A00_initialCalib.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/>.

%%
% this script is to calibrate:
% 1) general: to calculate the midline of CS+ and CS-
% 2) general: quick check of LEDs
% 3) lag: delay calib between led and vis stim
% 4) lag: delay calib betn led and shock

% lagvis and lagshock are special checks done once  in a while
% general is recommended to run before each experiment

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

Screen('Preference', 'VisualDebugLevel', 1);
%Screen('Preference', 'SkipSyncTests', 1); % may lead to some  synch timimng issue; 
%but can be used as long as the timimng is externally determined

%% initialise things here

% 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 = 1; % forcing screen #1
% to project stim

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


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

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

%% ask for the protocol here %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
protocol = input('Which protocol do you want to run?','s');% choose protocol

if isempty(protocol)
    protocol = 'cs';
end

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

%% setup arduino
ard = arduino('COM4', 'Uno'); % Initializes Arduino

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

%% 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);

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

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


%%
if (strcmp(protocol,'general'))

% 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 2
writeDigitalPin(ard, 'D9', 1); % CS1 LED ON
% Flip to the screen
Screen('Flip', window);

% Wait for few seconds
WaitSecs(2);

% Now fill the screen blank
Screen('DrawTexture', window, BGFullTexture, [], [], 0);

writeDigitalPin(ard, 'D9', 0); % CS1 LED OFF
Screen('Flip', window);
WaitSecs(2);
disp('press any key to continue to half texture');
pause('on');
pause();

% 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);

% Wait for one second
WaitSecs(2);

disp('press any key to proceed to check the LEDs');
pause('on');
pause();
writeDigitalPin(ard, 'D10', 0); % CS2 LED ON

WaitSecs(10);
%% %%%%%%%%%%%%%%%%%%%%%%%%%%% check the LEDs

writeDigitalPin(ard, 'D09', 1); % CS1 LED ON
WaitSecs(5);
writeDigitalPin(ard, 'D09', 0); % CS1 LED OFF

writeDigitalPin(ard, 'D10', 1); % CS2 LED ON
WaitSecs(5);
writeDigitalPin(ard, 'D10', 0); % CS2 LED OFF

writeDigitalPin(ard, 'D11', 1); % CSfull LED ON
WaitSecs(5);
writeDigitalPin(ard, 'D11', 0); % CSfull LED OFF

writeDigitalPin(ard, 'D12', 1); % US LED ON
WaitSecs(5);
writeDigitalPin(ard, 'D12', 0); % US LED OFF

writeDigitalPin(ard, 'D07', 1); % Shock ON
WaitSecs(5);
writeDigitalPin(ard, 'D07', 0); % Shock OFF

end

%% lagvis: check lag in visual stim and US delivery wrt to the LED proxy
if (strcmp(protocol,'lag'))

delay=10; % for arrival of US shock; all in secs
shock=2; % duration of the actual shock

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


for tr=1:12
    
% 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);
% Screen('FillRect', window, [0 0 0]);
% Screen('Flip', window);

WaitSecs(delay);
Screen('DrawTexture', window, csFullTexture, [], [], 0);
%Screen('FillRect', window, [1 1 1]);
writeDigitalPin(ard, 'D11', 1); % CSfull LED ON % MEASURE PIN11/ CS-FULL LED
Screen('Flip', window); % Flip to the screen % MEASURE ILLUMINACE Change of arena w/ a photodiode

% 
% % Wait for few secs for the US arrive
 WaitSecs(delay);
% 
 writeDigitalPin(ard, 'D12', 1); % US LED ON % MEASURE PIN12/ US LED
 writeDigitalPin(ard, 'D07', 1); % Shock ON % % MEASURE shock at PIN6/ shock stim
 WaitSecs(shock); % 2 secs of shock
 writeDigitalPin(ard, 'D12', 0); % US LED OFF
 writeDigitalPin(ard, 'D07', 0); % Shock OFF
% 
 WaitSecs(1); % wait for another sec and then switch off the vis stim
% 
% % Now fill the screen blank
Screen('DrawTexture', window, BGFullTexture, [], [], 0);
 writeDigitalPin(ard, 'D11', 0); % CSfull LED OFF
 % Flip to the screen
 Screen('Flip', window);

disp('press any key to repeat the stim for calibration');
pause('on');
pause();
end
    
end

%%
disp('press any key to exit the calibration');
pause('on');
pause();
% Clear the screen
sca;