CSF_regressor - mean(handles.CSF_regressor);
handles.WM_regressor = mean(handles.Data(handles.c3,:),1);
handles.WM_regressor = handles.WM_regressor - mean(handles.WM_regressor);

guidata(hObject,handles);



%% Data button: motion file
function DataButton3_Callback(hObject, eventdata, handles)

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

handles.Mot = textread(fullfile(pathname3,filename3));
handles.Mot = handles.Mot(:,1:6);

handles.IsMotLoaded = 1;

guidata(hObject,handles);



%% Detrending radio switch
function DetrendingButton_Callback(hObject, eventdata, handles)

guidata(hObject,handles);


%% Regression popup
function RegressionButton_Callback(hObject, eventdata, handles)

guidata(hObject,handles);

function RegressionButton_CreateFcn(hObject, eventdata, handles)

Regression_Types = {'None','Const','Const|Lin','Const|Lin|Quad',...
    'Const|Lin|Quad|CSF','Const|Lin|Quad|CSF|WM','Const|Lin|Quad|CSF|WM|Mot'};

set(hObject,'String',Regression_Types);

guidata(hObject,handles);


%% Preprocessing button
function PreproButton_Callback(hObject, eventdata, handles)

% Data from all 3 tissue types
tmp_GM = handles.Data(handles.c1,:);
tmp_WM = handles.Data(handles.c2,:);
tmp_CSF = handles.Data(handles.c3,:);

% If we asked to detrend, detrending is performed
if get(handles.DetrendingButton,'Value') == 1
    tmp_GM = (detrend(tmp_GM'))';
    tmp_WM = (detrend(tmp_WM'))';
    tmp_CSF = (detrend(tmp_CSF'))';
end

% X is the regressor matrix
X = [];

% Given the subcase asked for, the matrix is updated
switch get(handles.RegressionButton,'Value')
    case 1
        
    case 2
        X = [X,ones(size(tmp_GM,2),1)];
    case 3
        X = [X,ones(size(tmp_GM,2),1),(1:size(tmp_GM,2))'/size(tmp_GM,2)];
    case 4
        X = [X,ones(size(tmp_GM,2),1),(1:size(tmp_GM,2))'/size(tmp_GM,2),((1:size(tmp_GM,2)).^2)'/size(tmp_GM,2)];
    case 5
        X = [X,ones(size(tmp_GM,2),1),(1:size(tmp_GM,2))'/size(tmp_GM,2),((1:size(tmp_GM,2)).^2)'/size(tmp_GM,2),handles.CSF_regressor'];
    case 6
        X = [X,ones(size(tmp_GM,2),1),(1:size(tmp_GM,2))'/size(tmp_GM,2),((1:size(tmp_GM,2)).^2)'/size(tmp_GM,2),handles.CSF_regressor',handles.WM_regressor'];
    case 7
        X = [X,ones(size(tmp_GM,2),1),(1:size(tmp_GM,2))'/size(tmp_GM,2),((1:size(tmp_GM,2)).^2)'/size(tmp_GM,2),handles.CSF_regressor',handles.WM_regressor',handles.Mot];
end

% If we asked for at least one regressor, then we regress out the
% covariates from the data
if get(handles.RegressionButton,'Value') > 1
    
    for vox = 1:size(tmp_GM,1)
        [~,tmp_GM(vox,:)] = y_regress_ss(tmp_GM(vox,:)',X);
        tmp_GM(vox,:) = tmp_GM(vox,:) + mean(tmp_GM(vox,:));
    end
    
    for vox = 1:size(tmp_WM,1)
        [~,tmp_WM(vox,:)] = y_regress_ss(tmp_WM(vox,:)',X);
        tmp_WM(vox,:) = tmp_WM(vox,:) + mean(tmp_WM(vox,:));
    end
    
    for vox = 1:size(tmp_CSF,1)
        [~,tmp_CSF(vox,:)] = y_regress_ss(tmp_CSF(vox,:)',X);
        tmp_CSF(vox,:) = tmp_CSF(vox,:) + mean(tmp_CSF(vox,:));
    end
end

% Plotting
handles.GMPlot = JOVE_PlotTimeCourses(handles.GMPlot,tmp_GM,handles.TR);
handles.CSFWMPlot = JOVE_PlotMotion(handles.CSFWMPlot,[handles.CSF_regressor',handles.WM_regressor'],handles.TR);
handles.TransPlot = JOVE_PlotMotion(handles.TransPlot,handles.Mot(:,1:3),handles.TR);
handles.RotPlot = JOVE_PlotMotion(handles.RotPlot,handles.Mot(:,4:6),handles.TR);

guidata(hObject,handles);


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

ISFC_VX = handles.Data;
ISFC_VX(~handles.c1,:) = NaN;

save(fullfile(handles.FuncFolder,['ISFC_VX']),'ISFC_VX');

guidata(hObject,handles);


function TRBox_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]);
else 
    set(hObject,'BackgroundColor', [0.93 0.84 0.84]);
end

guidata(hObject,handles);


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

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


function TRBox_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)

TRBox_CreateFcn(handles.TRBox, eventdata, handles);
set(handles.TRBox,'BackgroundColor',240/255*[1 1 1]);
RegressionButton_CreateFcn(handles.RegressionButton, eventdata, handles)
set(handles.DetrendingButton,'Value',0);
set(handles.RegressionButton,'Value',1);
set(handles.TRBox,'Enable','off');

handles.Data = [];
handles.FuncLink = '';
handles.FuncFolder = '';

handles.c1 = [];
handles.c2 = [];
handles.c3 = [];

handles.IsFuncLoaded = 0;
handles.IsMotLoaded = 0;
handles.IsStructLoaded = 0;
handles.AreAllDataLoaded = 0;

handles.TR = 1;

handles.Mot = [];

% Makes the plots as we want
set(handles.CSFWMPlot,'Box','off');
set(handles.TransPlot,'Box','off');
set(handles.RotPlot,'Box','off');

set(handles.CSFWMPlot,'XTick',[]);
set(handles.TransPlot,'XTick',[]);

xlabel(handles.RotPlot,'Time [s]');

ylabel(handles.CSFWMPlot,'CSF/WM [a.u.]');
ylabel(handles.TransPlot,'Trans. [mm]');
ylabel(handles.RotPlot,'Rot. [deg]');

ylabel(handles.GMPlot,'GM voxels');

cla(handles.GMPlot);
cla(handles.TransPlot);
cla(handles.RotPlot);
cla(handles.CSFWMPlot);

guidata(hObject,handles);