main.m

clc
close all
clear

% Get config params
para = CONFIG;

%% MAIN ANALYSIS

% get list of animals to be analysed
Animal_IDs = para.Animal_IDs;

% Iterate though each animal in para.Animal_IDs
for mouseNum = 1:length(Animal_IDs) 

    Animal_ID = Animal_IDs(mouseNum);

    %% write intermediate variables and save locally
    
    % get list of files containing session-level behavioural data for each mouse
    filelist_behaviour = dir(fullfile(para.input_folder, Animal_ID,'**', ...
        '*experimental-data.csv'));
    
    % concatenate within-session data from all sessions for animal
    trial_data_mouse = table();
    
    % acquire trial-level information from ceph and save locally
    for sessionNum=1:length(filelist_behaviour)
    
        session_data_filepath = fullfile(filelist_behaviour(sessionNum).folder, ...
                filelist_behaviour(sessionNum).name);
        session_ID = get_session_ID(session_data_filepath);
    
        % output folder for session intermediate variables
        output_folder_session = fullfile(para.output_folder, 'intermediate_variables', ...
            Animal_ID, session_ID);
        filename = strcat(Animal_ID, '_', session_ID, '_trial_data.csv');
    
        if ~isfile(fullfile(output_folder_session, filename))
            trial_data_session = get_trial_data(session_data_filepath);
            save_table(trial_data_session, output_folder_session, filename);
        else % if trial summary already exists
           trial_data_session = read_trial_data(fullfile(output_folder_session, ...
               filename));
        end
    
        %concatenate across all sessions 
        trial_data_mouse = [trial_data_mouse;trial_data_session];
    
    end
    
    %% summarise session-level information
    
    % behavioural data summary and ephys metadata for each session
    sessions_summary = get_session_summary(para,trial_data_mouse);
    
    % save to local directory
    writetable(sessions_summary, fullfile(para.output_folder, 'intermediate_variables', ...
        strcat('sessions_summary_', Animal_ID, '.csv')));
    
    %% plot session summary information
    
    fig = plot_sessions_summary(para, sessions_summary);
    output_folder = fullfile(para.output_folder, 'plot_performance_across_sessions');
    filename = strcat('plot_session_bias_accuracy_', Animal_ID);
    save_figure(fig, output_folder, filename);
    
    %% plot changes in signal quality over time (if ephys signal quality metadata exists).
    if isfile(fullfile(para.output_folder, 'ephys_signal_quality', ...
            ['quality_metrics_KS3_metadata_', Animal_ID,'.csv']))
        fig = plot_signal_quality_across_sessions(para, sessions_summary);
        output_folder = fullfile(para.output_folder, 'plot_data_quality_across_sessions');
        filename = strcat('plot_data_quality_', Animal_ID);
        save_figure(fig, output_folder, filename);
    else
        warning(strcat("No ephys metadata found for animal ", Animal_ID, ...
            ". Skipping plot of signal quality."))
    end
    
    %% plot trial summary information (within each session)
    
    filelist = dir(fullfile(para.output_folder, 'intermediate_variables', ...
        Animal_ID, '*trial_data.csv'));
    
    % loop through all session with local trial-level data saved
    for sessionNum=1:length(filelist)
    
        % read trial-level information
        trial_data_session = read_trial_data(fullfile(filelist(sessionNum).folder, ...
            filelist(sessionNum).name));
        Session_ID = trial_data_session.Session_ID(1,:);
    
        % plot accuracy, choice / abort trial bias, response times
        output_folder = fullfile(para.output_folder, 'plot_performance_across_trials', ...
            Animal_ID);
        filename = strcat('plot_trial_bias_accuracy_', Animal_ID, '_', Session_ID);
        if ~isfile(fullfile(output_folder, strcat(filename, '.png')))
            fig = plot_trials_summary(para, trial_data_session);
            save_figure(fig, output_folder, filename);
            close
        else
            disp(strcat("Skipping ", Session_ID, " session plot as it already exists."))
        end
    
    end

end