headfix_GUI_camera.m

function varargout = headfix_GUI_camera(varargin)
% HEADFIX_GUI_CAMERA MATLAB code for headfix_GUI_camera.fig
%      HEADFIX_GUI_CAMERA, by itself, creates a new HEADFIX_GUI_CAMERA or raises the existing
%      singleton*.
%
%      H = HEADFIX_GUI_CAMERA returns the handle to a new HEADFIX_GUI_CAMERA or the handle to
%      the existing singleton*.
%
%      HEADFIX_GUI_CAMERA('CALLBACK',hObject,eventData,handles,...) calls the local
%      function named CALLBACK in HEADFIX_GUI_CAMERA.M with the given input arguments.
%
%      HEADFIX_GUI_CAMERA('Property','Value',...) creates a new HEADFIX_GUI_CAMERA or raises the
%      existing singleton*.  Starting from the left, property value pairs are
%      applied to the GUI before headfix_GUI_camera_OpeningFcn gets called.  An
%      unrecognized property name or invalid value makes property application
%      stop.  All inputs are passed to headfix_GUI_camera_OpeningFcn via varargin.
%
%      *See GUI Options on GUIDE's Tools menu.  Choose "GUI allows only one
%      instance to run (singleton)".
%
% See also: GUIDE, GUIDATA, GUIHANDLES

% Edit the above text to modify the response to help headfix_GUI_camera

% Last Modified by GUIDE v2.5 20-May-2022 13:48:56

% cd 'F:\acads\Stuber lab\headfix'; %Change to directory

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

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

% Update handles structure
guidata(hObject, handles);

% This sets up the initial plot - only do when we are invisible
% so window can get raised using headfix_GUI_camera.
% if strcmp(get(hObject,'Visible'),'off')
%     plot(rand(5));
% end

global actvAx saveDir cam

mainPath = 'C:\Users\namboodirilab\OneDrive - University of California, San Francisco\Behavioral_acquisition_and_analysis';
addpath(mainPath)
saveDir = [mainPath '\data\'];          % where to save data

actvAx  = handles.activityAxes;         % handle for activity plot

% Find available serial ports
serialInfo = instrhwinfo('serial');
port = serialInfo.AvailableSerialPorts;
if ~isempty(port)
    set(handles.availablePorts,'String',port)
end

%%
% Change window title
set(gcf,'name','Head-fixed behavior')

set(handles.csproperties, 'Enable', 'off');
set(handles.lickproperties, 'Enable', 'off');
set(handles.experimentmode, 'Enable', 'on');
set(handles.uploadButton, 'Enable', 'on');
set(handles.openButton, 'Enable', 'off');
set(handles.backgroundsolenoid, 'Enable', 'off');
set(handles.T_bgd, 'Enable', 'off');
set(handles.r_bgd, 'Enable', 'off');
set(handles.mindelaybgdtocue, 'Enable', 'off'); 
set(handles.mindelayfxdtobgd, 'Enable', 'off');
set(handles.totPoisssolenoid, 'Enable', 'off');
set(handles.checkboxtrialbytrial, 'Enable', 'off');
set(handles.checkboxrandlaser, 'Enable', 'off');
set(handles.lasertrialbytrial, 'Enable', 'off');
set(handles.laserlatency, 'Enable', 'off');
set(handles.laserduration, 'Enable', 'off');
set(handles.laserpulseperiod, 'Enable', 'off');
set(handles.laserpulseoffperiod, 'Enable', 'off');
set(handles.CS1lasercheck, 'Enable', 'off');
set(handles.CS2lasercheck, 'Enable', 'off');
set(handles.CS3lasercheck, 'Enable', 'off');
set(handles.CS4lasercheck, 'Enable', 'off');
set(handles.Rewardlasercheck, 'Enable', 'off');
set(handles.checkboxintervaldistribution, 'Enable', 'off');
set(handles.maxdelaycuetovacuum, 'Enable', 'off');
set(handles.meanITI, 'Enable', 'off');
set(handles.maxITI, 'Enable', 'off');
set(handles.minITI, 'Enable', 'off');
set(handles.testcs1, 'Enable', 'off');
set(handles.testcs2, 'Enable', 'off');
set(handles.testcs3, 'Enable', 'off');
set(handles.testlaser, 'Enable', 'off');
set(handles.solenoid1Button, 'Enable', 'off');
set(handles.solenoid2Button, 'Enable', 'off');
set(handles.solenoid3Button, 'Enable', 'off');
set(handles.solenoid4Button, 'Enable', 'off');
set(handles.lickretractsolenoid1Button, 'Enable','off')
set(handles.lickretractsolenoid2Button, 'Enable','off')
set(handles.primesolenoid1, 'Enable', 'off');
set(handles.primesolenoid2, 'Enable', 'off');
set(handles.primesolenoid3, 'Enable', 'off');
set(handles.primesolenoid4, 'Enable', 'off');
set(handles.primelickretractsolenoid1, 'Enable','off');
set(handles.primelickretractsolenoid2, 'Enable','off');
set(handles.clearlick1rewards, 'Enable','off');
set(handles.clearlick2rewards, 'Enable','off');


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

% --- Executes during object creation, after setting all properties.
% adjust the size of the gui
function figure1_CreateFcn(hObject, eventdata, handles) 
% hObject    handle to figure1 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called
set(hObject,'Units','pixels','Position',[60 80 1500 870])

% --- Outputs from this function are returned to the command line.
function varargout = headfix_GUI_camera_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;


% --------------------------------------------------------------------
function FileMenu_Callback(~, eventdata, handles)
% hObject    handle to FileMenu (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)


% --------------------------------------------------------------------
function prefs_Callback(~, eventdata, handles)
% hObject    handle to prefs (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)


% --------------------------------------------------------------------
function CloseMenuItem_Callback(hObject, eventdata, handles)
% hObject    handle to CloseMenuItem (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
selection = questdlg(['Close ' get(handles.figure1,'Name') '?'],...
                     ['Close ' get(handles.figure1,'Name') '...'],...
                     'Yes','No','Yes');
if strcmp(selection,'No')
    return;
end

delete(handles.figure1)


% --- Executes during object deletion, before destroying properties.
function figure1_DeleteFcn(hObject, eventdata, handles)
% hObject    handle to figure1 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

instrreset
if exist('s','var')
    fclose(s)
end


% --- Executes on button press in refreshButton.
function refreshButton_Callback(hObject, eventdata, handles)
% hObject    handle to refreshButton (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

serialInfo = instrhwinfo('serial');                             % get info on connected serial ports
port = serialInfo.AvailableSerialPorts;                         % get names of ports
if ~isempty(port)
    set(handles.availablePorts,'String',port)                   % update list of ports available
else
    set(handles.availablePorts,'String', ...
        'none found, please check connection and refresh')      % if none, indicate so
end


% --- Executes on button press in openButton.
function openButton_Callback(hObject, eventdata, handles)
% opens serial port (identified by user) for communication with arduino

global s cam


portList = get(handles.availablePorts,'String');    % get list from popup menu
selected = get(handles.availablePorts,'Value');     % find which is selected
port     = portList{selected};                      % selected port

s = serial(port,'BaudRate',57600,'Timeout',1);    % setup serial port with arduino, specify the terminator as a LF ('\n' in Arduino)
fopen(s)                                            % open serial port with arduino
% get(s)
set(handles.openButton,'String','Wait 5s');
pause(5);
set(handles.openButton,'String','Link');

set(handles.port,'String',port)                     % write out port selected in menu
%set(handles.sendButton,'Enable','on')               % enable 'send' button
set(handles.startButton,'Enable','off')             % disable 'send' button
set(handles.closeButton,'Enable','on')              % enable 'unlink' button
set(handles.openButton,'Enable','off')              % disable 'link' button
set(handles.refreshButton,'Enable','off')           % disable 'refresh' button

selectedmode = get(handles.experimentmode, 'Value');
if selectedmode == 1 || selectedmode == 4 || selectedmode ==6
    set(handles.sendButton,'Enable','on') 
    set(handles.csproperties, 'Enable', 'on');
    set(handles.checkboxtrialbytrial, 'Enable', 'on');
    set(handles.checkboxrandlaser, 'Enable', 'on');
    set(handles.lasertrialbytrial, 'Enable', 'on');
    set(handles.laserlatency, 'Enable', 'on');
    set(handles.laserduration, 'Enable', 'on');
    set(handles.laserpulseperiod, 'Enable', 'on');
    set(handles.laserpulseoffperiod, 'Enable', 'on');
    set(handles.CS1lasercheck, 'Enable', 'on');
    set(handles.CS2lasercheck, 'Enable', 'on');
    set(handles.CS3lasercheck, 'Enable', 'on');
    set(handles.CS4lasercheck, 'Enable', 'on');
    set(handles.Rewardlasercheck, 'Enable', 'on');
    set(handles.checkboxintervaldistribution, 'Enable', 'on');
    set(handles.maxdelaycuetovacuum, 'Enable', 'on');
    set(handles.meanITI, 'Enable', 'on');
    set(handles.maxITI, 'Enable', 'on');
    set(handles.minITI, 'Enable', 'on');
    set(handles.backgroundsolenoid, 'Enable', 'on');
    set(handles.T_bgd, 'Enable', 'on');
    set(handles.r_bgd, 'Enable', 'on');
    set(handles.mindelaybgdtocue, 'Enable', 'on'); 
    set(handles.mindelayfxdtobgd, 'Enable', 'on');    
elseif selectedmode == 2
    set(handles.sendButton,'Enable','on') 
    set(handles.backgroundsolenoid, 'Enable', 'on');
    set(handles.T_bgd, 'Enable', 'on');
    set(handles.r_bgd, 'Enable', 'on');
    set(handles.mindelaybgdtocue, 'Enable', 'on'); 
    set(handles.mindelayfxdtobgd, 'Enable', 'on');
    set(handles.totPoisssolenoid, 'Enable', 'on');
elseif selectedmode == 3 || selectedmode == 7
    set(handles.sendButton,'Enable','on') 
    set(handles.lickproperties, 'Enable', 'on');
elseif selectedmode == 5
    set(handles.testserialport, 'Enable', 'on');
end


% --- Executes on selection change in experimentmode.
function experimentmode_Callback(hObject, eventdata, handles)
% hObject    handle to experimentmode (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: contents = cellstr(get(hObject,'String')) returns experimentmode contents as cell array
%        contents{get(hObject,'Value')} returns selected item from experimentmode

set(handles.uploadButton, 'Enable', 'on');


% --- Executes on button press in uploadButton.
function uploadButton_Callback(hObject, eventdata, handles)
% hObject    handle to uploadButton (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
portList = get(handles.availablePorts,'String');    % get list from popup menu
selected = get(handles.availablePorts,'Value');     % find which is selected
port     = portList{selected};                      % selected port
           
basecmd = strcat('"C:\Program Files (x86)\Arduino\hardware\tools\avr/bin/avrdude" -C"C:\Program Files (x86)\Arduino\hardware\tools\avr/etc/avrdude.conf" -v -patmega2560 -cwiring -P',port,' -b115200 -D -Uflash:w:');
selectedmode = get(handles.experimentmode,'Value');

if selectedmode == 1
    [status,cmdout] = dos(strcat(basecmd,'C:\Users\namboodirilab\Desktop\Behavioral_acquisition_and_analysis\uploads\Namlab_behavior_cues.ino.hex',':i'));
elseif selectedmode == 2
    [status,cmdout] = dos(strcat(basecmd,'C:\Users\namboodirilab\Desktop\Behavioral_acquisition_and_analysis\uploads\Namlab_behavior_randomrewards.ino.hex',':i'));
elseif selectedmode == 3
    [status,cmdout] = dos(strcat(basecmd,'C:\Users\namboodirilab\Desktop\Behavioral_acquisition_and_analysis\uploads\Namlab_behavior_lickforreward.ino.hex',':i'));
elseif selectedmode == 4
    [status,cmdout] = dos(strcat(basecmd,'C:\Users\namboodirilab\Desktop\Behavioral_acquisition_and_analysis\uploads\Namlab_behavior_decisionmaking.ino.hex',':i'));
elseif selectedmode == 5
    [status,cmdout] = dos(strcat(basecmd,'C:\Users\namboodirilab\Desktop\Behavioral_acquisition_and_analysis\uploads\Serial_port_testing.ino.hex',':i'));
elseif selectedmode == 6
    [status,cmdout] = dos(strcat(basecmd,'C:\Users\namboodirilab\Desktop\Behavioral_acquisition_and_analysis\uploads\Namlab_behavior_ramptiming.ino.hex',':i'));    
elseif selectedmode == 7
    [status,cmdout] = dos(strcat(basecmd,'C:\Users\namboodirilab\Desktop\Behavioral_acquisition_and_analysis\uploads\Namlab_behavior_delaydiscounting_automated.ino.hex',':i'));    
end


if contains(cmdout, 'avrdude done.') && status==0
    set(handles.uploadButton, 'String', 'Successfully uploaded');
    set(handles.experimentmode, 'Enable', 'off');
    set(handles.uploadButton, 'Enable','off');
    set(handles.openButton, 'Enable','on');
else
    set(handles.uploadButton, 'String', 'Unable to upload');
    pause(5);
    set(handles.uploadButton, 'String', 'Upload');
end


% --- Executes on button press in closeButton.
function closeButton_Callback(hObject, eventdata, handles)

global s
fclose(s)
instrreset                                          % "closes serial"
set(handles.port,'String','port not selected')      % remove port from menu
set(handles.startButton,'Enable','off')             % turn off 'start' button
set(handles.stopButton,'Visible','on')
set(handles.stopButton,'Enable','off')              % turn off 'stop' button
set(handles.closeButton,'Enable','off')             % turn off 'unlink' button (self)
set(handles.openButton,'Enable','off')               % turn on 'link' button
set(handles.refreshButton,'Enable','on')            % turn on 'refresh' button
set(handles.sendButton,'Enable','off')
set(handles.experimentmode,'Enable','on')
set(handles.uploadButton,'Enable','on')
set(handles.uploadButton,'String','Upload')
set(handles.csproperties,'Enable','off')
set(handles.lickproperties,'Enable','off')
set(handles.backgroundsolenoid, 'Enable', 'off');
set(handles.T_bgd, 'Enable', 'off');
set(handles.r_bgd, 'Enable', 'off');
set(handles.mindelaybgdtocue, 'Enable', 'off'); 
set(handles.mindelayfxdtobgd, 'Enable', 'off');
set(handles.totPoisssolenoid, 'Enable', 'off');
set(handles.checkboxtrialbytrial, 'Enable', 'off');
set(handles.checkboxrandlaser, 'Enable', 'off');
set(handles.lasertrialbytrial, 'Enable', 'off');
set(handles.laserlatency, 'Enable', 'off');
set(handles.laserduration, 'Enable', 'off');
set(handles.laserpulseperiod, 'Enable', 'off');
set(handles.laserpulseoffperiod, 'Enable', 'off');
set(handles.CS1lasercheck, 'Enable', 'off');
set(handles.CS2lasercheck, 'Enable', 'off');
set(handles.CS3lasercheck, 'Enable', 'off');
set(handles.CS4lasercheck, 'Enable', 'off');
set(handles.Rewardlasercheck, 'Enable', 'off');
set(handles.checkboxintervaldistribution, 'Enable', 'off');
set(handles.maxdelaycuetovacuum, 'Enable', 'off');
set(handles.meanITI, 'Enable', 'off');
set(handles.maxITI, 'Enable', 'off');
set(handles.minITI, 'Enable', 'off');

set(handles.testcs1, 'Enable', 'off');
set(handles.testcs2, 'Enable', 'off');
set(handles.testcs3, 'Enable', 'off');
set(handles.testlaser, 'Enable', 'off');
set(handles.testserialport, 'Enable', 'off');
set(handles.solenoid1Button, 'Enable', 'off');
set(handles.solenoid2Button, 'Enable', 'off');
set(handles.solenoid3Button, 'Enable', 'off');
set(handles.solenoid4Button, 'Enable', 'off');
set(handles.lickretractsolenoid1Button, 'Enable','off');
set(handles.lickretractsolenoid2Button, 'Enable','off');
set(handles.primesolenoid1, 'Enable', 'off');
set(handles.primesolenoid2, 'Enable', 'off');
set(handles.primesolenoid3, 'Enable', 'off');
set(handles.primesolenoid4, 'Enable', 'off');
set(handles.primelickretractsolenoid1, 'Enable','off');
set(handles.primelickretractsolenoid2, 'Enable','off');
set(handles.clearlick1rewards, 'Enable','off');
set(handles.clearlick2rewards, 'Enable','off');



% --- Executes on button press in solenoid1Button.
function solenoid1Button_Callback(hObject, eventdata, handles)

global s
fprintf(s,'A');              % Send solenoid signal to arduino; 65 in the Arduino is the ASCII code for A


% --- Executes on button press in solenoid2Button.
function solenoid2Button_Callback(hObject, eventdata, handles)
% hObject    handle to solenoid2Button (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

global s
fprintf(s,'D');              % Send solenoid signal to arduino; 68 in the Arduino is the ASCII code for D


% --- Executes on button press in solenoid3Button.
function solenoid3Button_Callback(hObject, eventdata, handles)
% hObject    handle to solenoid3Button (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

global s 
fprintf(s, 'G');        % Send solenoid signal to arduino; 71 in the Arduino is the ASCII code for G
    
% --- Executes on button press in solenoid4Button.
function solenoid4Button_Callback(hObject, eventdata, handles)
% hObject    handle to solenoid4Button (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

global s
fprintf(s, 'J');       % Send solenoid signal to arduino; 74 in Arduino is the ASCII code for J


% --- Executes on button press in lickretractsolenoid1Button.
function lickretractsolenoid1Button_Callback(hObject, eventdata, handles)
% hObject    handle to lickretractsolenoid1Button (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

global s
fprintf(s, 'M');       % Send lickretractsolenoid signal to arduino; 77 in Arduino is teh ASCII code for M


% --- Executes on button press in lickretractsolenoid2Button.
function lickretractsolenoid2Button_Callback(hObject, eventdata, handles)
% hObject    handle to lickretractsolenoid2Button (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

global s
fprintf(s, 'P');       % Send lickretractsolenoid signal to arduino; 80 in Arduino is teh ASCII code for P


% --- Executes on button press in vacuumButton.
function vacuumButton_Callback(hObject, eventdata, handles)
% hObject    handle to vacuumButton (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

global s
fprintf(s,'V');              % Send vacuum signal to arduino; 86 in the Arduino is the ASCII code for V


% --- Executes on button press in primesolenoid1.
function primesolenoid1_Callback(hObject, eventdata, handles)
% hObject    handle to primesolenoid1 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hint: get(hObject,'Value') returns toggle state of primesolenoid1
global s

if get(hObject,'Value') == get(hObject,'Max')
    fprintf(s,'B');              % Send prime solenoid signal to arduino; 66 in the Arduino is the ASCII code for B
else
    fprintf(s,'C');              % Send stop solenoid signal to arduino; 67 in the Arduino is the ASCII code for C
end

% --- Executes on button press in primesolenoid2.
function primesolenoid2_Callback(hObject, eventdata, handles)
% hObject    handle to primesolenoid2 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hint: get(hObject,'Value') returns toggle state of primesolenoid2
global s

if get(hObject,'Value') == get(hObject,'Max')
    fprintf(s,'E');              % Send prime solenoid signal to arduino; 69 in the Arduino is the ASCII code for E
else
    fprintf(s,'F');              % Send stop solenoid signal to arduino; 70 in the Arduino is the ASCII code for F
end

% --- Executes on button press in primesolenoid3.
function primesolenoid3_Callback(hObject, eventdata, handles)
% hObject    handle to primesolenoid3 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hint: get(hObject,'Value') returns toggle state of primesolenoid3
global s

if get(hObject,'Value') == get(hObject,'Max')
    fprintf(s, 'H');            % Send prime solenoid signal to arduino; 72 in the Arduino is the ASCII code for H
else
    fprintf(s, 'I');            % Send prime solenoid signal to arduino; 73 in the Arduino is the ASCII code for I
end

% --- Executes on button press in primesolenoid4.
function primesolenoid4_Callback(hObject, eventdata, handles)
% hObject    handle to primesolenoid4 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hint: get(hObject,'Value') returns toggle state of primesolenoid4
global s

if get(hObject,'Value') == get(hObject,'Max')
    fprintf(s, 'K');            % Send prime solenoid signal to arduino; 75 in the Arduino is the ASCII code for K
else
    fprintf(s, 'L');            % Send prime solenoid signal to arduino; 76 in the Arduino is the ASCII code for L
end

% --- Executes on button press in primelickretractsolenoid1.
function primelickretractsolenoid1_Callback(hObject, eventdata, handles)
% hObject    handle to primelickretractsolenoid1 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hint: get(hObject,'Value') returns toggle state of primelickretractsolenoid1
global s

if get(hObject,'Value') == get(hObject,'Max')
    fprintf(s, 'N');            % Send prime lickretractsolenoid signal to arduino; 78 in the Arduino is the ASCII code for N
else
    fprintf(s, 'O');            % Send prime lickretractsolenoid signal to arduino; 79 in the Arduino is the ASCII code for O
end

% --- Executes on button press in primelickretractsolenoid2.
function primelickretractsolenoid2_Callback(hObject, eventdata, handles)
% hObject    handle to primelickretractsolenoid2 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hint: get(hObject,'Value') returns toggle state of primelickretractsolenoid2
global s

if get(hObject,'Value') == get(hObject,'Max')
    fprintf(s, 'Q');            % Send prime lickretractsolenoid signal to arduino; 81 in the Arduino is the ASCII code for Q
else
    fprintf(s, 'R');            % Send prime lickretractsolenoid signal to arduino; 82 in the Arduino is the ASCII code for R
end


% --- Executes on button press in clearlick1rewards.
function clearlick1rewards_Callback(hObject, eventdata, handles)
% hObject    handle to clearlick1rewards (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
global s
fprintf(s,'Y');              % Send clear lick 1 rewards signal to arduino; Y in the Arduino is the ASCII code for 89
set(handles.clearlick1rewards,'Enable','off')


% --- Executes on button press in clearlick2rewards.
function clearlick2rewards_Callback(hObject, eventdata, handles)
% hObject    handle to clearlick2rewards (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
global s
fprintf(s,'Z');              % Send clear lick 2 rewards signal to arduino; Y in the Arduino is the ASCII code for 90
set(handles.clearlick2rewards,'Enable','off')


% --- Executes on button press in testcs1.
function testcs1_Callback(hObject, eventdata, handles)
% hObject    handle to testcs1 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
global s
fprintf(s,'2');              % Send CS1 signal to arduino; 50 in the Arduino is the ASCII code for 2
flushinput(s)


% --- Executes on button press in testcs2.
function testcs2_Callback(hObject, eventdata, handles)
% hObject    handle to testcs2 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
global s
fprintf(s,'3');              % Send CS2 signal to arduino; 51 in the Arduino is the ASCII code for 3
flushinput(s)

% --- Executes on button press in testcs3.
function testcs3_Callback(hObject, eventdata, handles)
% hObject    handle to testcs3 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
global s
fprintf(s,'4');              % Send CS3 signal to arduino; 52 in the Arduino is the ASCII code for 4
flushinput(s)


% --- Executes on button press in testlaser.
function testlaser_Callback(hObject, eventdata, handles)
% hObject    handle to testlaser (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
global s
fprintf(s,'8');              % Send Laser signal to arduino; 56 in the Arduino is the ASCII code for 8
flushinput(s)


% --- Executes on button press in testserialport.
function testserialport_Callback(hObject, eventdata, handles)
% hObject    handle to testserialport (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
global s running actvAx saveDir

mainPath = 'C:\Users\namboodirilab\OneDrive - University of California, San Francisco\Behavioral_acquisition_and_analysis';	
addpath(mainPath)	
saveDir = [mainPath '\serialtest\'];          % save serial testing data here

fprintf(s,'T');                          % Send test serial port signal to arduino; 84 in the Arduino is the ASCII code for T
set(hObject,'Enable','off');
serial_port_testing                      % Start figure for serial port connection signal


% --- Executes during object creation, after setting all properties.
function csproperties_CreateFcn(hObject, eventdata, handles)
% hObject    handle to csproperties (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called
% temp = {'Number of trials', 33, 33, 33;
%         'Frequency(kHz)', 12, 3, 7;
%         'Predicted solenoid', '1+3', '2+3', '1+3';
%         'Probability of solenoid', '100+100', '100+100', '0+100';
%         'Solenoid open time (ms)', '30+30', '30+30', '0+30';
%         'Cue duration (ms)', 1000, 1000, 1000;
%         'Delay to solenoid (ms)', '1500+3000', '1500+3000', '0+3000';
%         'Pulse tone (1) or not (0)', 0, 1, 1;
%         'Speaker number', 1, 2, 1;
%         'Go lick requirement', 1, 1, 0;
%         'Go lick tube (or solenoid)', 1, 2, 3;
%         'Sound(1), light(2) or both(3)', 1, 1, 1};

%%%% DEFAULT FOR TIMING TASK
% temp = {'Number of trials', 100, 0, 0;
%         'Frequency(kHz)', 12, 3, 7;
%         'Predicted solenoid', '1+3', '2+3', '1+3';
%         'Probability of solenoid', '0+80', '0+0', '0+0';
%         'Solenoid open time (ms)', '0+30', '30+30', '0+30';
%         'Cue duration (ms)', 0, 0, 0;
%         'Delay to solenoid (ms)', '1500+0', '1500+3000', '0+3000';
%         'Pulse tone (1) or not (0)', 0, 1, 1;
%         'Speaker number', 1, 2, 1;
%         'Light number', 1, 2, 1;
%         'Go lick requirement', 0, 0, 0;
%         'Go lick tube (or solenoid)', 1, 2, 3;
%         'Sound(1), light(2) or both(3)', 1, 1, 1};

%%%% DEFAULT FOR LICK REQUIREMENT TASK
% temp = {'Number of trials', 50, 50, 0;
%         'Frequency(kHz)', 12, 3, 7;
%         'Predicted solenoid', '5+3', '5+3', '1+3';
%         'Probability of solenoid', '100+100', '100+0', '0+100';
%         'Solenoid open time (ms)', '3000+30', '3000+30', '0+30';
%         'Cue duration (ms)', 2000, 2000, 0;
%         'Delay to solenoid (ms)', '0+0', '0+0', '0+3000';
%         'Pulse tone (1) or not (0)', 0, 1, 1;
%         'Speaker number', 1, 2, 1;
%         'Light number', 1, 2, 1
%         'Go lick requirement', 3, 0, 0;
%         'Go lick tube (or solenoid)', 1, 1, 3;
%         'Sound(1), light(2) or both(3)', 1, 1, 1};

%%%% DEFAULT FOR DECISION MAKING TASK
% temp = {'Number of trials', 33, 33, 33;
%         'Frequency(kHz)', 12, 3, 12;
%         'Predicted solenoid', '5+3', '6+3', '56+0';
%         'Probability of solenoid', '100+100', '100+100', '100+100';
%         'Solenoid open time (ms)', '3000+60', '3000+30', '3000+30';
%         'Cue duration (ms)', 2000, 2000, 2000;
%         'Delay to solenoid (ms)', '0+3000', '0+5000', '0+3000';
%         'Pulse tone (1) or not (0)', 0, 1, 0;
%         'Speaker number', 1, 2, 1;
%         'Light number', 1, 2, 2
%         'Go lick requirement', 1, 1, 1;
%         'Go lick tube (or solenoid)', 1, 2, 1;
%         'Sound(1), light(2) or both(3)', 1, 2, 3};

%%% DEFAULT FOR PAVLOVIAN CONDITIONING
% temp = {'Number of trials', 50, 50, 0;
%         'Frequency(kHz)', 12, 3, 7;
%         'Predicted solenoid', '1+3', '2+3', '1+3';
%         'Probability of solenoid', '0+100', '0+0', '0+100';
%         'Solenoid open time (ms)', '30+30', '30+30', '0+30';
%         'Cue duration (ms)', 2000, 2000, 2000;
%         'Delay to solenoid (ms)', '1500+3000', '1500+3000', '0+3000';
%         'Pulse tone (1) or not (0)', 0, 1, 1;
%         'Speaker number', 1, 2, 1;
%         'Light number', 1, 2, 1;
%         'Go lick requirement', 0, 0, 0;
%         'Go lick tube (or solenoid)', 1, 2, 3;
%         'Sound(1), light(2) or both(3)', 1, 1, 1};
    
%%% DEFAULT FOR LASER PAVLOVIAN
temp = {'Number of trials', 25, 25, 50, 0;
        'Frequency(kHz)', 12, 3, 5, 0;
        'Predicted solenoid', '5+3', '5+3', '1+3', '1+3';
        'Probability of solenoid', '0+100', '0+100', '0+0', '0+0';
        'Solenoid open time (ms)', '3000+40', '3000+40', '0+30', '0+40';
        'Cue duration (ms)', 1000, 1000, 1000, 1000;
        'Delay to solenoid (ms)', '0+3000', '0+3000', '0+3000', '0+3000';
        'Pulse tone (1) or not (0)', 0, 0, 1, 0;
        'Speaker number', 1, 2, 2, 2;
        'Light number', 1, 2, 1, 2;
        'Go lick requirement', 0, 0, 0, 0;
        'Go lick tube (or solenoid)', 1, 1, 3, 1;
        'Sound(1), light(2)', 1, 1, 1, 1;
        'Ramp max delay', 5000, 5000,1200, 5000;
        'Ramp exponent', 1, 1, 1, 1;
        'Increasing cue (1) or not(0)', 0, 0, 0, 0;
        'Delay to deliver the second cue if there is one', 0, 0, 0, 0;
        'Second cue type: sound(1) light(2) nocue(0)', 0, 0, 0, 0;
        'Second cue frequency', 5, 5, 5, 5;
        'Second cue speaker number', 1, 1, 2, 2;
        'Second cue light number', 1, 1, 1, 1};
set(hObject, 'Data', temp);

% --- Executes during object creation, after setting all properties.
function lickproperties_CreateFcn(hObject, eventdata, handles)
% hObject    handle to lickproperties (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called
temp = {'Number of licks required',  5, 5;
        'Fixed/variable check',      0, 0;
        'Predicted solenoid',        3, 3;
        'Probability of solenoid', 100, 0;
        'Solenoid open time (ms)',  30, 30;
        'Delay to solenoid (ms)',    0, 0;
        'Delay to next lick (ms)',100, 100;
        'Fixed/variable check',      0, 0;                
        'Min number of rewards',    100, 0;
        'Sound(1), light(2) or both(3)' 1 1;
        'Pulse tone (1) or not (0)' 0 1;
        'Sound Frequency (kHz)' 12 3;
        'Sound Duration (ms)' 0 1000;
        'Speaker number' 1 2;
        'Light number' 1 2;
        'Fixed side check',          0, 0};
set(hObject, 'Data', temp);


% --- Executes on button press in sendButton.
function sendButton_Callback(hObject, eventdata, handles)
% hObject    handle to sendButton (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
global s cam;


% checkboxcamera
if get(handles.checkboxcamera,'Value')==1
    imaqreset;
    cam = videoinput('winvideo',1, 'YUY2_960x720');
    cam.FramesPerTrigger = Inf;
    cam.ReturnedColorSpace = 'grayscale';
    cam.FrameGrabInterval = 1; % reduce the sampling rate by x
    cam.LoggingMode = 'disk';
    cam.ROIposition = [400 150 450 400];
    preview(cam);
%     
%     satisfy = 0;
%     while satisfy==0
%         satisfy = input('satisfied? 1:yes, 0:no');
%         if satisfy==1
%             break;
%         end
%         roi = input('roi?');
%         cam.ROIposition = roi;
%     end
end

% Retrieve inputs

% Experiment mode 
experimentmode = get(handles.experimentmode,'Value');

% Cues
csproperties = get(handles.csproperties, 'Data');
assignin('base', 'csproperties', csproperties);
numtrials    = cell2mat(csproperties(1,2:end));
CSfreq       = cell2mat(csproperties(2,2:end));
CSsolenoid   = [str2double(split(csproperties(3,2),'+'))',...
                str2double(split(csproperties(3,3),'+'))',...
                str2double(split(csproperties(3,4),'+'))',...
                str2double(split(csproperties(3,5),'+'))'];
CSprob       = [str2double(split(csproperties(4,2),'+'))',...
                str2double(split(csproperties(4,3),'+'))',...
                str2double(split(csproperties(4,4),'+'))',...
                str2double(split(csproperties(4,5),'+'))'];
CSopentime   = [str2double(split(csproperties(5,2),'+'))',...
                str2double(split(csproperties(5,3),'+'))',...
                str2double(split(csproperties(5,4),'+'))',...
                str2double(split(csproperties(5,5),'+'))'];
CSdur        = cell2mat(csproperties(6,2:end));
CS_t_fxd     = [str2double(split(csproperties(7,2),'+'))',...
                str2double(split(csproperties(7,3),'+'))',...
                str2double(split(csproperties(7,4),'+'))',...
                str2double(split(csproperties(7,5),'+'))'];
CSpulse      = cell2mat(csproperties(8,2:end));
CSspeaker    = cell2mat(csproperties(9,2:end));
CSlight      = cell2mat(csproperties(10,2:end));
golickreq    = cell2mat(csproperties(11,2:end));
golicktube   = cell2mat(csproperties(12,2:end));
CSsignal = cell2mat(csproperties(13, 2:end));
CSrampmaxdelay = cell2mat(csproperties(14, 2:end));
CSrampexp    = cell2mat(csproperties(15,2:end));
CSincrease = cell2mat(csproperties(16, 2:end));
delayforsecondcue = cell2mat(csproperties(17, 2:end));
secondcuetype = cell2mat(csproperties(18, 2:end));
secondcuefreq = cell2mat(csproperties(19,2:end));
secondcuespeaker = cell2mat(csproperties(20,2:end));
secondcuelight = cell2mat(csproperties(21,2:end));

%ITI
meanITI = get(handles.meanITI,'String');
meanITI = str2double(meanITI);
minITI = get(handles.minITI,'String');
minITI = str2double(minITI);
maxITI = get(handles.maxITI,'String');
maxITI = str2double(maxITI);
intervaldistribution = get(handles.checkboxintervaldistribution,'Value');
maxdelaycuetovacuum = get(handles.maxdelaycuetovacuum,'String');
maxdelaycuetovacuum = str2double(maxdelaycuetovacuum);

%Bgd solenoids

backgroundsolenoid = get(handles.backgroundsolenoid,'String'); 
backgroundsolenoid = str2double(backgroundsolenoid);
T_bgd = get(handles.T_bgd,'String'); 
T_bgd = str2double(T_bgd);
r_bgd = get(handles.r_bgd,'String');
r_bgd = str2double(r_bgd);
mindelaybgdtocue = get(handles.mindelaybgdtocue,'String');
mindelaybgdtocue = str2double(mindelaybgdtocue);
mindelayfxdtobgd = get(handles.mindelayfxdtobgd,'String');
mindelayfxdtobgd = str2double(mindelayfxdtobgd);
trialbytrialbgdsolenoidflag = get(handles.checkboxtrialbytrial,'Value');
totPoisssolenoid = get(handles.totPoisssolenoid,'String'); % Total Poisson solenoids to deliver
totPoisssolenoid = str2double(totPoisssolenoid);

% Lick dependent rewards 

lickproperties  = get(handles.lickproperties, 'Data');
assignin('base', 'lickproperties', lickproperties);
reqlicknum      = cell2mat(lickproperties(1,2:end));
variableratioflag = cell2mat(lickproperties(2,2:end));
licksolenoid    = cell2mat(lickproperties(3,2:end));
lickprob        = cell2mat(lickproperties(4,2:end));
lickopentime    = cell2mat(lickproperties(5,2:end));
delaytoreward   = cell2mat(lickproperties(6,2:end));
delaytolick     = cell2mat(lickproperties(7,2:end));
variableintervalflag = cell2mat(lickproperties(8,2:end));
minrewards      = cell2mat(lickproperties(9,2:end));
signaltolickreq = cell2mat(lickproperties(10,2:end));
soundsignalpulse   = cell2mat(lickproperties(11,2:end));
soundfreq       = cell2mat(lickproperties(12,2:end));
sounddur        = cell2mat(lickproperties(13,2:end));
lickspeaker     = cell2mat(lickproperties(14,2:end));
licklight       = cell2mat(lickproperties(15,2:end));
fixedsidecheck  = cell2mat(lickproperties(16,2:end));

%Laser
laserlatency = get(handles.laserlatency,'String');
laserlatency = str2double(laserlatency);
laserduration = get(handles.laserduration,'String');
laserduration = str2double(laserduration);
randlaserflag = get(handles.checkboxrandlaser,'Value');
laserpulseperiod = get(handles.laserpulseperiod,'String');
laserpulseperiod = str2double(laserpulseperiod);
laserpulseoffperiod = get(handles.laserpulseoffperiod,'String');
laserpulseoffperiod = str2double(laserpulseoffperiod);
lasertrialbytrialflag = get(handles.lasertrialbytrial,'Value');
CS1lasercheck = get(handles.CS1lasercheck, 'Value');
CS2lasercheck = get(handles.CS2lasercheck, 'Value');
CS3lasercheck = get(handles.CS3lasercheck, 'Value');
CS4lasercheck = get(handles.CS4lasercheck, 'Value');
Rewardlasercheck = get(handles.Rewardlasercheck, 'Value');

% Validate inputs
inputs = [numtrials, CSfreq, CSsolenoid, CSprob, CSopentime, CSdur, CS_t_fxd,...
          CSpulse, CSspeaker, golickreq, golicktube, CSsignal, meanITI, maxITI, minITI, intervaldistribution,...
          backgroundsolenoid, T_bgd, r_bgd, mindelaybgdtocue, mindelayfxdtobgd,...
          experimentmode, trialbytrialbgdsolenoidflag, totPoisssolenoid,...
          reqlicknum, licksolenoid, lickprob, lickopentime, delaytoreward, delaytolick,...
          minrewards, signaltolickreq, soundsignalpulse, soundfreq, sounddur, lickspeaker,...
          laserlatency, laserduration, randlaserflag, laserpulseperiod, laserpulseoffperiod,...
          lasertrialbytrialflag, maxdelaycuetovacuum, CSlight,variableratioflag, variableintervalflag,...
          licklight, CS1lasercheck, CS2lasercheck, CS3lasercheck, CS4lasercheck,...
          fixedsidecheck, Rewardlasercheck, CSrampmaxdelay, CSrampexp, CSincrease,delayforsecondcue,...
          secondcuetype, secondcuefreq, secondcuespeaker, secondcuelight]; % collect all inputs into array

negIn  = inputs < 0;
intIn  = inputs - fix(inputs);
negIn(53) = 0;
negIn(54) = 0;
negIn(55) = 0;
negIn(56) = 0; % Go lick requirement can be negative for no go task

if any([negIn intIn])
    errordlg('Invalid inputs')
    error('Invalid inputs')
end
if inputs(37) < inputs(137) || inputs(38) < inputs(137)
    errordlg('Invalid inputs')
    error('Invalid inputs: delay to solenoids must be bigger or same with delay to second cue')
end
if inputs(39) < inputs(138) || inputs(40) < inputs(138)
    errordlg('Invalid inputs')
    error('Invalid inputs: delay to solenoids must be bigger or same with delay to second cue')
end
if inputs(41) < inputs(139) || inputs(42) < inputs(139)
    errordlg('Invalid inputs')
    error('Invalid inputs: delay to solenoids must be bigger or same with delay to second cue')
end
if inputs(43) < inputs(140) || inputs(44) < inputs(140)
    errordlg('Invalid inputs')
    error('Invalid inputs: delay to solenoids must be bigger or same with delay to second cue')
end

% disable/enable certain options
set(handles.startButton,'Enable','on')
set(handles.sendButton,'Enable','off')
set(handles.csproperties,'Enable','off')
set(handles.lickproperties,'Enable','off')
set(handles.experimentmode,'Enable','off')
set(handles.uploadButton,'Enable','off')

set(handles.meanITI,'Enable','off')
set(handles.maxITI,'Enable','off')
set(handles.minITI,'Enable','off')
set(handles.maxdelaycuetovacuum,'Enable','off')

set(handles.backgroundsolenoid,'Enable','off')
set(handles.T_bgd,'Enable','off')
set(handles.r_bgd,'Enable','off')
set(handles.mindelaybgdtocue,'Enable','off')
set(handles.mindelayfxdtobgd,'Enable','off')
set(handles.checkboxtrialbytrial,'Enable','off')
set(handles.checkboxintervaldistribution,'Enable','off')
set(handles.totPoisssolenoid,'Enable','off')

set(handles.laserlatency,'Enable','off')
set(handles.laserduration,'Enable','off')
set(handles.checkboxrandlaser,'Enable','off')
set(handles.laserpulseperiod,'Enable','off')
set(handles.laserpulseoffperiod,'Enable','off')
set(handles.lasertrialbytrial,'Enable','off')
set(handles.CS1lasercheck,'Enable','off');
set(handles.CS2lasercheck,'Enable','off');
set(handles.CS3lasercheck,'Enable','off');
set(handles.CS4lasercheck,'Enable','off');
set(handles.Rewardlasercheck,'Enable','off');

set(handles.testcs1,'Enable','on')
set(handles.testcs2,'Enable','on')
set(handles.testcs3,'Enable','on')
set(handles.solenoid1Button,'Enable','on')
set(handles.primesolenoid1,'Visible','on')
set(handles.primesolenoid1,'Enable','on')
set(handles.solenoid2Button,'Enable','on')
set(handles.primesolenoid2,'Visible','on')
set(handles.primesolenoid2,'Enable','on')
set(handles.solenoid3Button,'Enable','on')
set(handles.primesolenoid3,'Visible','on')
set(handles.primesolenoid3,'Enable','on')
set(handles.solenoid4Button,'Enable','on')
set(handles.primesolenoid4,'Visible','on')
set(handles.primesolenoid4,'Enable','on')
set(handles.lickretractsolenoid1Button,'Enable','on')
set(handles.primelickretractsolenoid1,'Visible','on')
set(handles.primelickretractsolenoid1,'Enable','on')
set(handles.lickretractsolenoid2Button,'Enable','on')
set(handles.primelickretractsolenoid2,'Visible','on')
set(handles.primelickretractsolenoid2,'Enable','on')
set(handles.vacuumButton,'Enable','on')
set(handles.testlaser,'Enable','on')

params = sprintf('%G+', numtrials, CSfreq, CSsolenoid, CSprob, CSopentime,...
                 CSdur, CS_t_fxd, CSpulse, CSspeaker, golickreq, golicktube, CSsignal,...
                 meanITI, maxITI, minITI, intervaldistribution, backgroundsolenoid, T_bgd, r_bgd,...
                 mindelaybgdtocue, mindelayfxdtobgd, experimentmode, trialbytrialbgdsolenoidflag,... 
                 totPoisssolenoid, reqlicknum, licksolenoid, lickprob, lickopentime, delaytoreward,...
                 delaytolick, minrewards, signaltolickreq, soundsignalpulse, soundfreq, sounddur, lickspeaker,...
                 laserlatency, laserduration, randlaserflag, laserpulseperiod,...
                 laserpulseoffperiod, lasertrialbytrialflag, maxdelaycuetovacuum, CSlight,...
                 variableratioflag,variableintervalflag,licklight,...
                 CS1lasercheck, CS2lasercheck, CS3lasercheck,CS4lasercheck,fixedsidecheck,...
                 Rewardlasercheck, CSrampmaxdelay, CSrampexp, CSincrease,delayforsecondcue,...
                 secondcuetype, secondcuefreq, secondcuespeaker, secondcuelight);
params = params(1:end-1);

% Run arduino code
fprintf(s,params);                                  % send info to arduino
flushinput(s)

% --- Executes on button press in startButton.
function startButton_Callback(hObject, eventdata, handles)

% global s running actvAx saveDir
global s running actvAx saveDir cam
% Retrieve inputs

% Experiment mode 
experimentmode = get(handles.experimentmode,'Value');

% Cues
csproperties = get(handles.csproperties, 'Data');
assignin('base', 'csproperties', csproperties);
numtrials    = cell2mat(csproperties(1,2:end));
CSfreq       = cell2mat(csproperties(2,2:end));
CSsolenoid   = [str2double(split(csproperties(3,2),'+'))',...
                str2double(split(csproperties(3,3),'+'))',...
                str2double(split(csproperties(3,4),'+'))',...
                str2double(split(csproperties(3,5),'+'))'];
CSprob       = [str2double(split(csproperties(4,2),'+'))',...
                str2double(split(csproperties(4,3),'+'))',...
                str2double(split(csproperties(4,4),'+'))',...
                str2double(split(csproperties(4,5),'+'))'];
CSopentime   = [str2double(split(csproperties(5,2),'+'))',...
                str2double(split(csproperties(5,3),'+'))',...
                str2double(split(csproperties(5,4),'+'))',...
                str2double(split(csproperties(5,5),'+'))'];
CSdur        = cell2mat(csproperties(6,2:end));
CS_t_fxd     = [str2double(split(csproperties(7,2),'+'))',...
                str2double(split(csproperties(7,3),'+'))',...
                str2double(split(csproperties(7,4),'+'))',...
                str2double(split(csproperties(7,5),'+'))'];
CSpulse      = cell2mat(csproperties(8,2:end));
CSspeaker    = cell2mat(csproperties(9,2:end));
CSlight      = cell2mat(csproperties(10,2:end));
golickreq    = cell2mat(csproperties(11,2:end));
golicktube   = cell2mat(csproperties(12,2:end));
CSsignal     = cell2mat(csproperties(13, 2:end));
CSrampmaxdelay = cell2mat(csproperties(14, 2:end));
CSrampexp    = cell2mat(csproperties(15,2:end));
CSincrease = cell2mat(csproperties(16, 2:end));
delayforsecondcue = cell2mat(csproperties(17, 2:end));
secondcuetype = cell2mat(csproperties(18, 2:end));
secondcuefreq = cell2mat(csproperties(19, 2:end));
secondcuespeaker = cell2mat(csproperties(20, 2:end));
secondcuelight = cell2mat(csproperties(21,2:end));

%ITI
meanITI = get(handles.meanITI,'String');
meanITI = str2double(meanITI);
maxITI = get(handles.maxITI,'String');
maxITI = str2double(maxITI);
minITI = get(handles.minITI,'String');
minITI = str2double(minITI);
intervaldistribution = get(handles.checkboxintervaldistribution,'Value');
maxdelaycuetovacuum = get(handles.maxdelaycuetovacuum,'String');
maxdelaycuetovacuum = str2double(maxdelaycuetovacuum);

%Bgd solenoids

backgroundsolenoid = get(handles.backgroundsolenoid,'String'); 
backgroundsolenoid = str2double(backgroundsolenoid);
T_bgd = get(handles.T_bgd,'String'); 
T_bgd = str2double(T_bgd);
r_bgd = get(handles.r_bgd,'String');
r_bgd = str2double(r_bgd);
mindelaybgdtocue = get(handles.mindelaybgdtocue,'String');
mindelaybgdtocue = str2double(mindelaybgdtocue);
mindelayfxdtobgd = get(handles.mindelayfxdtobgd,'String');
mindelayfxdtobgd = str2double(mindelayfxdtobgd);
trialbytrialbgdsolenoidflag = get(handles.checkboxtrialbytrial,'Value');
totPoisssolenoid = get(handles.totPoisssolenoid,'String'); % Total Poisson solenoids to deliver
totPoisssolenoid = str2double(totPoisssolenoid);

% Lick dependent rewards 

lickproperties  = get(handles.lickproperties, 'Data');
assignin('base', 'lickproperties', lickproperties);
reqlicknum      = cell2mat(lickproperties(1,2:end));
variableratioflag = cell2mat(lickproperties(2,2:end));
licksolenoid    = cell2mat(lickproperties(3,2:end));
lickprob        = cell2mat(lickproperties(4,2:end));
lickopentime    = cell2mat(lickproperties(5,2:end));
delaytoreward   = cell2mat(lickproperties(6,2:end));
delaytolick     = cell2mat(lickproperties(7,2:end));
variableintervalflag = cell2mat(lickproperties(8,2:end));
minrewards      = cell2mat(lickproperties(9,2:end));
signaltolickreq = cell2mat(lickproperties(10,2:end));
soundsignalpulse   = cell2mat(lickproperties(11,2:end));
soundfreq       = cell2mat(lickproperties(12,2:end));
sounddur        = cell2mat(lickproperties(13,2:end));
lickspeaker     = cell2mat(lickproperties(14,2:end));
licklight       = cell2mat(lickproperties(15,2:end));
fixedsidecheck  = cell2mat(lickproperties(16,2:end));

%Laser
laserlatency = get(handles.laserlatency,'String');
laserlatency = str2double(laserlatency);
laserduration = get(handles.laserduration,'String');
laserduration = str2double(laserduration);
randlaserflag = get(handles.checkboxrandlaser,'Value');
laserpulseperiod = get(handles.laserpulseperiod,'String');
laserpulseperiod = str2double(laserpulseperiod);
laserpulseoffperiod = get(handles.laserpulseoffperiod,'String');
laserpulseoffperiod = str2double(laserpulseoffperiod);
lasertrialbytrialflag = get(handles.lasertrialbytrial,'Value');
CS1lasercheck = get(handles.CS1lasercheck, 'Value');
CS2lasercheck = get(handles.CS2lasercheck, 'Value');
CS3lasercheck = get(handles.CS3lasercheck, 'Value');
CS4lasercheck = get(handles.CS4lasercheck, 'Value');
Rewardlasercheck = get(handles.Rewardlasercheck, 'Value');

% Validate inputs
inputs = [numtrials, CSfreq, CSsolenoid, CSprob, CSopentime, CSdur, CS_t_fxd,...
          CSpulse, CSspeaker, golickreq, golicktube, CSsignal, meanITI, maxITI, minITI, intervaldistribution,...
          backgroundsolenoid, T_bgd, r_bgd, mindelaybgdtocue, mindelayfxdtobgd,...
          experimentmode, trialbytrialbgdsolenoidflag, totPoisssolenoid,...
          reqlicknum, licksolenoid, lickprob, lickopentime, delaytoreward,...                
          delaytolick, minrewards, signaltolickreq, soundsignalpulse, soundfreq, sounddur, lickspeaker,...
          laserlatency, laserduration, randlaserflag, laserpulseperiod, laserpulseoffperiod,...
          lasertrialbytrialflag, maxdelaycuetovacuum, CSlight,variableratioflag,...
          variableintervalflag,licklight, CS1lasercheck,...
          CS2lasercheck, CS3lasercheck, CS4lasercheck, fixedsidecheck, Rewardlasercheck,...
          CSrampmaxdelay, CSrampexp, CSincrease, delayforsecondcue,...
          secondcuetype, secondcuefreq, secondcuespeaker, secondcuelight]; % collect all inputs into array
          
negIn  = inputs < 0;
intIn  = inputs - fix(inputs);
negIn(53) = 0;
negIn(54) = 0;
negIn(55) = 0;
negIn(56) = 0; % Go lick requirement can be negative for no go task

if any([negIn intIn])
    errordlg('Invalid inputs')
    error('Invalid inputs')
end
if inputs(37) < inputs(137) || inputs(38) < inputs(137)
    errordlg('Invalid inputs')
    error('Invalid inputs: delay to solenoids must be bigger or same with delay to second cue')
end
if inputs(39) < inputs(138) || inputs(40) < inputs(138)
    errordlg('Invalid inputs')
    error('Invalid inputs: delay to solenoids must be bigger or same with delay to second cue')
end
if inputs(41) < inputs(139) || inputs(42) < inputs(139)
    errordlg('Invalid inputs')
    error('Invalid inputs: delay to solenoids must be bigger or same with delay to second cue')
end
if inputs(43) < inputs(140) || inputs(44) < inputs(140)
    errordlg('Invalid inputs')
    error('Invalid inputs: delay to solenoids must be bigger or same with delay to second cue')
end

set(handles.licks1Edit,'String','0')
set(handles.licks2Edit,'String','0')
set(handles.licks3Edit,'String','0')
set(handles.cues1Edit,'String','0')
set(handles.cues2Edit,'String','0')
set(handles.cues3Edit,'String','0')
set(handles.cues4Edit,'String','0')
set(handles.light1Edit,'String','0')
set(handles.light2Edit,'String','0')
set(handles.light3Edit,'String','0')
set(handles.light4Edit,'String','0')
set(handles.bgdsolenoidsEdit,'String','0')
set(handles.fxdsolenoids1Edit,'String','0')
set(handles.fxdsolenoids2Edit,'String','0')
set(handles.fxdsolenoids3Edit,'String','0')
set(handles.fxdsolenoids4Edit,'String','0')
set(handles.lickretractsolenoid1Edit,'String','0')
set(handles.lickretractsolenoid2Edit,'String','0')
set(handles.primesolenoid1,'Visible','off')
set(handles.primesolenoid2,'Visible','off')
set(handles.primesolenoid3,'Visible','off')
set(handles.primesolenoid4,'Visible','off')
set(handles.primelickretractsolenoid1, 'Visible','off')
set(handles.primelickretractsolenoid2, 'Visible','off')

% disable/enable certain options
set(handles.startButton,'Enable','off')
set(handles.stopButton,'Enable','on')
set(handles.closeButton,'Enable','off')
set(handles.sendButton,'Enable','off')
set(handles.testcs1,'Enable','off')
set(handles.testcs2,'Enable','off')
set(handles.testcs3,'Enable','off')
set(handles.testlaser,'Enable','off')
set(handles.closeButton,'Enable','off')
set(handles.experimentmode,'Enable','off')
set(handles.uploadButton,'Enable','off')

if experimentmode==2
    set(handles.vacuumButton,'Enable', 'off')
end

if experimentmode==3 || experimentmode==7
    set(handles.clearlick1rewards,'Enable','on');
    set(handles.clearlick2rewards,'Enable','on');
end

fname = get(handles.fileName,'String');
format = 'yymmdd-HHMMSS';
date = datestr(now,format);

params = sprintf('%G+', numtrials, CSfreq, CSsolenoid, CSprob, CSopentime,...
                 CSdur, CS_t_fxd, CSpulse, CSspeaker, golickreq, golicktube, CSsignal,...
                 meanITI, maxITI, minITI, intervaldistribution, backgroundsolenoid, T_bgd, r_bgd, ...
                 mindelaybgdtocue, mindelayfxdtobgd, experimentmode, ...
                 trialbytrialbgdsolenoidflag, totPoisssolenoid, reqlicknum,...
                 licksolenoid, lickprob, lickopentime, delaytoreward, delaytolick,...
                 minrewards, signaltolickreq, soundsignalpulse, soundfreq, sounddur, lickspeaker,...
                 laserlatency, laserduration, randlaserflag, laserpulseperiod, laserpulseoffperiod,...
                 lasertrialbytrialflag, maxdelaycuetovacuum, CSlight,variableratioflag,...
                 variableintervalflag,licklight, CS1lasercheck,...
                 CS2lasercheck, CS3lasercheck,CS4lasercheck, fixedsidecheck, Rewardlasercheck,...
                 CSrampmaxdelay, CSrampexp, CSincrease, delayforsecondcue,...
                 secondcuetype, secondcuefreq, secondcuespeaker, secondcuelight);
             
params = params(1:end-1);
% disp(params)
% Run arduino code
fprintf(s,'0');                          % Signals to Arduino to start the experiment

if get(handles.checkboxcamera,'Value')==1
    logfile = VideoWriter([saveDir fname '_' date '.avi']);
    logfile.FrameRate = 15;
    cam.DiskLogger = logfile;
end
conditioning_prog_camera

% Reset GUI
set(handles.stopButton,'Visible','off')
% set(handles.stopButton,'Enable','off')             % disable 'start' button
set(handles.startButton,'Enable','off')             % disable 'start' button
set(handles.sendButton,'Enable','off')              % enable 'send' button
set(handles.closeButton,'Enable','on')              % enable 'unlink' button
set(handles.openButton,'Enable','off')              % disable 'link' button
set(handles.refreshButton,'Enable','off')           % disable 'refresh' button

set(handles.testcs1, 'Enable', 'off');
set(handles.testcs2, 'Enable', 'off');
set(handles.testcs3, 'Enable', 'off');
set(handles.testlaser, 'Enable', 'off');
set(handles.testserialport, 'Enable', 'off');
set(handles.solenoid1Button, 'Enable', 'off');
set(handles.solenoid2Button, 'Enable', 'off');
set(handles.solenoid3Button, 'Enable', 'off');
set(handles.solenoid4Button, 'Enable', 'off');
set(handles.lickretractsolenoid1Button, 'Enable','off')
set(handles.lickretractsolenoid2Button, 'Enable','off')
set(handles.primesolenoid1, 'Enable', 'off');
set(handles.primesolenoid2, 'Enable', 'off');
set(handles.primesolenoid3, 'Enable', 'off');
set(handles.primesolenoid4, 'Enable', 'off');
set(handles.primelickretractsolenoid1, 'Enable','off')
set(handles.primelickretractsolenoid2, 'Enable','off')

flushinput(s);                                  % clear serial input buffer



% --- Executes on button press in stopButton.
function stopButton_Callback(hObject, eventdata, handles)


global s running     
running = false;            % Stop running MATLAB code for monitoring arduino
fprintf(s,'1');              % Send stop signal to arduino; 49 in the Arduino is the ASCII code for 1

set(handles.stopButton,'Visible','off')
% set(handles.stopButton,'Enable','off')             % disable 'start' button
set(handles.startButton,'Enable','off')             % disable 'start' button
set(handles.sendButton,'Enable','off')              % enable 'send' button
set(handles.closeButton,'Enable','on')              % enable 'unlink' button
set(handles.openButton,'Enable','off')              % disable 'link' button
set(handles.refreshButton,'Enable','off')           % disable 'refresh' button

set(handles.testcs1, 'Enable', 'off');
set(handles.testcs2, 'Enable', 'off');
set(handles.testcs3, 'Enable', 'off')
set(handles.testlaser, 'Enable', 'off');
set(handles.testserialport, 'Enable', 'off');
set(handles.solenoid1Button, 'Enable', 'off');
set(handles.solenoid2Button, 'Enable', 'off');
set(handles.solenoid3Button, 'Enable', 'off');
set(handles.solenoid4Button, 'Enable', 'off');
set(handles.lickretractsolenoid1Button, 'Enable','off')
set(handles.lickretractsolenoid2Button, 'Enable','off')
set(handles.primesolenoid1, 'Enable', 'off');
set(handles.primesolenoid2, 'Enable', 'off');
set(handles.primesolenoid3, 'Enable', 'off');
set(handles.primesolenoid4, 'Enable', 'off');
set(handles.primelickretractsolenoid1, 'Enable','off')
set(handles.primelickretractsolenoid2, 'Enable','off')
set(handles.clearlick1rewards,'Enable','off');
set(handles.clearlick2rewards,'Enable','off');

function minITI_Callback(hObject, eventdata, handles)
% hObject    handle to minITI (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
% Hints: get(hObject,'String') returns contents of minITI as text
%        str2double(get(hObject,'String')) returns contents of minITI as a double
% --- Executes during object creation, after setting all properties.
function minITI_CreateFcn(hObject, eventdata, handles)
% hObject    handle to minITI (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called
% Hint: edit controls usually have a white background on Windows.
%       See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor','white');
end


% --- Executes on button press in checkboxcamera.
function checkboxcamera_Callback(hObject, eventdata, handles)
% hObject    handle to checkboxcamera (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hint: get(hObject,'Value') returns toggle state of checkboxcamera