function make_paper_figures(target)
%MAKE_PAPER_FIGURES Journal figures for Paper 2 Sections 2 and 3.2.
%   Writes to writing/figures of the main checkout (white background).
if nargin < 1, target = 0.4; end
here = fileparts(mfilename('fullpath'));
main = fileparts(here);
out = fullfile(main, '..', '..', '..', 'figures');   % worktree -> writing/figures
if ~isfolder(out), mkdir(out), end
set(groot, 'defaultAxesFontName', 'Times New Roman', 'defaultTextFontName', 'Times New Roman', ...
    'defaultAxesFontSize', 8, 'defaultAxesTickDir', 'out', 'defaultAxesBox', 'off', ...
    'defaultAxesTickLabelInterpreter', 'tex')
copper = '#AC6420'; blue = '#007CA8'; green = '#39BF5E'; red = '#901500'; gray = [0.55 0.55 0.55];

%% open- and closed-loop frequency responses (Section 2.4)
dt = 1/2048;
E0 = load(fullfile(main, 'saved_results', 'exp_tf', 'tf_sp1_7000_20260627_210411.mat'));
Ed = load(fullfile(main, 'saved_results', 'exp_tf', 'tf_sp1_5000_20260627_233333.mat'));
pv = Ed.pid_values;
C = pid(pv.P, pv.I, pv.D, 1/pv.derivative_filter_N, dt, 'IFormula', 'ForwardEuler', 'DFormula', 'ForwardEuler');
f = logspace(0, 2, 600)';
L = [squeeze(freqresp(C*c2d(E0.H_dc_dm, dt, 'zoh'), 2*pi*f)), squeeze(freqresp(C*c2d(Ed.H_dc_dm, dt, 'zoh'), 2*pi*f))];
T = L./(1 + L);
chord = @(l) abs(1 + l)./sqrt(2*(1 + abs(l).^2));
kap = chord(L);
X = {E0.H_dc_dm_xfunc, Ed.H_dc_dm_xfunc}; fm = cell(1, 2); Lm = cell(1, 2);   % measured points (>= 1 Hz)
for j = 1:2, k = X{j}.freq_hz >= 1; fm{j} = X{j}.freq_hz(k); Lm{j} = squeeze(freqresp(C, 2*pi*fm{j})).*X{j}.points(k); end
st = {'-', '--'}; col = {'k', red}; mk = {'o', 's'}; nm = {'Initial, k_0', 'Damaged, 0.75k_0'};

fig = newFig(3.5, 4.2);
tl = tiledlayout(fig, 3, 1, 'TileSpacing', 'compact', 'Padding', 'compact');
ax = nexttile(tl); hold on
for j = 1:2, plot(fm{j}, 20*log10(abs(Lm{j})), mk{j}, 'Color', col{j}, 'MarkerSize', 1.5, 'HandleVisibility', 'off'); end
for j = 1:2, semilogx(f, 20*log10(abs(L(:, j))), st{j}, 'Color', col{j}, 'LineWidth', 1); end
set(ax, 'XScale', 'log', 'XTickLabel', []); ylabel('|L| (dB)'); grid on
legend(nm, 'Location', 'southwest', 'Box', 'off')
ax = nexttile(tl); hold on
for j = 1:2
    ph = unwrap(angle(L(:, j)))*180/pi; phm = angle(Lm{j})*180/pi;
    phm = phm + 360*round((interp1(f, ph, fm{j}) - phm)/360);
    plot(fm{j}, phm, mk{j}, 'Color', col{j}, 'MarkerSize', 1.5); semilogx(f, ph, st{j}, 'Color', col{j}, 'LineWidth', 1);
end
set(ax, 'XScale', 'log', 'XTickLabel', []); ylabel('\angleL (deg)'); grid on
ax = nexttile(tl); hold on
for j = 1:2, plot(fm{j}, chord(Lm{j}), mk{j}, 'Color', col{j}, 'MarkerSize', 1.5, 'HandleVisibility', 'off'); semilogx(f, kap(:, j), st{j}, 'Color', col{j}, 'LineWidth', 1, 'HandleVisibility', 'off'); end
yline(0.4, ':', 'Color', gray, 'LineWidth', 1, 'HandleVisibility', 'off')
set(ax, 'XScale', 'log'); ylim([0.2 0.8]); ylabel('\chi'); xlabel('Frequency (Hz)'); grid on
[m, i] = min(kap); plot(f(i), m, 'o', 'MarkerFaceColor', blue, 'MarkerEdgeColor', 'w', 'MarkerSize', 5)
legend('NCF margin', 'Location', 'southwest', 'Box', 'off')
print(fig, fullfile(out, 'fig_open_loop.svg'), '-dsvg'); print(fig, fullfile(out, 'fig_open_loop.png'), '-dpng', '-r300'); close(fig)

fig = newFig(3.5, 3.0);
tl = tiledlayout(fig, 2, 1, 'TileSpacing', 'compact', 'Padding', 'compact');
ax = nexttile(tl); hold on
for j = 1:2, semilogx(f, 20*log10(abs(T(:, j))), st{j}, 'Color', col{j}, 'LineWidth', 1); end
set(ax, 'XScale', 'log', 'XTickLabel', []); ylabel('|T| (dB)'); grid on
legend(nm, 'Location', 'southwest', 'Box', 'off')
ax = nexttile(tl); hold on
for j = 1:2, semilogx(f, unwrap(angle(T(:, j)))*180/pi, st{j}, 'Color', col{j}, 'LineWidth', 1); end
set(ax, 'XScale', 'log'); ylabel('\angleT (deg)'); xlabel('Frequency (Hz)'); grid on
close(fig)

%% calibration cases (Section 3.2)
S = load(fullfile(here, sprintf('paper_benchmark_target_%03d.mat', round(100*target))));
R = S.R;
for g = 1:2
    ids = (1:4) + 4*(g - 1);
    fig = newFig(7.0, 4.6);
    tl = tiledlayout(fig, 3, 4, 'TileSpacing', 'compact', 'Padding', 'compact');
    for k = 1:4
        c = R.cases(ids(k));
        ax = nexttile(tl, k); hold on
        h1 = plot(c.t, c.dc, '-', 'Color', copper, 'LineWidth', 0.4);
        h2 = plot(c.t, c.dm, '-', 'Color', blue, 'LineWidth', 0.4);
        title(sprintf('Case %d: %s, %s', c.id, lower(c.history), lower(c.band)), 'FontWeight', 'normal')
        xlim([0 120]); ylim([-0.6 0.6]); set(ax, 'XTickLabel', []); grid on
        if k == 1, ylabel('Displacement (mm)'); end
        ax = nexttile(tl, k + 4);
        plot(c.tc, c.delta, 'k-', 'LineWidth', 1)
        xlim([0 120]); ylim([-0.05 1.1]); set(ax, 'XTickLabel', []); grid on
        if k == 1, ylabel('\delta'); end
        ax = nexttile(tl, k + 8); hold on
        if c.adaptive, yyaxis(ax, 'left'), end
        h3 = plot(c.tc, c.b_true, 'k-', 'LineWidth', 1);
        h4 = plot(c.tc, c.b_est, '-', 'Color', green, 'LineWidth', 1);
        h5 = plot([0 120], [target target], '--', 'Color', gray, 'LineWidth', 0.8);
        ylim([0.15 0.75]); ax.YColor = 'k';
        if k == 1, ylabel('NCF margin'); end
        if c.adaptive
            yyaxis(ax, 'right')
            h6 = plot(c.tc, c.lambda, '-', 'Color', red, 'LineWidth', 1);
            ylim([0 1.1]); ax.YColor = red;
            if k == 4, ylabel('\lambda'); end
        end
        xlim([0 120]); xlabel('Time (s)'); grid on
    end
    hs = [h1 h2 h3 h4 h5]; nm = {'Command', 'Measured', 'True margin b_{NCF}', 'Estimate b_{OSI}', 'Target b_{tar}'};
    if g == 2, hs(end+1) = h6; nm{end+1} = 'Adaptive factor \lambda'; end
    lg = legend(hs, nm, 'Orientation', 'horizontal', 'Box', 'off');
    lg.Layout.Tile = 'north';
    tag = {'fixed', 'adaptive'};
    print(fig, fullfile(out, ['fig_calibration_' tag{g} '.png']), '-dpng', '-r300'); close(fig)
end
end

function fig = newFig(w, h)
fig = figure('Color', 'w', 'Units', 'inches', 'Position', [1 1 w h], 'Visible', 'off', ...
    'PaperUnits', 'inches', 'PaperSize', [w h], 'PaperPosition', [0 0 w h], 'InvertHardcopy', 'off');
end