fnirsPlotWithBaselineDev.m

function fnirsPlotWithBaselineDev(time, HbO, HbR, titleString, con, avgBool, saveOption, subject, directory, folder)
% Authors: Ivy Hill, Iris Li
% Created: July 16th, 2024
% Last edited: Jul 27, 2024 by Iris


%% 1.0 Plots all HbR & HbO data + overlays avg value of each of HbO + HbR baseline

startIdx = find(time == time(and(time >= 0, time < max(diff(time))))); %Finds start index of data / end index of baseline

fig1 = figure('Visible', 'off'); hold on; grid on;

% baseline lines
HbOBaseline = yline(mean(HbO(1:(startIdx-1))), '-', 'Color', [200, 100, 50]/255, 'LineWidth', 1);
HbRBaseline = yline(mean(HbR(1:(startIdx-1))), '-', 'Color', [110, 240, 120]/255, 'LineWidth', 1);

% HbO + HbR values
if avgBool == true % preferred
    lineHbO = plot(time(startIdx:end), mean(HbO(:, startIdx:end)), 'r');
    lineHbR = plot(time(startIdx:end), mean(HbR(:, startIdx:end)), 'b');
elseif avgBool == false % test - not preferred
    lineHbO = plot(time(startIdx:end), HbO(:, startIdx:end), 'r');
    lineHbR = plot(time(startIdx:end), HbR(:, startIdx:end), 'b');
end

title(strcat("Entire ", con, " Session: ", titleString, " Hb Data & Baseline"));
legend([HbOBaseline, HbRBaseline, lineHbO(1), lineHbR(1)], {'HbO Baseline', 'HbR Baseline', 'HbO Trial Data (All Chans Avg)', 'HbR Trial Data (All Chans Avg)'}, 'Location', 'best');
xlabel('Time (s)');
ylabel('Relative Concentration (mmol/L)'); 

% save plots:
if saveOption == "save"
        saveas(fig1, fullfile(directory, folder, strcat(subject, '_', con, '_entire_ses_', titleString, 'baseline_HbO-HbR.png')));
        close(fig1);
else
    set(fig1, 'Visible', 'on');
end


%% 2.0 Plot single values (horiz. lines) of the baselines and the means of HbO and HbR -- may not use

if titleString == "Filtered"
    fig2 = figure('Visible', 'off'); hold on; grid on;

    % baselines
    baselineHbO = yline(mean(HbO(1:(startIdx-1))), '-', 'Color', [200, 100, 50]/255, 'LineWidth', 1);
    baselineHbR = yline(mean(HbR(1:(startIdx-1))), '-', 'Color', [110, 240, 120]/255, 'LineWidth', 1);
    
    % HbO and HbR
    meanHbO = yline(mean(HbO(:, startIdx:end), 2), 'r');
    meanHbR = yline(mean(HbR(:, startIdx:end), 2), 'b');
    
    title(strcat("Entire ", con, " Session: ", titleString, " Hb Data & Baseline"));
    legend([baselineHbO, baselineHbR, meanHbO(1), meanHbR(1)], {'HbO Baseline', 'HbR Baseline', 'HbO Trial Data Mean Value', 'HbR Trial Data Mean Value'}, 'Location', 'best');
    xlabel('Time (s)');
    
    % save plots:
    if saveOption == "save"
        saveas(fig2, fullfile(directory, folder, strcat(subject, '_', con, '_entire_ses_', titleString, '_means-baselines_HbO-HbR.png')));
        close(fig2);
    else
        set(fig2, 'Visible', 'on');
    end

end


end