update_parameters.m

function update_parameters
% UPDATE_PARAMETERS Update parameters at each trial.

    global   association_flag response_window trial_duration quiet_window lick_threshold...
        artifact_window iti camera_flag is_stim is_auditory is_whisker is_light is_opto...
        reward_valve_duration  aud_reward wh_reward wh_vec aud_vec light_vec ...
        light_prestim_delay stim_flag perf lick_flag ...
        false_alarm_punish_flag false_alarm_timeout early_lick_punish_flag early_lick_timeout ...
        Stim_S Log_S wh_stim_duration  aud_stim_duration  aud_stim_amp  aud_stim_freq  Stim_S_SR ScansTobeAcquired ...
        Reward_S Reward_S_SR  Trigger_S fid_lick_trace mouse_licked_flag reaction_time ...
        trial_started_flag  trial_number main_pool_size_old opto_stim_proba_old folder_name handles2give...
        stim_proba_old aud_stim_proba_old wh_stim_proba_old opto_aud_proba_old opto_wh_proba_old opto_ctrl_proba_old...
        light_flag baseline_window camera_vec deliver_reward_flag ...
        wh_stim_amp wh_scaling_factor response_window_start response_window_end...
        perf_and_save_results_flag reward_delivered_flag update_parameters_flag...
        is_reward reward_pool partial_reward_flag reward_proba_old...
        light_duration light_freq light_amp light_duty camera_freq SITrigger_vec main_trial_pool...
        whisker_trial_counter mouse_rewarded_context context_block context_flag block_id wh_rewarded_context...
        pink_noise_player brown_noise_player identical_block_count extra_time Context_S...
        WF_S wf_cam_vec LED1_vec LED2_vec opto_vec galv_x galv_y ...
        passive_stim_flag_enable passive_stim_flag passive_trial_max passive_iti passive_trial_counter is_passive
       

    outputSingleScan(Trigger_S,[0 0 0])
    pause(.5)
    outputSingleScan(Trigger_S,[0 0 0])
    
    trial_number = trial_number+1;

   %% GENERAL SETTINGS FROM BEHAVIOUR GUI

    association_flag=handles2give.association_flag; % 0 detection 1 assosiation
    light_flag=handles2give.light_flag;
    
    % Context info flag
    context_flag = handles2give.context_flag;
    context_block_size = handles2give.context_block_size;

    % Camera settings
    camera_freq=handles2give.camera_freq; % Hz
    camera_duty_cycle=0.5;
    
    trial_duration=handles2give.trial_duration; % ms

    % Lick sensor threshold
    lick_threshold=handles2give.lick_threshold; %in volts

    % Trial timeline settings
    min_quiet_window = handles2give.min_quiet_window; % in ms
    max_quiet_window = handles2give.max_quiet_window; % in ms
    if min_quiet_window > max_quiet_window
        set(handles2give.OnlineTextTag,'String','Error: Minimum quiet window should be smaller than maximum quiet window!');
    
    elseif min_quiet_window==max_quiet_window
        set(handles2give.OnlineTextTag,'String','Warning: quiet window will be constant.');
        quiet_window=min_quiet_window;
    else
        quiet_window=randsample(min_quiet_window:.1:max_quiet_window,1);
    end

    response_window=handles2give.response_window; % in ms
    artifact_window=handles2give.artifact_window; % in ms
    baseline_window=handles2give.baseline_window; % in ms

    % Inter-trial interval range
    min_iti=handles2give.min_iti; % InterStimInterval in ms
    max_iti=handles2give.max_iti; % InterStimInterval in ms
    if min_iti > max_iti
        set(handles2give.OnlineTextTag,'String','Error: Minimum ITI should be smaller than maximum ITI!');

    elseif min_iti==max_iti %constant ITI
        set(handles2give.OnlineTextTag,'String','Warning: ITI will be constant.');
        iti=min_iti;
    else
        iti=randsample(min_iti:.1:max_iti,1);
    end
       
    % Timeout
    false_alarm_punish_flag = handles2give.false_alarm_punish_flag;
    false_alarm_timeout=handles2give.false_alarm_timeout; % in ms
    early_lick_punish_flag = handles2give.early_lick_punish_flag;
    early_lick_timeout=handles2give.early_lick_timeout; % in ms

    % Stimuli parameters
    aud_stim_amp =  handles2give.aud_stim_amp;
    aud_stim_duration = handles2give.aud_stim_duration;
    aud_stim_freq = handles2give.aud_stim_freq;
    
    wh_stim_amp = handles2give.wh_stim_amp_1; % default amplitude, overwritten at stim. definition
    wh_stim_duration = handles2give.wh_stim_duration;
    wh_scaling_factor = handles2give.wh_scaling_factor;

    aud_stim_weight = handles2give.aud_stim_weight;
    wh_stim_weight = get_whisker_weight(handles2give);
    no_stim_weight = handles2give.no_stim_weight;
    
    if light_flag % If light stimulus, to be implemented
        light_amp = handles2give.light_amp;
        light_duration = handles2give.light_duration;
        light_prestim_delay = handles2give.light_prestim_delay;
        light_freq = handles2give.light_freq;
        light_duty = handles2give.light_duty;
        light_stim_weight = handles2give.light_stim_weight;
    end

    % Passive stimulation 
    passive_stim_flag_enable = handles2give.passive_stim_flag_enable;
    passive_stim_flag = handles2give.passive_stim_flag;
    passive_trial_max = handles2give.passive_trial_max;
    passive_iti = handles2give.passive_iti;
    is_passive = 0;

    if passive_stim_flag_enable
        contexts = {'active', 'passive'};
        if passive_stim_flag
            if passive_trial_counter < passive_trial_max
                is_passive = 1;
                association_flag = 1; % to exclude from performance and plots
                trial_duration = 1000;
                quiet_window = 0;
                iti = passive_iti;
    
                passive_trial_counter = passive_trial_counter + 1;
                context_block = contexts(is_passive+1)
                disp(['Passive trial ' num2str(passive_trial_counter)]);
            else
                is_passive = 0;
                association_flag = 0;
                passive_stim_flag=0;
                context_block = contexts(is_passive+1)
                set(handles2give.PassiveOnToggleButton,'Value',0);
                handles2give.passive_stim_flag = 0; % this will be reset when toggle button pressed again
                disp('End of passive stimulation.')
            end
        else
           context_block = contexts(is_passive+1)
           passive_trial_counter = 0; % keep counter
        end
    else
        is_passive=0;
    end


    
  
  
    %% Compute stimulus probability
    stim_proba = (aud_stim_weight + wh_stim_weight)/(aud_stim_weight + wh_stim_weight + no_stim_weight);
    %stim_proba = compute_stim_proba(handles2give);
    if isempty(stim_proba_old)
        stim_proba_old = stim_proba;
    end

    aud_stim_proba = (aud_stim_weight)/(aud_stim_weight + wh_stim_weight + no_stim_weight);
    if isempty(aud_stim_proba_old)
        aud_stim_proba_old = aud_stim_proba;
    end

    wh_stim_proba = (wh_stim_weight)/(aud_stim_weight + wh_stim_weight + no_stim_weight);
    if isempty(wh_stim_proba_old)
        wh_stim_proba_old = wh_stim_proba;
    end


    %% Compute opto-stimulus probability
    if handles2give.opto_session
        global Opto_info
        opto_stim_proba = Opto_info.nostim_proba; % proportion of light trials
        if isempty(opto_stim_proba_old)
            opto_stim_proba_old = opto_stim_proba;
        end
    
        opto_aud_proba = Opto_info.aud_proba; % proportion of light trials
        if isempty(opto_aud_proba_old)
            opto_aud_proba_old = opto_aud_proba;
        end

        opto_wh_proba = Opto_info.wh_proba; % proportion of light trials
        if isempty(opto_wh_proba_old)
            opto_wh_proba_old = opto_wh_proba;
        end

        opto_ctrl_proba = Opto_info.ctrl_proba;
        if isempty(opto_ctrl_proba_old)
            opto_ctrl_proba_old = opto_ctrl_proba;
        end
    else
        opto_stim_proba = 0;
        opto_aud_proba = 0;
        opto_wh_proba = 0;
        opto_ctrl_proba = 0;
    end
    
    %% Define new pool of stimuli

    if trial_number > 1
        results=readtable(strcat(folder_name, '\results.csv'));
        n_completed_trials=sum(results.perf~=6);
    else
        n_completed_trials=0;
    end

    % Size of pool (i.e. trial block) to get trials from
    % If context is not used:
    main_pool_size = aud_stim_weight + wh_stim_weight + no_stim_weight; %in an non-light task
    if isempty(main_pool_size_old)
        main_pool_size_old = main_pool_size;
    end

    stim_light_list=[900,901,902,903,904,905,906]; % code for stimuli: stim, aud, wh, opto_stim, opto_aud, opto_wh, opto_ctrl(tbd)
    

    % --- Creation of pseudo-random pool of trials (= block) ---
    % Create new trial pool when current pool finished, or, when change in parameters
    if mod(n_completed_trials, main_pool_size)==0 || main_pool_size_old ~= main_pool_size||...
            stim_proba_old ~= stim_proba || aud_stim_proba_old ~= aud_stim_proba|| wh_stim_proba_old ~= wh_stim_proba ||... 
            opto_stim_proba_old ~= opto_stim_proba || opto_aud_proba_old ~= opto_aud_proba || opto_wh_proba_old ~= opto_wh_proba ||...
            opto_ctrl_proba_old ~= opto_ctrl_proba

            % Save old probabilities and pool size
            opto_aud_proba_old = opto_aud_proba;
            opto_stim_proba_old = opto_stim_proba;
            opto_wh_proba_old = opto_wh_proba;
            opto_ctrl_proba_old = opto_ctrl_proba; % TBD: proba of trials stimulating in control location vs. no stimulation

            aud_stim_proba_old = aud_stim_proba;
            wh_stim_proba_old = wh_stim_proba;
            stim_proba_old = stim_proba;

            main_pool_size_old = main_pool_size;

        % Stim. probability and trial pool when opto-stimulus
        if handles2give.opto_session

            no_stim_opto_proba =(1-stim_proba)*opto_stim_proba;
            no_stim_no_opto_proba = (1-stim_proba)*(1-opto_stim_proba);
            aud_stim_opto = aud_stim_proba*opto_aud_proba;
            aud_stim_no_opto = aud_stim_proba*(1-opto_aud_proba);
            wh_stim_opto = wh_stim_proba*opto_wh_proba;
            wh_stim_no_opto = wh_stim_proba*(1-opto_wh_proba);

            main_trial_pool=[stim_light_list(1)*ones(1,round(round(no_stim_no_opto_proba*main_pool_size*100)/100)),...
                stim_light_list(2)*ones(1,round(round(aud_stim_no_opto*main_pool_size*100)/100)),...
                stim_light_list(3)*ones(1,round(round(wh_stim_no_opto*main_pool_size*100)/100)),...
                stim_light_list(4)*ones(1,round(round(no_stim_opto_proba*main_pool_size*100)/100)),...
                stim_light_list(5)*ones(1,round(round(aud_stim_opto*main_pool_size*100)/100)),...
                stim_light_list(6)*ones(1,round(round(wh_stim_opto*main_pool_size*100)/100)),...
                ];

        % Stim. probability and trial pool when no opto-stimulus
        else
            main_trial_pool=[stim_light_list(1)*ones(1,round(round(((1-stim_proba)*main_pool_size)*100)/100)) ,...
                stim_light_list(2)*ones(1,round(round(aud_stim_proba*main_pool_size*100)/100)),...
                stim_light_list(3)*ones(1,round(round(wh_stim_proba*main_pool_size*100)/100)),...
                ];
        end

        %Randomize occurrence of trials in pool
        main_trial_pool=main_trial_pool(randperm(numel(main_trial_pool)));

        if passive_stim_flag_enable
            contexts = {'active', 'passive'};
        else
            context_block = {'NA'};
        end

        % if context task
        if context_flag
            contexts = {'pink', 'brown'};
            if trial_number==1
                identical_block_count = 1;
                [pink_noise_player, brown_noise_player] = create_context_background_noise(handles2give.bckg_noise_directory);
                mouse_rewarded_context = get_or_determine_mouse_rewarded_context(handles2give.context_table_directory, handles2give.mouse_name, contexts);
                block_id = randi([1, size(contexts, 2)], 1); 
                context_block = contexts(block_id);
                outputSingleScan(Context_S, [0])
                if handles2give.context_sound_on
                    play_context_background(context_block, pink_noise_player, brown_noise_player, Context_S)
                else
                   outputSingleScan(Context_S, [1]) 
                end
            else
                old_block_id = block_id;
                block_id = randi([1, size(contexts, 2)], 1);
                if block_id == old_block_id
                    identical_block_count = identical_block_count + 1;
                else
                    identical_block_count = 1;
                end
                if identical_block_count > context_block_size  % We don't want more than 2 consecutive context A or B block
                     new_block_id = block_id;
                     while new_block_id == block_id
                         new_block_id = randi([1, size(contexts, 2)], 1);
                     end
                block_id = new_block_id;
                identical_block_count = 1;
                end
                context_block = contexts(block_id);
                outputSingleScan(Context_S, [0])
                if handles2give.context_sound_on
                    play_context_background(context_block, pink_noise_player, brown_noise_player, Context_S)
                else
                   outputSingleScan(Context_S, [1]) 
                end
            end
            wh_rewarded_context = strcmp(context_block, mouse_rewarded_context);    
        else
            block_id = 1;
        end
    end
    % --- End of trial pool creation ---

   

    % Select next trial 
    %trial_type = main_trial_pool(mod(n_completed_trials,main_pool_size)+1); %0 noLight 1 Light
    
    if is_passive
        
        main_trial_pool_passive = main_trial_pool((main_trial_pool~=900) & (main_trial_pool~=903)); % remove no stim trials
        main_pool_passive_size = wh_stim_weight + aud_stim_weight;
%         trial_type = main_trial_pool_passive(mod(n_completed_trials,main_pool_passive_size)+1); %0 noLight 1 Light
        trial_type = randsample(main_trial_pool_passive, 1);
        
        switch trial_type

            case stim_light_list(2) % AUDITORY TRIAL
                is_stim=1;
                is_auditory=1;
                is_whisker=0;
                is_light=0;
                is_opto=0;
            case stim_light_list(3) % WHISKER TRIAL
                is_stim=1;
                is_auditory=0;
                is_whisker=1;
                is_light=0;
                is_opto=0;
                whisker_trial_counter=whisker_trial_counter+1; %for proba. reward pool indexing

            case stim_light_list(5) % LIGHT AUDITORY TRIAL
                is_stim=1;
                is_auditory=1;
                is_whisker=0;
                is_light=0;
                is_opto=1;
            case stim_light_list(6)  % LIGHT WHISKER TRIAL
                is_stim=1;
                is_auditory=0;
                is_whisker=1;
                is_light=0;
                is_opto=1;
                whisker_trial_counter=whisker_trial_counter+1; %for proba. reward pool indexing
        end
    else

        trial_type = main_trial_pool(mod(n_completed_trials,main_pool_size)+1); %0 noLight 1 Light

        switch trial_type
            case stim_light_list(1) % NO STIM TRIAL
                is_stim=0;
                is_auditory=0;
                is_whisker=0;
                is_light=0;
                is_opto=0;
            case stim_light_list(2) % AUDITORY TRIAL
                is_stim=1;
                is_auditory=1;
                is_whisker=0;
                is_light=0;
                is_opto=0;
            case stim_light_list(3) % WHISKER TRIAL
                is_stim=1;
                is_auditory=0;
                is_whisker=1;
                is_light=0;
                is_opto=0;
                whisker_trial_counter=whisker_trial_counter+1; %for proba. reward pool indexing
            case stim_light_list(4) % LIGHT NO STIM TRIAL
                is_stim=0;
                is_auditory=0;
                is_whisker=0;
                is_light=0;
                is_opto=1;
            case stim_light_list(5) % LIGHT AUDITORY TRIAL
                is_stim=1;
                is_auditory=1;
                is_whisker=0;
                is_light=0;
                is_opto=1;
            case stim_light_list(6)  % LIGHT WHISKER TRIAL
                is_stim=1;
                is_auditory=0;
                is_whisker=1;
                is_light=0;
                is_opto=1;
                whisker_trial_counter=whisker_trial_counter+1; %for proba. reward pool indexing
        end
    end

    % Set light parameters to zero if not a light trial
    if ~is_light || ~light_flag
        is_light=0;
        light_prestim_delay=0;
        light_amp=0;
        light_duration=0;
        light_freq=0;
    end


    %% Reward Settings
    reward_valve_duration=handles2give.reward_valve_duration;    % duration valve open in milliseconds

    if handles2give.reward_delay_flag
        reward_delay_time=handles2give.reward_delay_time;         % delay in milisecond for delivering reward after stim (if Association=1)
    else
        reward_delay_time = 0;
    end

    
    aud_reward = handles2give.aud_reward; % is auditory rewarded
    if context_flag
        if wh_rewarded_context
            wh_reward=1;
        else
            wh_reward=0;
        end
    else
        wh_reward = handles2give.wh_reward;  % is whisker rewarded
    end

    partial_reward_flag=handles2give.partial_reward_flag; 
    n_pool_partial = 10; 

    % PROBABILISTIC reward delivery for whisker
    if partial_reward_flag && not(association_flag)

        reward_proba=handles2give.reward_proba; % proportion of rewarded whisker hits
        if isempty('reward_proba_old')
            reward_proba_old = reward_proba;
        end

        % Update pool of rewarded and unrewarded trials (1s and 0s) -> this
        % could be deleted
        if all(mod(whisker_trial_counter, n_pool_partial)==1)|| all(reward_proba_old ~= reward_proba)  %check if reward_proba has changed
            reward_proba_old = reward_proba;
            reward_pool=[zeros(1,round((1-reward_proba)*n_pool_partial)) ones(1,round(reward_proba*n_pool_partial))]; % zero for no stim, one for Reward
            reward_pool=reward_pool(randperm(numel(reward_pool))); 
        end

        % Set reward flag per trial type
        if is_whisker 
            is_reward = double(rand(1)<reward_proba);
        elseif is_auditory
            is_reward=aud_reward;
        end 

    % CONSTANT reward delivery (also for association trials)
    elseif not(partial_reward_flag) || association_flag
        is_reward=1;
    end

    
    % Define reward vector
    rew_vec_amp = 5; %volt
    reward_vec = [zeros(1,reward_delay_time) rew_vec_amp*ones(1,reward_valve_duration*Reward_S_SR/1000) zeros(1,Reward_S_SR/2)];

    if ~is_reward || ~is_stim
        reward_vec=zeros(1,numel(reward_vec));
    end

    %% Get trial duration
    trial_duration = max(trial_duration, (light_prestim_delay + artifact_window + baseline_window + max(response_window, (light_duration-light_prestim_delay))) /1000);


    %% Define stimulus parameters and vectors
    % Catch trials, set stimulus vectors to 0
    if ~is_stim
        aud_stim_duration = 0;
        aud_stim_amp = 0;
        aud_stim_freq = 0;
        wh_stim_duration = 0;
        wh_stim_amp = 0;

        wh_vec = zeros(1,(trial_duration)*(Stim_S_SR/1000));
        aud_vec = zeros(1,(trial_duration)*(Stim_S_SR/1000));

    % Stimulus trial parameters and vectors
    else
        % Sinusoidal auditory stimulus
        if is_auditory

            aud_vec = aud_stim_amp*[zeros(1,(baseline_window)*Stim_S_SR/1000)...
                sin(linspace(0, aud_stim_duration* aud_stim_freq*2*pi/1000, round(aud_stim_duration*Stim_S_SR/1000))) 0];
            aud_vec=[aud_vec zeros(1,trial_duration*Stim_S_SR/1000-length(aud_vec))];
            
            % Set whisker vec to zero
            wh_stim_duration = 0;
            wh_stim_amp = 0;
            wh_vec = zeros(1,(trial_duration)*(Stim_S_SR/1000));

        % Biphasic cosine whisker stimulus
        elseif is_whisker
            % Set auditory vector to 0
            aud_stim_duration = 0; 
            aud_stim_amp = 0;
            aud_stim_freq = 0;

            aud_vec=zeros(1,(trial_duration)*(Stim_S_SR/1000));
            
            wh_stim_duration_up = wh_stim_duration/2*Stim_S_SR/1000;
            wh_stim_duration_down = wh_stim_duration/2*Stim_S_SR/1000;

            impulse_up = tukeywin(wh_stim_duration_up,1);
            impulse_up = impulse_up(1:end-1);
            impulse_down = -tukeywin(wh_stim_duration_down,1);
            impulse_down = impulse_down(2:end);
            impulse = [impulse_up' wh_scaling_factor*impulse_down'];
            
            wh_stim_amp = get_whisker_stim_amp(handles2give); 
            wh_vec = wh_stim_amp * [zeros(1,baseline_window*Stim_S_SR/1000) impulse];
            wh_vec = [wh_vec zeros(1,trial_duration*Stim_S_SR/1000 - numel(wh_vec))];

        end
    end

    % If optogenetics, get opto-stimulus
    if handles2give.opto_session
        global opto_gui Opto_S variables_to_save_opto voltage_x voltage_y bregma_x bregma_y opto_count
        if is_opto
            [ML, AP, grid_no, count] = get_next_grid;
            power = opto_gui.amplitude;
            [opto_vec, galv_x, galv_y] = load_opto_vec(ML,AP);
            opto_count = opto_count+1;

        else
            [opto_vec, galv_x, galv_y] = load_opto_vec(5,-5);
            
            AP = -5;
            ML = 5;
            power = -1;
            grid_no = nan;
            count = trial_number - opto_count;

            opto_gui.plot_grid
            scatter(opto_gui.UIAxes, -5, 5, 'filled', 'MarkerEdgeColor','#DC143C', 'MarkerFaceColor', '#DC143C');
            text(opto_gui.UIAxes, 1, 6.5, {['No opto trial: ' num2str(count) '/' num2str(trial_number)]})
        end
        
        % Get optogenetic data to save
        variables_to_save_opto = {trial_number is_opto is_stim is_auditory is_whisker context_block opto_gui.baseline*1000 power opto_gui.frequency...
            opto_gui.duration opto_gui.pulse_width grid_no count AP ML ...
            voltage_x voltage_y bregma_x bregma_y};
    end
    %% Light define vector - To update
    if is_light

%         disp(['Light' num2str(is_light)])
%         time_vec_light = 1/Stim_S_SR : 1/Stim_S_SR : (light_duration/1000);
% 
%         light_pulse_train=[ones(1,round(Stim_S_SR*(light_duty/light_freq))) zeros(1,round(Stim_S_SR*((1-light_duty)/light_freq)))];
%         light_pulse_train=repmat(light_pulse_train,1,light_duration*light_freq/1000);
% 
%         switch light_stim_shape
%             case 'sin'
%                 light_vec=light_amp/2+light_amp/2*[-ones(1,baseline_window*Stim_S_SR/1000) -ones(1,(light_prestim_delay)*Stim_S_SR/1000) -cos(2*pi*light_freq*time_vec_light)];
%                 light_vec=[light_vec zeros(1,(trial_duration)*(Stim_S_SR/1000)-numel(light_vec))];
% 
%                 light_vec_shadow= [zeros(1,baseline_window*Stim_S_SR/1000) zeros(1,(light_prestim_delay)*Stim_S_SR/1000) [ones(1,1*length(light_pulse_train)-ramp_down_duration*Stim_S_SR/1000) fliplr(linspace(0,1,ramp_down_duration*Stim_S_SR/1000))]];
%                 light_vec_shadow =[light_vec_shadow zeros(1,(trial_duration)*(Stim_S_SR/1000)-numel(light_vec_shadow))];
% 
%                 light_vec=light_vec.*light_vec_shadow;
% 
%             otherwise
%                 light_vec=light_amp*[(zeros(1,(baseline_window - light_prestim_delay)*Stim_S_SR/1000)) light_pulse_train];
%                 light_vec=[light_vec zeros(1,(trial_duration)*(Stim_S_SR/1000)-numel(light_vec))];
%                 %
%                 light_vec_shadow= [zeros(1,(baseline_window-light_prestim_delay)*Stim_S_SR/1000) [ones(1,1*length(light_pulse_train)-ramp_down_duration*Stim_S_SR/1000) fliplr(linspace(0,1,ramp_down_duration*Stim_S_SR/1000))]];
%                 light_vec_shadow =[light_vec_shadow zeros(1,(trial_duration)*(Stim_S_SR/1000)-numel(light_vec_shadow))];
% 
%                 light_vec=light_vec.*light_vec_shadow;
% 
%         end

    % No light, set light vector to 0
    else
        light_vec=zeros(1,(trial_duration)*(Stim_S_SR/1000));
    end

    %% For Video Filming - Make pulse train for Trigger_S Camera

    camera_vec = [ones(1, Stim_S_SR*(camera_duty_cycle/camera_freq)) zeros(1,Stim_S_SR*((1-camera_duty_cycle)/camera_freq))];
    camera_vec = repmat(camera_vec, 1, trial_duration*camera_freq/1000);

    %% For WF imaging - Load vectors in single trial imaging
    if handles2give.wf_session 
        global WF_FileInfo
        if ~WF_FileInfo.RecordingContinuous 
            wf_imaging
            if ~handles2give.opto_session
                WF_S.start()
                WF_S.write([wf_cam_vec; LED1_vec; LED2_vec;]')
            end
        end
    end
    
    %% Plotting the whisker/auditory stim and camera vector signals
    
    % Set plotting params
    acolor = [0 0.4470 0.7410];
    acolor_str = '0 0.4470 0.7410';
    if wh_reward
        wcolor = [0.4660 0.6740 0.1880]';
        wcolor_str = '0.4660 0.6740 0.1880';
    else
        wcolor = [0.6350 0.0780 0.1840];
        wcolor_str = '0.6350 0.0780 0.1840';
    end

    %% Online performance for plotting
    if trial_number>1
        
        % Load results data
        results=readtable(strcat(folder_name, '\results.csv'));
        
        % Compute performance and display on GUI
        [aud_hit_rate, wh_hit_rate, fa_rate, stim_trial_number, aud_stim_number, wh_stim_number] = compute_performance(results);

        set(handles2give.PerformanceText1Tag, 'String', ...
            ['AHR=' num2str(aud_hit_rate) ', ' ...
            ' WHR=' num2str(wh_hit_rate) ', ' ...
            ' FAR=' num2str(fa_rate) ', ' ...
            ' Stim='  num2str(stim_trial_number) ', '...
            ' AudStim=' num2str(aud_stim_number) ', '...
            ' WhStim=' num2str(wh_stim_number)], ...
            'FontWeight', 'Bold');
        
        % Make performance plot
        perf_win_size=handles2give.last_recent_trials;
        plot_performance(results, perf_win_size);
        
        % Compute approx. reward volume obtained and display on GUI
        volume_per_reward = 5; % in microliter <- THIS MUST BE CALIBRATED 
        [aud_tot_volume, wh_tot_volume, asso_tot_volume] = compute_reward_volume(results, volume_per_reward);
        if wh_reward
            wh_tot_volume = wh_tot_volume;
        else
            wh_tot_volume = 0;
        end        
 
        set(handles2give.PerformanceText2Tag, 'String', ...
            ['Reward: Auditory=' num2str(aud_tot_volume) 'uL, '  ...
            ' Whisker=' num2str(wh_tot_volume) 'uL, ' ...
            ' Total=' num2str(aud_tot_volume+wh_tot_volume) 'uL, ' ...
            ' (Asso.=' num2str(asso_tot_volume) 'uL)'], ...
             'FontWeight', 'Bold');

    end

    %% Printing out the next trial specs
    trial_titles={'No stimulus', ...
        ['Amp=' num2str(wh_stim_amp) ', ' 'Duration=' num2str(wh_stim_duration)], ...
        ['Amp=' num2str(aud_stim_amp) ', ' 'Duration=' num2str(aud_stim_duration) ', ' 'Frequency=' num2str(aud_stim_freq)]};

    if is_passive
        association_titles={'', ''};
        reward_titles={'Passive', 'Passive'};
    else
        association_titles={'', ' Association'};
        reward_titles={'Not rewarded', 'Rewarded'};
    end

    if is_opto
            opto_titles={'Opto OFF', 'Opto ON'};
    else
            opto_titles={'', ''};
    end


    if is_stim

        if is_auditory

            set(handles2give.TrialTimeLineTextTag,'String', ['Next trial: Auditory.  ' char(trial_titles(is_stim+2)) ' '...
                char(association_titles(association_flag+1)) '   ' char(reward_titles(aud_reward+1)) '     ' char(opto_titles(is_opto+1))],'ForegroundColor',acolor);

        else
            if is_reward==1 && wh_reward==1 % =1 always when no partial rewards
                reward_title = 'Rewarded';
                wcolor = [0.4660 0.6740 0.1880]';
            else
                reward_title = 'Not rewarded';
                wcolor = [0.6350 0.0780 0.1840];
            end

            if is_passive
                reward_title = 'Passive';
            end
            
            set(handles2give.TrialTimeLineTextTag,'String',['Next trial: Whisker. ' char(trial_titles(is_stim+1)) ' '...
                char(association_titles(association_flag+1)) '   ' char(reward_title) '     ' char(opto_titles(is_opto+1))],'ForegroundColor', wcolor);

        end

    else
        set(handles2give.TrialTimeLineTextTag,'String',['Next trial:   ' char(trial_titles(is_stim+1)) ' '...
            char(association_titles(association_flag+1))  '     ' char(opto_titles(is_opto+1))], 'ForegroundColor','k');
    end

    %% Parameters are updated: now send signal vectors and triggers
    
    SITrigger_vec=[ones(1,numel(wh_vec)-2) 0 0]; % ScanImage trigger vector
    queueOutputData(Stim_S,[wh_vec; aud_vec; camera_vec; SITrigger_vec]')

    while Stim_S.IsRunning
        disp('Here') %?????
    end
    Stim_S.startBackground()

    outputSingleScan(Trigger_S,[0 0 0])

    if handles2give.opto_session && ~handles2give.wf_session
        try
            queueOutputData(Opto_S, [opto_vec; galv_x; galv_y]')
            pause(.1)

        catch
            disp(['Error preloading Opto_S coords ap ml: ' num2str(AP) ' ' num2str(ML)])
            disp(Opto_S)
        end
        Opto_S.startBackground();

    elseif handles2give.opto_session && handles2give.wf_session
        try
            queueOutputData(Opto_S, [opto_vec(1:end-1); galv_x(1:end-1); galv_y(1:end-1); wf_cam_vec]')
            pause(.1)

        catch
            disp(['Error preloading Opto_S coords ap ml: ' num2str(AP) ' ' num2str(ML)])
            disp(Opto_S)
        end
        Opto_S.startBackground();
    end

    % Queue reward vector
     if ~Reward_S.ScansQueued 
        queueOutputData(Reward_S, reward_vec')
        while Reward_S.IsRunning
            disp('Here 2') 
        end
        Reward_S.startBackground();
     end
     
    %% Define response window boundaries
    
    response_window_start = (artifact_window + baseline_window)/1000;
    response_window_end = (artifact_window + baseline_window + response_window)/1000;

    %% Update current trial flags
    handles2give.ReportPause=1; %not currently paused

    trial_started_flag=0;
    stim_flag=1;
    deliver_reward_flag=0;
    perf_and_save_results_flag=0;
    mouse_licked_flag=0;
    reward_delivered_flag=0;
    update_parameters_flag=0;

    % Reset variables
    reaction_time=0;

    % Give user extra time to start video and 2P acquisition before 1st trial start.
    % Added to iti condition for trial start in main_control.
    if trial_number == 1
        extra_time = 10;
    else
        extra_time = 0;
    end



end