A01_fullProtocol_classicalCond.m

%% 
% HT-LMD - High-Throughput Learning, Memory, and Drug-Testing Platform for Small Aquatic Models
% Copyright (C) 2025 Gokul Rajan
%
% This program is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation, either version 3 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program. If not, see <https://www.gnu.org/licenses/>.

%% L&M protocols

%protocol 1 (full protocol - train/ctrl/reverse): bias 2' +  bias(flip) 2' + train x N + test 2' + test(flip) 2'
%protocol 2 (test): test1 2' + test2 2' (flip)
%protocol 3 (extinction): (test 1' + exposure 3") x N times


%% Clear the workspace and the screen
sca;
close all;
clearvars;

Screen('Preference', 'VisualDebugLevel', 1); % skip the initialization screen
Screen('Preference', 'SkipSyncTests', 1); % may lead to some  synch timimng issue; 

%% some initialization before we start

% Here we call some default settings for setting up Psychtoolbox
PsychDefaultSetup(2);

% Get the screen numbers
%screens = Screen('Screens');

% Draw to the external screen if avaliable
screenNumber = 2;
% to project stim

% Define black and white
white = WhiteIndex(screenNumber);
black = BlackIndex(screenNumber);
grey = white / 2;
inc = white - grey;

%% get BG
BGFullLocation = 'C:\Users\orger\Desktop\Gokul\stim\rev1.png';
BGFullImage = imread(BGFullLocation);

BGFullLocationRev = 'C:\Users\orger\Desktop\Gokul\stim\csfull.png';
BGFullImageRev = imread(BGFullLocationRev);

%%
% Open an on screen window
[window, windowRect] = PsychImaging('OpenWindow', screenNumber,  0.7);
% Screen('DrawTexture', window, BGFullTexture, [], [], 0);
% Screen('Flip', window);

%% setup arduino
ard = arduino('COM3', 'Uno'); % Initializes Arduino

% D9 for CS1 LED
% D10 for CS2 LED
% D11 for CSfull LED
% D12 for US LED
% D07 for shock

%writeDigitalPin(ard, 'D09', 1); % CS1 LED ON
%writeDigitalPin(ard, 'D09', 0); % CS1 LED OFF

%writeDigitalPin(ard, 'D10', 1); % CS2 LED ON
%writeDigitalPin(ard, 'D10', 0); % CS2 LED OFF

%writeDigitalPin(ard, 'D11', 1); % CSfull LED ON
%writeDigitalPin(ard, 'D11', 0); % CSfull LED OFF

%writeDigitalPin(ard, 'D12', 1); % US LED ON
%writeDigitalPin(ard, 'D12', 0); % US LED OFF

%writeDigitalPin(ard, 'D07', 1); % Shock ON
%writeDigitalPin(ard, 'D07', 0); % Shock OFF

%% more initialization stuff

% Get the size of the on screen window
[screenXpixels, screenYpixels] = Screen('WindowSize', window);

% Query the frame duration
ifi = Screen('GetFlipInterval', window);

% Get the centre coordinate of the window
[xCenter, yCenter] = RectCenter(windowRect);

% Set up alpha-blending for smooth (anti-aliased) lines
Screen('BlendFunction', window, 'GL_SRC_ALPHA', 'GL_ONE_MINUS_SRC_ALPHA');

%%
% Here we load in an image from file. 
csHalfLocation = ['C:\Users\orger\Desktop\Gokul\stim\cs1.png'];
csHalfImage = imread(csHalfLocation);
csHalfLocationRev='C:\Users\orger\Desktop\Gokul\stim\cs1.png';
csHalfImageRev=imread(csHalfLocationRev);

csFullLocation = ['C:\Users\orger\Desktop\Gokul\stim\csfull.png'];
csFullImage = imread(csFullLocation);
csFullLocationRev = ['C:\Users\orger\Desktop\Gokul\stim\rev1.png'];
csFullImageRev = imread(csFullLocation);

BGFullTexture = Screen('MakeTexture', window, BGFullImage);
BGFullTextureRev = Screen('MakeTexture', window, BGFullImageRev);

% %% CS bias evaluation %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% 
% % Bias check phase 1
% 
% if (strcmp(,'train') | strcmp(protocol,'ctrl')| strcmp(protocol,'reverse'))
% 
% % biasTime var is the time the projection stays on (on 1 side)
% biasTime=120;
% 
% 
% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% 
% if (strcmp(protocol,'train')| strcmp(protocol,'ctrl'))
% 
% % Get the size of the image
% [s1, s2, s3] = size(csHalfImage);
% 
% % Here we check if the image is too big to fit on the screen and abort if
% % it is. See ImageRescaleDemo to see how to rescale an image.
% if s1 > screenYpixels || s2 > screenYpixels
%     disp('ERROR! Image is too big to fit on the screen');
%     sca;
%     return;
% end
% 
% % Make the image into a texture
% csHalfTexture = Screen('MakeTexture', window, csHalfImage);
% 
% % Draw the image to the screen, unless otherwise specified PTB will draw
% % the texture full size in the center of the screen. We first draw the
% % image in its correct orientation.
% Screen('DrawTexture', window, csHalfTexture, [], [], 0);
% 
% % Bias check phase 1
% writeDigitalPin(ard, 'D9', 1); % CS1 LED ON
% % Flip to the screen
% Screen('Flip', window);
% % Wait for few seconds
% WaitSecs(biasTime);
% writeDigitalPin(ard, 'D9', 0); % CS1 LED off
% 
% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% % Bias phase 2 (flip)
% % Draw the image to the screen for a second time this time upside down and
% % drawn onto our updated blue background
% Screen('DrawTexture', window, csHalfTexture, [], [], 180);
% writeDigitalPin(ard, 'D10', 1); % CS2 LED ON
% % Flip to the screen
% Screen('Flip', window);
% WaitSecs(biasTime);
% writeDigitalPin(ard, 'D10', 0); % CS2 LED off
% 
% elseif (strcmp(protocol,'reverse'))
%     
%     % Get the size of the image
% [s1, s2, s3] = size(csHalfImageRev);
% 
% % Here we check if the image is too big to fit on the screen and abort if
% % it is. See ImageRescaleDemo to see how to rescale an image.
% if s1 > screenYpixels || s2 > screenYpixels
%     disp('ERROR! Image is too big to fit on the screen');
%     sca;
%     return;
% end
% 
% % Make the image into a texture
% csHalfTextureRev = Screen('MakeTexture', window, csHalfImageRev);
% 
% % Draw the image to the screen, unless otherwise specified PTB will draw
% % the texture full size in the center of the screen. We first draw the
% % image in its correct orientation.
% Screen('DrawTexture', window, csHalfTextureRev, [], [], 0);
% 
% % Bias check phase 1
% writeDigitalPin(ard, 'D9', 1); % CS1 LED ON
% % Flip to the screen
% Screen('Flip', window);
% % Wait for few seconds
% WaitSecs(biasTime);
% writeDigitalPin(ard, 'D9', 0); % CS1 LED Off
% 
%
% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% % Bias phase 2 (flip)
% % Draw the image to the screen for a second time this time upside down and
% % drawn onto our updated blue background
% Screen('DrawTexture', window, csHalfTextureRev, [], [], 180);
% writeDigitalPin(ard, 'D10', 1); % CS2 LED ON
% % Flip to the screen
% Screen('Flip', window);
% WaitSecs(biasTime);
% writeDigitalPin(ard, 'D10', 0); % CS2 LED Off
% 
%     
% end
% 
% end


%%

disp('press any key to start the experiment the stimulus');
pause('on');
pause()
pause('off');

%% 
for ii=1:4
    
    %% SELECT PROTOCOL SEQUENCE HERE
    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
    if ii==1 || ii==3 
        protocol='test';
    elseif ii==2
        protocol='train';
    elseif ii==3
        protocol='test';
    elseif ii==4
        protocol='exit';
    end

%% TRAINING PHASE %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

delay=2; % all in secs
isi=25; % rest between the reinforcement trials
shock=0.1; % duration of the actual shock in sec
trials=75; % # of trials

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
for tr=1:trials

    if (strcmp(protocol,'train')| strcmp(protocol,'ctrl'))

% Make the image into a texture
csFullTexture = Screen('MakeTexture', window, csFullImage);
    
    if tr==1
        WaitSecs(60); % wait few secs before starting training after bias evaluation; helps dispersion
    end
    
% Get the size of the image
[u1, u2, u3] = size(csFullImage);

% Here we check if the image is too big to fit on the screen and abort if
% it is. See ImageRescaleDemo to see how to rescale an image.
if u1 > screenYpixels || u2 > screenYpixels
    disp('ERROR! Image is too big to fit on the screen');
    sca;
    return;
end

% Draw the image to the screen, unless otherwise specified PTB will draw
% the texture full size in the center of the screen. We first draw the
% image in its correct orientation.
Screen('DrawTexture', window, csFullTexture, [], [], 0);
writeDigitalPin(ard, 'D11', 1); % CSfull LED ON
Screen('Flip', window); % Flip to the screen

% Wait for few secs for the US arrive
WaitSecs(delay);

writeDigitalPin(ard, 'D04', 1); % US LED ON
writeDigitalPin(ard, 'D07', 1); % Shock ON
WaitSecs(shock); % 70 msecs of shock
writeDigitalPin(ard, 'D04', 0); % US LED OFF
writeDigitalPin(ard, 'D07', 0); % Shock OFF

% Now fill the screen blank
Screen('DrawTexture', window, BGFullTexture, [], [], 0);
writeDigitalPin(ard, 'D11', 0); % CSfull LED OFF
% Flip to the screen
Screen('Flip', window);
WaitSecs(isi); %wait for isi before the next training trial

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

elseif (strcmp(protocol,'reverse'))
    
    % Make the image into a texture
csFullTextureRev = Screen('MakeTexture', window, csFullImageRev);

% for tr=1:trials
%     
%     if tr==1
%         WaitSecs(300); % wait few mins before starting training after bias evaluation
%     end
    
% Get the size of the image
[u1, u2, u3] = size(csFullImageRev);

% Here we check if the image is too big to fit on the screen and abort if
% it is. See ImageRescaleDemo to see how to rescale an image.
if u1 > screenYpixels || u2 > screenYpixels
    disp('ERROR! Image is too big to fit on the screen');
    sca;
    return;
end

% Draw the image to the screen, unless otherwise specified PTB will draw
% the texture full size in the center of the screen. We first draw the
% image in its correct orientation.
Screen('DrawTexture', window, BGFullTexture, [], [], 0);
writeDigitalPin(ard, 'D11', 1); % CSfull LED ON
Screen('Flip', window); % Flip to the screen

% Wait for few secs for the US arrive
WaitSecs(delay);

writeDigitalPin(ard, 'D12', 1); % US LED ON
writeDigitalPin(ard, 'D07', 1); % Shock ON
WaitSecs(shock); % 70 msecs of shock
writeDigitalPin(ard, 'D12', 0); % US LED OFF
writeDigitalPin(ard, 'D07', 0); % Shock OFF

% Now fill the screen blank
Screen('DrawTexture', window, BGFullTextureRev, [], [], 0);
writeDigitalPin(ard, 'D11', 0); % CSfull LED OFF
% Flip to the screen
Screen('Flip', window);
WaitSecs(isi); %wait for another minute before the next training trial
    
    end
end


%% Testing phase %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

if (strcmp(protocol,'test'))

testTime=300;

% test phase 1
% Get the size of the image
[s1, s2, s3] = size(csHalfImage);

% Here we check if the image is too big to fit on the screen and abort if
% it is. See ImageRescaleDemo to see how to rescale an image.
if s1 > screenYpixels || s2 > screenYpixels
    disp('ERROR! Image is too big to fit on the screen');
    sca;
    return;
end

% Make the image into a texture
csHalfTexture = Screen('MakeTexture', window, csHalfImage);

% Draw the image to the screen, unless otherwise specified PTB will draw
% the texture full size in the center of the screen. We first draw the
% image in its correct orientation.
Screen('DrawTexture', window, csHalfTexture, [], [], 0);
writeDigitalPin(ard, 'D9', 1); % CS1 LED ON
Screen('Flip', window); % Flip to the screen

% Wait for few seconds
WaitSecs(testTime);
writeDigitalPin(ard, 'D9', 0); % CS1 LED Off

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Test phase 2 (flip)
% Draw the image to the screen for a second time this time upside down and
% drawn onto our updated blue background
Screen('DrawTexture', window, csHalfTexture, [], [], 180);
writeDigitalPin(ard, 'D10', 1); % CS2 LED ON
% Flip to the screen
Screen('Flip', window);
WaitSecs(testTime);

if (strcmp(protocol,'reverse'))
% Now fill the screen blank
Screen('DrawTexture', window, BGFullTextureRev, [], [], 0);
writeDigitalPin(ard, 'D10', 0); % CS2 LED OFF
Screen('Flip', window);

else
    % Now fill the screen blank
Screen('DrawTexture', window, BGFullTexture, [], [], 0);
writeDigitalPin(ard, 'D10', 0); % CS2 LED OFF
Screen('Flip', window);
end

end

%% Extinction %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if (strcmp(protocol,'extinction'))
    
    exposure=3;
    extinctionTest=60; % 20 trials/ 21 mins
    extTrials=1;

    
    while (extTrials<21)
        
            % Make the image into a texture
        csFullTexture = Screen('MakeTexture', window, csFullImage);

        % Get the size of the image
        [u1, u2, u3] = size(csFullImage);

        % Here we check if the image is too big to fit on the screen and abort if
        % it is. See ImageRescaleDemo to see how to rescale an image.
        if u1 > screenYpixels || u2 > screenYpixels
            disp('ERROR! Image is too big to fit on the screen');
            sca;
            return;
        end

        % Draw the image to the screen, unless otherwise specified PTB will draw
        % the texture full size in the center of the screen. We first draw the
        % image in its correct orientation.
        Screen('DrawTexture', window, csFullTexture, [], [], 0);
        writeDigitalPin(ard, 'D11', 1); % CSfull LED ON
        Screen('Flip', window); % Flip to the screen
        writeDigitalPin(ard, 'D12', 1); % US LED ON
        WaitSecs(exposure);
        writeDigitalPin(ard, 'D12', 0); % US LED OFF

        % Get the size of the image
        [s1, s2, s3] = size(csHalfImage);

        % Here we check if the image is too big to fit on the screen and abort if
        % it is. See ImageRescaleDemo to see how to rescale an image.
        if s1 > screenYpixels || s2 > screenYpixels
            disp('ERROR! Image is too big to fit on the screen');
            sca;
            return;
        end

        % Make the image into a texture
        csHalfTexture = Screen('MakeTexture', window, csHalfImage);

        % Draw the image to the screen, unless otherwise specified PTB will draw
        % the texture full size in the center of the screen. We first draw the
        % image in its correct orientation.
        Screen('DrawTexture', window, csHalfTexture, [], [], 0);
        writeDigitalPin(ard, 'D9', 1); % CS1 LED ON
        Screen('Flip', window); % Flip to the screen
        % Wait for few seconds
        WaitSecs(extinctionTest);

        extTrials=extTrials+1;
    end
    
end

if (strcmp(protocol,'exit'))
% Wait for few second
disp('press any key to exit the stimulus');
pause('on');
pause()
pause('off');
% Clear the screen
sca;
end

end