#+TITLE: ESRF Double Crystal Monochromator - Feedback Controller
:DRAWER:
#+LANGUAGE: en
#+EMAIL: dehaeze.thomas@gmail.com
#+AUTHOR: Dehaeze Thomas

#+HTML_LINK_HOME: ../index.html
#+HTML_LINK_UP:   ../index.html

#+HTML_HEAD: <link rel="stylesheet" type="text/css" href="https://research.tdehaeze.xyz/css/style.css"/>
#+HTML_HEAD: <script type="text/javascript" src="https://research.tdehaeze.xyz/js/script.js"></script>

#+BIND: org-latex-image-default-option "scale=1"
#+BIND: org-latex-image-default-width ""

#+LaTeX_CLASS: scrreprt
#+LaTeX_CLASS_OPTIONS: [a4paper, 10pt, DIV=12, parskip=full]
#+LaTeX_HEADER_EXTRA: \input{preamble.tex}
#+LATEX_HEADER_EXTRA: \bibliography{ref}

#+PROPERTY: header-args:matlab  :session *MATLAB*
#+PROPERTY: header-args:matlab+ :comments org
#+PROPERTY: header-args:matlab+ :exports both
#+PROPERTY: header-args:matlab+ :results none
#+PROPERTY: header-args:matlab+ :tangle no
#+PROPERTY: header-args:matlab+ :eval no-export
#+PROPERTY: header-args:matlab+ :noweb yes
#+PROPERTY: header-args:matlab+ :mkdirp yes
#+PROPERTY: header-args:matlab+ :output-dir figs

#+PROPERTY: header-args:latex  :headers '("\\usepackage{tikz}" "\\usepackage{import}" "\\import{$HOME/Cloud/tikz/org/}{config.tex}")
#+PROPERTY: header-args:latex+ :imagemagick t :fit yes
#+PROPERTY: header-args:latex+ :iminoptions -scale 100% -density 150
#+PROPERTY: header-args:latex+ :imoutoptions -quality 100
#+PROPERTY: header-args:latex+ :results file raw replace
#+PROPERTY: header-args:latex+ :buffer no
#+PROPERTY: header-args:latex+ :tangle no
#+PROPERTY: header-args:latex+ :eval no-export
#+PROPERTY: header-args:latex+ :exports results
#+PROPERTY: header-args:latex+ :mkdirp yes
#+PROPERTY: header-args:latex+ :output-dir figs
#+PROPERTY: header-args:latex+ :post pdf2svg(file=*this*, ext="png")
:END:

#+begin_export html
  <hr>
  <p>This report is also available as a <a href="./dcm-feedback-control.pdf">pdf</a>.</p>
  <hr>
#+end_export

#+latex: \clearpage

* Introduction                                                        :ignore:

* Estimation of Sensitivity Function
** Matlab Init                                              :noexport:ignore:
#+begin_src matlab :tangle no :exports none :results silent :noweb yes :var current_dir=(file-name-directory buffer-file-name)
<<matlab-dir>>
#+end_src

#+begin_src matlab :exports none :results silent :noweb yes
<<matlab-init>>
#+end_src

#+begin_src matlab :tangle no :noweb yes
<<m-init-path>>
#+end_src

#+begin_src matlab :eval no :noweb yes
<<m-init-path-tangle>>
#+end_src

#+begin_src matlab :noweb yes
<<m-init-other>>
#+end_src

** Load Data
Two scans are performed:
- =1.1= in mode B
- =3.1= in mode C

The difference between the two is that mode C adds the feedback controller.

#+begin_src matlab
%% Load Data of the new LUT method
Ts = 0.1;

ol_drx = 1e-9*double(h5read('xanes_0003.h5','/1.1/measurement/xtal_111_drx_filter')); % Rx [rad]
cl_drx = 1e-9*double(h5read('xanes_0003.h5','/3.1/measurement/xtal_111_drx_filter')); % Rx [rad]

ol_dry = 1e-9*double(h5read('xanes_0003.h5','/1.1/measurement/xtal_111_dry_filter')); % Ry [rad]
cl_dry = 1e-9*double(h5read('xanes_0003.h5','/3.1/measurement/xtal_111_dry_filter')); % Ry [rad]

t = linspace(Ts, Ts*length(ol_drx), length(ol_drx));
#+end_src

By comparison the frequency content of the crystal orientation errors between mode B and mode C, it is possible to estimate the Sensitivity transfer function (Figure [[fig:sensitivity_function_drx_est]]).
#+begin_src matlab
win = hanning(ceil(1/Ts));

[pxx_ol_drx, f] = pwelch(ol_drx, win, [], [], 1/Ts);
[pxx_cl_drx, ~] = pwelch(cl_drx, win, [], [], 1/Ts);

[pxx_ol_dry, ~] = pwelch(ol_dry, win, [], [], 1/Ts);
[pxx_cl_dry, ~] = pwelch(cl_dry, win, [], [], 1/Ts);
#+end_src

#+begin_src matlab :exports none
%% Estimation of Sensitivity function
figure;
hold on;
plot(f, sqrt(pxx_cl_drx)./sqrt(pxx_ol_drx), 'DisplayName', '$R_x$');
plot(f, sqrt(pxx_cl_dry)./sqrt(pxx_ol_dry), 'DisplayName', '$R_y$');
hold off;
set(gca, 'XScale', 'log'); set(gca, 'YScale', 'log');
xlabel('Frequency [Hz]'); ylabel('Sensitivity Function');
legend('location', 'northwest');
#+end_src

#+begin_src matlab :tangle no :exports results :results file replace
exportFig('figs/sensitivity_function_drx_est.pdf', 'width', 'wide', 'height', 'normal');
#+end_src

#+name: fig:sensitivity_function_drx_est
#+caption: Estimation of the sensitivity transfer function magnitude
#+RESULTS:
[[file:figs/sensitivity_function_drx_est.png]]


** Controller
#+begin_src matlab
load('X_tal_cage_PID.mat', 'K');
#+end_src

#+begin_src matlab :exports none
%% Bode plot for the controller
figure;
tiledlayout(3, 1, 'TileSpacing', 'Compact', 'Padding', 'None');

ax1 = nexttile([2,1]);
hold on;
plot(freqs, abs(squeeze(freqresp(K(1,1), freqs, 'Hz'))));
hold off;
set(gca, 'XScale', 'log'); set(gca, 'YScale', 'log');
ylabel('Amplitude [-]'); set(gca, 'XTickLabel',[]);

ax2 = nexttile;
hold on;
plot(freqs, 180/pi*angle(squeeze(freqresp(K(1,1), freqs, 'Hz'))));
hold off;
set(gca, 'XScale', 'log'); set(gca, 'YScale', 'lin');
xlabel('Frequency [Hz]'); ylabel('Phase [deg]');
hold off;
yticks(-360:90:360);
ylim([-180, 180]);

linkaxes([ax1,ax2],'x');
xlim([freqs(1), freqs(end)]);
#+end_src

#+begin_src matlab :tangle no :exports results :results file replace
exportFig('figs/bode_plot_cur_controller.pdf', 'width', 'wide', 'height', 'tall');
#+end_src

#+name: fig:bode_plot_cur_controller
#+caption: Bode Plot of the Controller
#+RESULTS:
[[file:figs/bode_plot_cur_controller.png]]

** Test
#+begin_src matlab
Ts = 5e-3;
cl_drx = 1e-9*double(h5read('xanes_0003.h5','/16.1/measurement/xtal_111_drx_filter')); % Rx [rad]
ol_drx = 1e-9*double(h5read('xanes_0003.h5','/18.1/measurement/xtal_111_drx_filter')); % Rx [rad]

t = linspace(Ts, Ts*length(ol_drx), length(ol_drx));
#+end_src

#+begin_src matlab
figure;
hold on;
plot(t, ol_drx)
plot(t, cl_drx)
#+end_src

#+begin_src matlab
win = hanning(ceil(10/Ts));

[pxx_ol_drx, f] = pwelch(ol_drx, win, [], [], 1/Ts);
[pxx_cl_drx, ~] = pwelch(cl_drx, win, [], [], 1/Ts);
#+end_src

#+begin_src matlab :exports none
%% Estimation of Sensitivity function
figure;
hold on;
plot(f, sqrt(pxx_cl_drx)./sqrt(pxx_ol_drx), 'DisplayName', '$R_x$');
hold off;
set(gca, 'XScale', 'log'); set(gca, 'YScale', 'log');
xlabel('Frequency [Hz]'); ylabel('Sensitivity Function');
legend('location', 'northwest');
#+end_src

#+begin_src matlab :exports none
%% Estimation of Sensitivity function
figure;
hold on;
plot(f, sqrt(pxx_ol_drx), 'DisplayName', '$R_x$ - OL');
plot(f, sqrt(pxx_cl_drx), 'DisplayName', '$R_x$ - CL');
hold off;
set(gca, 'XScale', 'log'); set(gca, 'YScale', 'log');
xlabel('Frequency [Hz]'); ylabel('Amplitude Spectral Density [$m/\sqrt{Hz}$]');
legend('location', 'northwest');
#+end_src

* System Identification
** Matlab Init                                              :noexport:ignore:
#+begin_src matlab :tangle no :exports none :results silent :noweb yes :var current_dir=(file-name-directory buffer-file-name)
<<matlab-dir>>
#+end_src

#+begin_src matlab :exports none :results silent :noweb yes
<<matlab-init>>
#+end_src

#+begin_src matlab :tangle no :noweb yes
<<m-init-path>>
#+end_src

#+begin_src matlab :eval no :noweb yes
<<m-init-path-tangle>>
#+end_src

#+begin_src matlab :noweb yes
<<m-init-other>>
#+end_src

** Identification ID24
#+begin_src matlab
load('test_id_id24_3.mat')
#+end_src

#+begin_src matlab
t = 1e-4*ones(size(fjpur, 1), 1);

ur.dz  = fjpur(:,1) - mean(fjpur(:,1));
ur.dry = fjpur(:,2) - mean(fjpur(:,2));
ur.drx = fjpur(:,3) - mean(fjpur(:,3));
ur.u   = fjpur(:,7) - mean(fjpur(:,7));

uh.dz  = fjpuh(:,1) - mean(fjpuh(:,1));
uh.dry = fjpuh(:,2) - mean(fjpuh(:,2));
uh.drx = fjpuh(:,3) - mean(fjpuh(:,3));
uh.u   = fjpuh(:,8) - mean(fjpuh(:,8));

d.dz  = fjpd(:,1) - mean(fjpd(:,1));
d.dry = fjpd(:,2) - mean(fjpd(:,2));
d.drx = fjpd(:,3) - mean(fjpd(:,3));
d.u   = fjpd(:,9) - mean(fjpd(:,9));
#+end_src

#+begin_src matlab
J_a_311 = [1,  0.14, -0.0675
           1,  0.14,  0.1525
           1, -0.14,  0.0425];

J_a_111 = [1,  0.14, -0.1525
           1,  0.14,  0.0675
           1, -0.14, -0.0425];

ur.y = [J_a_311 * [-ur.dz, ur.dry,-ur.drx]']';
uh.y = [J_a_311 * [-uh.dz, uh.dry,-uh.drx]']';
d.y  = [J_a_311 * [-d.dz,  d.dry, -d.drx]']';
#+end_src

#+begin_src matlab
%% Sampling Time and Frequency
Ts = 1e-4; % [s]
Fs = 1/Ts; % [Hz]

% Hannning Windows
win = hanning(ceil(1*Fs));
#+end_src

#+begin_src matlab
%% And we get the frequency vector
[G_ur, f] = tfestimate(ur.u, ur.y, win, [], [], 1/Ts);
[G_uh, ~] = tfestimate(uh.u, uh.y, win, [], [], 1/Ts);
[G_d,  ~] = tfestimate(d.u,  d.y,  win, [], [], 1/Ts);
#+end_src

#+begin_src matlab
[coh_ur, ~] = mscohere(ur.u, ur.y, win, [], [], 1/Ts);
[coh_uh, ~] = mscohere(uh.u, uh.y, win, [], [], 1/Ts);
[coh_d,  ~] = mscohere(d.u,  d.y,  win, [], [], 1/Ts);
#+end_src

#+begin_src matlab :exports none
%% Coherence
figure;
tiledlayout(1, 1, 'TileSpacing', 'Compact', 'Padding', 'None');
hold on;
plot(f, coh_ur(:,1), 'DisplayName', '$u_r$');
plot(f, coh_uh(:,2), 'DisplayName', '$u_h$');
plot(f, coh_d( :,3), 'DisplayName', '$u_d$');
hold off;
set(gca, 'XScale', 'log'); set(gca, 'YScale', 'lin');
xlabel('Frequency [Hz]'); ylabel('Coherence');
legend('location', 'southeast');
xlim([1, 1e3]);
#+end_src

#+begin_src matlab :exports none
%% Bode plot of the DCM dynamics in the frame of the Fast Jacks
figure;
tiledlayout(3, 1, 'TileSpacing', 'Compact', 'Padding', 'None');

ax1 = nexttile([2,1]);
hold on;
plot(f, abs(G_ur(:,1)), 'DisplayName', '$u_r$');
plot(f, abs(G_uh(:,2)), 'DisplayName', '$u_h$');
plot(f, abs(G_d( :,3)), 'DisplayName', '$u_d$');
plot(f, abs(G_ur(:,2)), 'color', [0, 0, 0, 0.2], ...
     'DisplayName', 'Off Diagonal');
plot(f, abs(G_ur(:,3)), 'color', [0, 0, 0, 0.2], ...
     'HandleVisibility', 'off');
plot(f, abs(G_uh(:,1)), 'color', [0, 0, 0, 0.2], ...
     'HandleVisibility', 'off');
plot(f, abs(G_uh(:,3)), 'color', [0, 0, 0, 0.2], ...
     'HandleVisibility', 'off');
plot(f, abs(G_d(:,1)), 'color', [0, 0, 0, 0.2], ...
     'HandleVisibility', 'off');
plot(f, abs(G_d(:,2)), 'color', [0, 0, 0, 0.2], ...
     'HandleVisibility', 'off');
hold off;
set(gca, 'XScale', 'log'); set(gca, 'YScale', 'log');
ylabel('Amplitude'); set(gca, 'XTickLabel',[]);
ylim([1e-2, 1e2]);
legend('location', 'northwest');

ax2 = nexttile;
hold on;
plot(f, 180/pi*angle(G_ur(:,1)));
plot(f, 180/pi*angle(G_uh(:,2)));
plot(f, 180/pi*angle(G_d(:,3)));
hold off;
set(gca, 'XScale', 'log'); set(gca, 'YScale', 'lin');
xlabel('Frequency [Hz]'); ylabel('Phase [deg]');
hold off;
yticks(-360:90:360);
% ylim([-45, 45]);

linkaxes([ax1,ax2],'x');
xlim([1, 1e3]);
#+end_src

** Identification
#+begin_src matlab
ur = load('FJPUR_step.mat');
uh = load('FJPUH_step.mat');
d  = load('FJPD_step.mat');
#+end_src

|  1 | dz311  |
|  2 | dry311 |
|  3 | drx311 |
|  4 | dz111  |
|  5 | dry111 |
|  6 | drx111 |
|  7 | fjpur  |
|  8 | fjpuh  |
|  9 | fjpd   |
| 10 | bragg  |

#+begin_src matlab
ur.time = ur.time - ur.time(1);
ur.allValues(:, 1) = ur.allValues(:, 1) - mean(ur.allValues(ur.time<1, 1));
ur.allValues(:, 2) = ur.allValues(:, 2) - mean(ur.allValues(ur.time<1, 2));
ur.allValues(:, 3) = ur.allValues(:, 3) - mean(ur.allValues(ur.time<1, 3));

t_filt = ur.time > 48 & ur.time < 60;

ur.u = ur.allValues(t_filt, 7);
ur.y_111 = [-ur.allValues(t_filt, 1), ur.allValues(t_filt, 2), ur.allValues(t_filt, 3)];
#+end_src

#+begin_src matlab
uh.time = uh.time - uh.time(1);
uh.allValues(:, 1) = uh.allValues(:, 1) - mean(uh.allValues(uh.time<1, 1));
uh.allValues(:, 2) = uh.allValues(:, 2) - mean(uh.allValues(uh.time<1, 2));
uh.allValues(:, 3) = uh.allValues(:, 3) - mean(uh.allValues(uh.time<1, 3));

uh.u = uh.allValues(t_filt, 8);
uh.y_111 = [-uh.allValues(t_filt, 1), uh.allValues(t_filt, 2), uh.allValues(t_filt, 3)];
#+end_src

#+begin_src matlab
d.time = d.time - d.time(1);
d.allValues(:, 1) = d.allValues(:, 1) - mean(d.allValues(d.time<1, 1));
d.allValues(:, 2) = d.allValues(:, 2) - mean(d.allValues(d.time<1, 2));
d.allValues(:, 3) = d.allValues(:, 3) - mean(d.allValues(d.time<1, 3));

d.u = d.allValues(t_filt, 9);
d.y_111 = [-d.allValues(t_filt, 1), d.allValues(t_filt, 2), d.allValues(t_filt, 3)];
#+end_src

#+begin_src matlab
J_a_111 = [1,  0.14, -0.0675
           1,  0.14,  0.1525
           1, -0.14,  0.0425];

J_a_311 = [1,  0.14, -0.1525
           1,  0.14,  0.0675
           1, -0.14, -0.0425];

ur.y = [J_a_311 * ur.y_111']';
uh.y = [J_a_311 * uh.y_111']';
d.y  = [J_a_311 * d.y_111']';
#+end_src

#+begin_src matlab
%% Sampling Time and Frequency
Ts = 1e-4; % [s]
Fs = 1/Ts; % [Hz]

% Hannning Windows
win = hanning(ceil(5*Fs));
#+end_src

#+begin_src matlab
%% And we get the frequency vector
[G_ur, f] = tfestimate(ur.u, ur.y, win, [], [], 1/Ts);
[G_uh, ~] = tfestimate(uh.u, uh.y, win, [], [], 1/Ts);
[G_d,  ~] = tfestimate(d.u,  d.y,  win, [], [], 1/Ts);
#+end_src

#+begin_src matlab
[coh_ur, ~] = mscohere(ur.u, ur.y, win, [], [], 1/Ts);
[coh_uh, ~] = mscohere(uh.u, uh.y, win, [], [], 1/Ts);
[coh_d,  ~] = mscohere(d.u,  d.y,  win, [], [], 1/Ts);
#+end_src

#+begin_src matlab :exports none
%% Coherence
figure;
tiledlayout(1, 1, 'TileSpacing', 'Compact', 'Padding', 'None');
hold on;
plot(f, coh_ur(:,1), 'DisplayName', '$u_r$');
plot(f, coh_uh(:,2), 'DisplayName', '$u_h$');
plot(f, coh_d( :,3), 'DisplayName', '$u_d$');
hold off;
set(gca, 'XScale', 'log'); set(gca, 'YScale', 'lin');
xlabel('Frequency [Hz]'); ylabel('Coherence');
legend('location', 'southeast');
xlim([1, 1e3]);
#+end_src

#+begin_src matlab :tangle no :exports results :results file replace
exportFig('figs/coherence_id_dcm_dyn.pdf', 'width', 'wide', 'height', 'normal');
#+end_src

#+name: fig:coherence_id_dcm_dyn
#+caption: Coherence
#+RESULTS:
[[file:figs/coherence_id_dcm_dyn.png]]


#+begin_src matlab :exports none
%% Bode plot of the DCM dynamics in the frame of the Fast Jacks
figure;
tiledlayout(3, 1, 'TileSpacing', 'Compact', 'Padding', 'None');

ax1 = nexttile([2,1]);
hold on;
plot(f, abs(G_ur(:,1)), 'DisplayName', '$u_r$');
plot(f, abs(G_uh(:,2)), 'DisplayName', '$u_h$');
plot(f, abs(G_d( :,3)), 'DisplayName', '$u_d$');
plot(f, abs(G_ur(:,2)), 'color', [0, 0, 0, 0.2], ...
     'DisplayName', 'Off Diagonal');
plot(f, abs(G_ur(:,3)), 'color', [0, 0, 0, 0.2], ...
     'HandleVisibility', 'off');
plot(f, abs(G_uh(:,1)), 'color', [0, 0, 0, 0.2], ...
     'HandleVisibility', 'off');
plot(f, abs(G_uh(:,3)), 'color', [0, 0, 0, 0.2], ...
     'HandleVisibility', 'off');
plot(f, abs(G_d(:,1)), 'color', [0, 0, 0, 0.2], ...
     'HandleVisibility', 'off');
plot(f, abs(G_d(:,2)), 'color', [0, 0, 0, 0.2], ...
     'HandleVisibility', 'off');
hold off;
set(gca, 'XScale', 'log'); set(gca, 'YScale', 'log');
ylabel('Amplitude'); set(gca, 'XTickLabel',[]);
ylim([1e-2, 1e2]);
legend('location', 'southeast');

ax2 = nexttile;
hold on;
plot(f, 180/pi*angle(G_ur(:,1)));
plot(f, 180/pi*angle(G_uh(:,2)));
plot(f, 180/pi*angle(G_d(:,3)));
hold off;
set(gca, 'XScale', 'log'); set(gca, 'YScale', 'lin');
xlabel('Frequency [Hz]'); ylabel('Phase [deg]');
hold off;
yticks(-360:90:360);
% ylim([-45, 45]);

linkaxes([ax1,ax2],'x');
xlim([1, 1e3]);
#+end_src

#+begin_src matlab :tangle no :exports results :results file replace
exportFig('figs/bode_plot_dcm_dynamics.pdf', 'width', 'wide', 'height', 'tall');
#+end_src

#+name: fig:bode_plot_dcm_dynamics
#+caption: Bode Plot of the DCM dynamics in the frame of the fast jack.
#+RESULTS:
[[file:figs/bode_plot_dcm_dynamics.png]]


#+begin_src matlab
%% Previously used controller
load('X_tal_cage_PID.mat', 'K');
#+end_src

#+begin_src matlab
%% Controller design
s = tf('s');

% Lead
a  = 4;  % Amount of phase lead / width of the phase lead / high frequency gain
wc = 2*pi*20; % Frequency with the maximum phase lead [rad/s]

% Low Pass Filter
w0 = 2*pi*100; % Cut-off frequency [rad/s]
xi = 0.4; % Damping Ratio

Kb = eye(3)*(2*pi*20)^2/(s^2) *1/(sqrt(a))* (1 + s/(wc/sqrt(a)))/(1 + s/(wc*sqrt(a))) * 1/(1 + 2*xi/w0*s + s^2/w0^2);;
#+end_src

#+begin_src matlab :exports none
%% Loop Gain
figure;
tiledlayout(3, 1, 'TileSpacing', 'Compact', 'Padding', 'None');

ax1 = nexttile([2,1]);
hold on;
plot(f, abs(G_ur(:,1).*squeeze(freqresp(Kb(1,1), f, 'Hz'))), 'DisplayName', '$u_r$');
plot(f, abs(G_uh(:,2).*squeeze(freqresp(Kb(2,2), f, 'Hz'))), 'DisplayName', '$u_h$');
plot(f, abs(G_d( :,3).*squeeze(freqresp(Kb(3,3), f, 'Hz'))), 'DisplayName', '$d$');
hold off;
set(gca, 'XScale', 'log'); set(gca, 'YScale', 'log');
ylabel('Amplitude'); set(gca, 'XTickLabel',[]);
ylim([1e-4, 1e2]);
legend('location', 'northeast');

ax2 = nexttile;
hold on;
plot(f, 180/pi*angle(G_ur(:,1).*squeeze(freqresp(K(1,1), f, 'Hz'))));
plot(f, 180/pi*angle(G_uh(:,2).*squeeze(freqresp(K(2,2), f, 'Hz'))));
plot(f, 180/pi*angle(G_d(:,3).*squeeze(freqresp(K(3,3), f, 'Hz'))));
hold off;
set(gca, 'XScale', 'log'); set(gca, 'YScale', 'lin');
xlabel('Frequency [Hz]'); ylabel('Phase [deg]');
hold off;
yticks(-360:90:360);

linkaxes([ax1,ax2],'x');
xlim([1, 1e3]);
#+end_src

#+begin_src matlab :tangle no :exports results :results file replace
exportFig('figs/loop_gain_dcm_contr_simple.pdf', 'width', 'wide', 'height', 'tall');
#+end_src

#+name: fig:loop_gain_dcm_contr_simple
#+caption: Loop gain
#+RESULTS:
[[file:figs/loop_gain_dcm_contr_simple.png]]


#+begin_src matlab :exports none
%% Loop Gain
figure;
tiledlayout(3, 1, 'TileSpacing', 'Compact', 'Padding', 'None');

ax1 = nexttile([2,1]);
hold on;
plot(f, abs(G_d(:,3).*squeeze(freqresp(K(1,1), f, 'Hz'))));
plot(f, abs(G_d(:,3).*squeeze(freqresp(Kb(1,1), f, 'Hz'))));
hold off;
set(gca, 'XScale', 'log'); set(gca, 'YScale', 'log');
ylabel('Amplitude'); set(gca, 'XTickLabel',[]);
ylim([1e-4, 1e2]);

ax2 = nexttile;
hold on;
plot(f, 180/pi*angle(G_d(:,3).*squeeze(freqresp(K(1,1), f, 'Hz'))));
plot(f, 180/pi*angle(G_d(:,3).*squeeze(freqresp(Kb(1,1), f, 'Hz'))));
hold off;
set(gca, 'XScale', 'log'); set(gca, 'YScale', 'lin');
xlabel('Frequency [Hz]'); ylabel('Phase [deg]');
hold off;
yticks(-360:90:360);

linkaxes([ax1,ax2],'x');
xlim([1, 1e3]);
#+end_src

#+begin_src matlab :tangle no :exports results :results file replace
exportFig('figs/loop_gain_diag_old_new_contr.pdf', 'width', 'wide', 'height', 'tall');
#+end_src

#+name: fig:loop_gain_diag_old_new_contr
#+caption: Loop gain
#+RESULTS:
[[file:figs/loop_gain_diag_old_new_contr.png]]

Compare Sensitivity functions
#+begin_src matlab :exports none
%% Sensitivity function
figure;
tiledlayout(1, 1, 'TileSpacing', 'Compact', 'Padding', 'None');

hold on;
plot(f, 1./abs(1 + G_d(:,3).*squeeze(freqresp(K(1,1), f, 'Hz'))));
plot(f, 1./abs(1 + G_d(:,3).*squeeze(freqresp(Kb(1,1), f, 'Hz'))));
hold off;
set(gca, 'XScale', 'log'); set(gca, 'YScale', 'log');
xlabel('Frequency [Hz]'); ylabel('Amplitude');
ylim([1e-2, 1e1]); xlim([1, 1e3]);
#+end_src

#+begin_src matlab :tangle no :exports results :results file replace
exportFig('figs/sensitivity_comp.pdf', 'width', 'wide', 'height', 'normal');
#+end_src

#+name: fig:sensitivity_comp
#+caption: Comparison of sensitivity functions
#+RESULTS:
[[file:figs/sensitivity_comp.png]]


#+begin_src matlab
L  = zeros(3, 3, length(f));
Lb = zeros(3, 3, length(f));

for i_f = 1:length(f)
    L(:,:,i_f)  = [G_ur(i_f,:); G_uh(i_f,:); G_d(i_f,:)]*freqresp(K , f(i_f), 'Hz');
    Lb(:,:,i_f) = [G_ur(i_f,:); G_uh(i_f,:); G_d(i_f,:)]*freqresp(Kb, f(i_f), 'Hz');
end
#+end_src

#+begin_src matlab :exports none
%% Compute the Eigenvalues of the loop gain
Ldet  = zeros(3, length(f));
Ldetb = zeros(3, length(f));

% Loop gain
for i_f = 1:length(f)
    Ldet( :, i_f) = eig(squeeze(L( :,:,i_f)));
    Ldetb(:, i_f) = eig(squeeze(Lb(:,:,i_f)));
end
#+end_src

#+begin_src matlab :exports none
%% Plot of the eigenvalues of L in the complex plane
figure;
hold on;
for i = 1:size(Ldet,1)
    plot(real(Ldet(i,:)),  imag(Ldet(i,:)), '.', 'color', colors(1, :));
    plot(real(Ldet(i,:)), -imag(Ldet(i,:)), '.', 'color', colors(1, :));

    plot(real(Ldetb(i,:)),  imag(Ldetb(i,:)), '.', 'color', colors(2, :));
    plot(real(Ldetb(i,:)), -imag(Ldetb(i,:)), '.', 'color', colors(2, :));
end
plot(-1, 0, 'kx', 'HandleVisibility', 'off');
hold off;
set(gca, 'XScale', 'lin'); set(gca, 'YScale', 'lin');
xlabel('Real'); ylabel('Imag');
xlim([-3, 1]); ylim([-2, 2]);
#+end_src

#+begin_src matlab :tangle no :exports results :results file replace
exportFig('figs/loci_loop_gain_comp_controllers.pdf', 'width', 'wide', 'height', 'tall');
#+end_src

#+caption: Root Locus
#+RESULTS:
[[file:figs/loci_loop_gain_comp_controllers.png]]


** Identification - New
#+begin_src matlab
ur = load('FJPUR_step_new.mat');
uh = load('FJPUH_step_new.mat');
d  = load('FJPD_step_new.mat');
#+end_src

|  1 | dz311  |
|  2 | dry311 |
|  3 | drx311 |
|  4 | dz111  |
|  5 | dry111 |
|  6 | drx111 |
|  7 | fjpur  |
|  8 | fjpuh  |
|  9 | fjpd   |
| 10 | bragg  |

#+begin_src matlab
ur.time = ur.time - ur.time(1);
ur.allValues(:, 1) = ur.allValues(:, 1) - mean(ur.allValues(ur.time<0.1, 1));
ur.allValues(:, 2) = ur.allValues(:, 2) - mean(ur.allValues(ur.time<0.1, 2));
ur.allValues(:, 3) = ur.allValues(:, 3) - mean(ur.allValues(ur.time<0.1, 3));

t_filt = ur.time < 5;

ur.u = ur.allValues(t_filt, 7);
ur.y_111 = [-ur.allValues(t_filt, 1), ur.allValues(t_filt, 2), ur.allValues(t_filt, 3)];
#+end_src

#+begin_src matlab
uh.time = uh.time - uh.time(1);
uh.allValues(:, 1) = uh.allValues(:, 1) - mean(uh.allValues(uh.time<0.1, 1));
uh.allValues(:, 2) = uh.allValues(:, 2) - mean(uh.allValues(uh.time<0.1, 2));
uh.allValues(:, 3) = uh.allValues(:, 3) - mean(uh.allValues(uh.time<0.1, 3));

uh.u = uh.allValues(t_filt, 8);
uh.y_111 = [-uh.allValues(t_filt, 1), uh.allValues(t_filt, 2), uh.allValues(t_filt, 3)];
#+end_src

#+begin_src matlab
d.time = d.time - d.time(1);
d.allValues(:, 1) = d.allValues(:, 1) - mean(d.allValues(d.time<0.1, 1));
d.allValues(:, 2) = d.allValues(:, 2) - mean(d.allValues(d.time<0.1, 2));
d.allValues(:, 3) = d.allValues(:, 3) - mean(d.allValues(d.time<0.1, 3));

d.u = d.allValues(t_filt, 9);
d.y_111 = [-d.allValues(t_filt, 1), d.allValues(t_filt, 2), d.allValues(t_filt, 3)];
#+end_src

#+begin_src matlab
J_a_111 = [1,  0.14, -0.0675
           1,  0.14,  0.1525
           1, -0.14,  0.0425];

J_a_311 = [1,  0.14, -0.1525
           1,  0.14,  0.0675
           1, -0.14, -0.0425];

ur.y = [J_a_311 * ur.y_111']';
uh.y = [J_a_311 * uh.y_111']';
d.y  = [J_a_311 * d.y_111']';
#+end_src

#+begin_src matlab
%% Sampling Time and Frequency
Ts = 1e-4; % [s]
Fs = 1/Ts; % [Hz]

% Hannning Windows
win = hanning(ceil(5*Fs));
#+end_src

#+begin_src matlab
%% And we get the frequency vector
[G_ur, f] = tfestimate(ur.u, ur.y, win, [], [], 1/Ts);
[G_uh, ~] = tfestimate(uh.u, uh.y, win, [], [], 1/Ts);
[G_d,  ~] = tfestimate(d.u,  d.y,  win, [], [], 1/Ts);
#+end_src

#+begin_src matlab
[coh_ur, ~] = mscohere(ur.u, ur.y, win, [], [], 1/Ts);
[coh_uh, ~] = mscohere(uh.u, uh.y, win, [], [], 1/Ts);
[coh_d,  ~] = mscohere(d.u,  d.y,  win, [], [], 1/Ts);
#+end_src

#+begin_src matlab :exports none
%% Coherence
figure;
tiledlayout(1, 1, 'TileSpacing', 'Compact', 'Padding', 'None');
hold on;
plot(f, coh_ur(:,1), 'DisplayName', '$u_r$');
plot(f, coh_uh(:,2), 'DisplayName', '$u_h$');
plot(f, coh_d( :,3), 'DisplayName', '$u_d$');
hold off;
set(gca, 'XScale', 'log'); set(gca, 'YScale', 'lin');
xlabel('Frequency [Hz]'); ylabel('Coherence');
legend('location', 'southeast');
xlim([1, 1e3]);
#+end_src

#+begin_src matlab :exports none
%% Bode plot of the DCM dynamics in the frame of the Fast Jacks
figure;
tiledlayout(3, 1, 'TileSpacing', 'Compact', 'Padding', 'None');

ax1 = nexttile([2,1]);
hold on;
plot(f, abs(G_ur(:,1)), 'DisplayName', '$u_r$');
plot(f, abs(G_uh(:,2)), 'DisplayName', '$u_h$');
plot(f, abs(G_d( :,3)), 'DisplayName', '$u_d$');
plot(f, abs(G_ur(:,2)), 'color', [0, 0, 0, 0.2], ...
     'DisplayName', 'Off Diagonal');
plot(f, abs(G_ur(:,3)), 'color', [0, 0, 0, 0.2], ...
     'HandleVisibility', 'off');
plot(f, abs(G_uh(:,1)), 'color', [0, 0, 0, 0.2], ...
     'HandleVisibility', 'off');
plot(f, abs(G_uh(:,3)), 'color', [0, 0, 0, 0.2], ...
     'HandleVisibility', 'off');
plot(f, abs(G_d(:,1)), 'color', [0, 0, 0, 0.2], ...
     'HandleVisibility', 'off');
plot(f, abs(G_d(:,2)), 'color', [0, 0, 0, 0.2], ...
     'HandleVisibility', 'off');
hold off;
set(gca, 'XScale', 'log'); set(gca, 'YScale', 'log');
ylabel('Amplitude'); set(gca, 'XTickLabel',[]);
ylim([1e-2, 1e2]);
legend('location', 'southeast');

ax2 = nexttile;
hold on;
plot(f, 180/pi*angle(G_ur(:,1)));
plot(f, 180/pi*angle(G_uh(:,2)));
plot(f, 180/pi*angle(G_d(:,3)));
hold off;
set(gca, 'XScale', 'log'); set(gca, 'YScale', 'lin');
xlabel('Frequency [Hz]'); ylabel('Phase [deg]');
hold off;
yticks(-360:90:360);
% ylim([-45, 45]);

linkaxes([ax1,ax2],'x');
xlim([1, 1e3]);
#+end_src

#+begin_src matlab
%% Previously used controller
load('X_tal_cage_PID.mat', 'K');
#+end_src

#+begin_src matlab
%% Controller design
s = tf('s');

% Lead
a  = 4;  % Amount of phase lead / width of the phase lead / high frequency gain
wc = 2*pi*20; % Frequency with the maximum phase lead [rad/s]

% Low Pass Filter
w0 = 2*pi*100; % Cut-off frequency [rad/s]
xi = 0.4; % Damping Ratio

Kb = eye(3)*(2*pi*20)^2/(s^2) *1/(sqrt(a))* (1 + s/(wc/sqrt(a)))/(1 + s/(wc*sqrt(a))) * 1/(1 + 2*xi/w0*s + s^2/w0^2);;
#+end_src

#+begin_src matlab :exports none
%% Loop Gain
figure;
tiledlayout(3, 1, 'TileSpacing', 'Compact', 'Padding', 'None');

ax1 = nexttile([2,1]);
hold on;
plot(f, abs(G_ur(:,1).*squeeze(freqresp(Kb(1,1), f, 'Hz'))), 'DisplayName', '$u_r$');
plot(f, abs(G_uh(:,2).*squeeze(freqresp(Kb(2,2), f, 'Hz'))), 'DisplayName', '$u_h$');
plot(f, abs(G_d( :,3).*squeeze(freqresp(Kb(3,3), f, 'Hz'))), 'DisplayName', '$d$');
hold off;
set(gca, 'XScale', 'log'); set(gca, 'YScale', 'log');
ylabel('Amplitude'); set(gca, 'XTickLabel',[]);
ylim([1e-4, 1e2]);
legend('location', 'northeast');

ax2 = nexttile;
hold on;
plot(f, 180/pi*angle(G_ur(:,1).*squeeze(freqresp(K(1,1), f, 'Hz'))));
plot(f, 180/pi*angle(G_uh(:,2).*squeeze(freqresp(K(2,2), f, 'Hz'))));
plot(f, 180/pi*angle(G_d(:,3).*squeeze(freqresp(K(3,3), f, 'Hz'))));
hold off;
set(gca, 'XScale', 'log'); set(gca, 'YScale', 'lin');
xlabel('Frequency [Hz]'); ylabel('Phase [deg]');
hold off;
yticks(-360:90:360);

linkaxes([ax1,ax2],'x');
xlim([1, 1e3]);
#+end_src

Compare Sensitivity functions
#+begin_src matlab :exports none
%% Sensitivity function
figure;
tiledlayout(1, 1, 'TileSpacing', 'Compact', 'Padding', 'None');


hold on;
plot(f, 1./abs(1 + G_d(:,3).*squeeze(freqresp(K(1,1), f, 'Hz'))));
plot(f, 1./abs(1 + G_d(:,3).*squeeze(freqresp(Kb(1,1), f, 'Hz'))));
hold off;
set(gca, 'XScale', 'log'); set(gca, 'YScale', 'log');
xlabel('Frequency [Hz]'); ylabel('Amplitude');
ylim([1e-2, 1e1]); xlim([1, 1e3]);
#+end_src

#+begin_src matlab :tangle no :exports results :results file replace
exportFig('figs/sensitivity_comp.pdf', 'width', 'wide', 'height', 'normal');
#+end_src

#+name: fig:sensitivity_comp
#+caption: Comparison of sensitivity functions
#+RESULTS:
[[file:figs/sensitivity_comp.png]]


#+begin_src matlab
L  = zeros(3, 3, length(f));
Lb = zeros(3, 3, length(f));

for i_f = 1:length(f)
    L(:,:,i_f)  = [G_ur(i_f,:); G_uh(i_f,:); G_d(i_f,:)]*freqresp(K , f(i_f), 'Hz');
    Lb(:,:,i_f) = [G_ur(i_f,:); G_uh(i_f,:); G_d(i_f,:)]*freqresp(Kb, f(i_f), 'Hz');
end
#+end_src

#+begin_src matlab :exports none
%% Compute the Eigenvalues of the loop gain
Ldet  = zeros(3, length(f));
Ldetb = zeros(3, length(f));

% Loop gain
for i_f = 1:length(f)
    Ldet( :, i_f) = eig(squeeze(L( :,:,i_f)));
    Ldetb(:, i_f) = eig(squeeze(Lb(:,:,i_f)));
end
#+end_src

#+begin_src matlab :exports none
%% Plot of the eigenvalues of L in the complex plane
figure;
hold on;
for i = 1:size(Ldet,1)
    plot(real(Ldet(i,:)),  imag(Ldet(i,:)), '.', 'color', colors(1, :));
    plot(real(Ldet(i,:)), -imag(Ldet(i,:)), '.', 'color', colors(1, :));

    plot(real(Ldetb(i,:)),  imag(Ldetb(i,:)), '.', 'color', colors(2, :));
    plot(real(Ldetb(i,:)), -imag(Ldetb(i,:)), '.', 'color', colors(2, :));
end
plot(-1, 0, 'kx', 'HandleVisibility', 'off');
hold off;
set(gca, 'XScale', 'lin'); set(gca, 'YScale', 'lin');
xlabel('Real'); ylabel('Imag');
xlim([-3, 1]); ylim([-2, 2]);
#+end_src

#+begin_src matlab :tangle no :exports results :results file replace
exportFig('figs/loci_loop_gain_comp_controllers.pdf', 'width', 'wide', 'height', 'tall');
#+end_src

#+caption: Root Locus
#+RESULTS:
[[file:figs/loci_loop_gain_comp_controllers.png]]


** Identification - White noise
#+begin_src matlab
ur = load('fjpur_white_noise.mat');
uh = load('fjpuh_white_noise.mat');
d  = load('fjpd_white_noise.mat');
#+end_src

| 1 | dz111  |
| 2 | dry111 |
| 3 | drx111 |
| 4 | fjpur  |
| 5 | fjpuh  |
| 6 | fjpd   |
| 7 | bragg  |

#+begin_src matlab
ur.time = ur.time - ur.time(1);

ur.drx = ur.drx - mean(ur.drx);
ur.dry = ur.dry - mean(ur.dry);
ur.dz  = ur.dz  - mean(ur.dz);
#+end_src

#+begin_src matlab
uh.time = uh.time - uh.time(1);

uh.drx = uh.drx - mean(uh.drx);
uh.dry = uh.dry - mean(uh.dry);
uh.dz  = uh.dz  - mean(uh.dz);
#+end_src

#+begin_src matlab
d.time = d.time - d.time(1);

d.drx = d.drx - mean(d.drx);
d.dry = d.dry - mean(d.dry);
d.dz  = d.dz  - mean(d.dz);
#+end_src

#+begin_src matlab
J_a_111 = [1,  0.14, -0.0675
           1,  0.14,  0.1525
           1, -0.14,  0.0425];

ur.y = [J_a_111 * [-ur.dz, ur.dry, ur.drx]']';
uh.y = [J_a_111 * [-uh.dz, uh.dry, uh.drx]']';
d.y  = [J_a_111 * [-d.dz, d.dry, d.drx]']';
#+end_src

#+begin_src matlab
%% Sampling Time and Frequency
Ts = 1e-4; % [s]
Fs = 1/Ts; % [Hz]

% Hannning Windows
win = hanning(ceil(0.5*Fs));
#+end_src

#+begin_src matlab
%% And we get the frequency vector
[G_ur, f] = tfestimate(ur.fjpur, ur.y, win, [], [], 1/Ts);
[G_uh, ~] = tfestimate(uh.fjpuh, uh.y, win, [], [], 1/Ts);
[G_d,  ~] = tfestimate(d.fjpd,   d.y,  win, [], [], 1/Ts);
#+end_src

#+begin_src matlab
[coh_ur, ~] = mscohere(ur.fjpur, ur.y, win, [], [], 1/Ts);
[coh_uh, ~] = mscohere(uh.fjpuh, uh.y, win, [], [], 1/Ts);
[coh_d,  ~] = mscohere(d.fjpd,   d.y,  win, [], [], 1/Ts);
#+end_src

#+begin_src matlab :exports none
%% Coherence
figure;
tiledlayout(1, 1, 'TileSpacing', 'Compact', 'Padding', 'None');
hold on;
plot(f, coh_ur(:,1), 'DisplayName', '$u_r$');
plot(f, coh_uh(:,2), 'DisplayName', '$u_h$');
plot(f, coh_d(:,3),  'DisplayName', '$d$');
hold off;
set(gca, 'XScale', 'log'); set(gca, 'YScale', 'lin');
xlabel('Frequency [Hz]'); ylabel('Coherence');
legend('location', 'southeast');
xlim([1, 1e3]);
#+end_src

#+begin_src matlab :tangle no :exports results :results file replace
exportFig('figs/coherence_ident_noise.pdf', 'width', 'wide', 'height', 'normal');
#+end_src

#+name: fig:coherence_ident_noise
#+caption: description
#+RESULTS:
[[file:figs/coherence_ident_noise.png]]

#+begin_src matlab :exports none
%% Bode plot of the DCM dynamics in the frame of the Fast Jacks
figure;
tiledlayout(3, 1, 'TileSpacing', 'Compact', 'Padding', 'None');

ax1 = nexttile([2,1]);
hold on;
plot(f, abs(G_ur(:,1)), 'DisplayName', '$u_r$');
plot(f, abs(G_uh(:,2)), 'DisplayName', '$u_h$');
plot(f, abs(G_d( :,3)), 'DisplayName', '$u_d$');
plot(f, abs(G_ur(:,2)), 'color', [0, 0, 0, 0.2], ...
     'DisplayName', 'Off Diagonal');
plot(f, abs(G_ur(:,3)), 'color', [0, 0, 0, 0.2], ...
     'HandleVisibility', 'off');
plot(f, abs(G_uh(:,1)), 'color', [0, 0, 0, 0.2], ...
     'HandleVisibility', 'off');
plot(f, abs(G_uh(:,3)), 'color', [0, 0, 0, 0.2], ...
     'HandleVisibility', 'off');
plot(f, abs(G_d(:,1)), 'color', [0, 0, 0, 0.2], ...
     'HandleVisibility', 'off');
plot(f, abs(G_d(:,2)), 'color', [0, 0, 0, 0.2], ...
     'HandleVisibility', 'off');
hold off;
set(gca, 'XScale', 'log'); set(gca, 'YScale', 'log');
ylabel('Amplitude'); set(gca, 'XTickLabel',[]);
ylim([1e-2, 1e2]);
legend('location', 'northwest');

ax2 = nexttile;
hold on;
plot(f, 180/pi*angle(G_ur(:,1)));
plot(f, 180/pi*angle(G_uh(:,2)));
plot(f, 180/pi*angle(G_d(:,3)));
hold off;
set(gca, 'XScale', 'log'); set(gca, 'YScale', 'lin');
xlabel('Frequency [Hz]'); ylabel('Phase [deg]');
hold off;
yticks(-360:90:360);
% ylim([-45, 45]);

linkaxes([ax1,ax2],'x');
xlim([1, 1e3]);
#+end_src

#+begin_src matlab :tangle no :exports results :results file replace
exportFig('figs/bode_plot_ident_noise.pdf', 'width', 'full', 'height', 'tall');
#+end_src

#+name: fig:bode_plot_ident_noise
#+caption: Bode Plot of the DCM dynamics in the frame of the fast jack.
#+RESULTS:
[[file:figs/bode_plot_ident_noise.png]]


#+begin_src matlab
%% Previously used controller
load('X_tal_cage_PID.mat', 'K');
#+end_src

#+begin_src matlab
%% Controller design
s = tf('s');

% Lead
a  = 8;  % Amount of phase lead / width of the phase lead / high frequency gain
wc = 2*pi*20; % Frequency with the maximum phase lead [rad/s]

% Low Pass Filter
w0 = 2*pi*80; % Cut-off frequency [rad/s]
xi = 0.4; % Damping Ratio

Kb = eye(3)*(2*pi*20)^2/(s^2) *1/(sqrt(a))* (1 + s/(wc/sqrt(a)))/(1 + s/(wc*sqrt(a))) * 1/(1 + 2*xi/w0*s + s^2/w0^2);;
#+end_src

#+begin_src matlab :exports none
%% Loop Gain
figure;
tiledlayout(3, 1, 'TileSpacing', 'Compact', 'Padding', 'None');

ax1 = nexttile([2,1]);
hold on;
plot(f, abs(G_ur(:,1).*squeeze(freqresp(Kb(1,1), f, 'Hz'))), 'DisplayName', '$u_r$');
plot(f, abs(G_uh(:,2).*squeeze(freqresp(Kb(2,2), f, 'Hz'))), 'DisplayName', '$u_h$');
plot(f, abs(G_d( :,3).*squeeze(freqresp(Kb(3,3), f, 'Hz'))), 'DisplayName', '$d$');
hold off;
set(gca, 'XScale', 'log'); set(gca, 'YScale', 'log');
ylabel('Amplitude'); set(gca, 'XTickLabel',[]);
ylim([1e-4, 1e2]);
legend('location', 'northeast');

ax2 = nexttile;
hold on;
plot(f, 180/pi*angle(G_ur(:,1).*squeeze(freqresp(Kb(1,1), f, 'Hz'))));
plot(f, 180/pi*angle(G_uh(:,2).*squeeze(freqresp(Kb(2,2), f, 'Hz'))));
plot(f, 180/pi*angle(G_d(:,3).*squeeze(freqresp(Kb(3,3), f, 'Hz'))));
hold off;
set(gca, 'XScale', 'log'); set(gca, 'YScale', 'lin');
xlabel('Frequency [Hz]'); ylabel('Phase [deg]');
yticks(-360:90:360);

linkaxes([ax1,ax2],'x');
xlim([1, 1e3]);
#+end_src

#+begin_src matlab :tangle no :exports results :results file replace
exportFig('figs/loop_gain_dcm_contr_simple.pdf', 'width', 'full', 'height', 'tall');
#+end_src

#+name: fig:loop_gain_dcm_contr_simple
#+caption: Loop gain
#+RESULTS:
[[file:figs/loop_gain_dcm_contr_simple.png]]

#+begin_src matlab :exports none
%% Loop Gain
figure;
tiledlayout(3, 1, 'TileSpacing', 'Compact', 'Padding', 'None');

ax1 = nexttile([2,1]);
hold on;
plot(f, abs(G_ur(:,1).*squeeze(freqresp(K(1,1), f, 'Hz'))), 'color', colors(1,:), 'DisplayName', 'Old K');
plot(f, abs(G_uh(:,2).*squeeze(freqresp(K(2,2), f, 'Hz'))), 'color', colors(1,:), 'HandleVisibility', 'off');
plot(f, abs(G_d(:,3).*squeeze(freqresp(K(3,3), f, 'Hz'))), 'color', colors(1,:), 'HandleVisibility', 'off');
plot(f, abs(G_ur(:,1).*squeeze(freqresp(Kb(1,1), f, 'Hz'))), 'color', colors(2,:), 'DisplayName', 'New K');
plot(f, abs(G_uh(:,2).*squeeze(freqresp(Kb(2,2), f, 'Hz'))), 'color', colors(2,:), 'HandleVisibility', 'off');
plot(f, abs(G_d(:,3).*squeeze(freqresp(Kb(3,3), f, 'Hz'))), 'color', colors(2,:), 'HandleVisibility', 'off');
hold off;
set(gca, 'XScale', 'log'); set(gca, 'YScale', 'log');
ylabel('Amplitude'); set(gca, 'XTickLabel',[]);
ylim([1e-4, 1e2]);
legend('location', 'northeast');

ax2 = nexttile;
hold on;
plot(f, 180/pi*angle(G_ur(:,1).*squeeze(freqresp(K(1,1), f, 'Hz'))), 'color', colors(1,:));
plot(f, 180/pi*angle(G_uh(:,2).*squeeze(freqresp(K(2,2), f, 'Hz'))), 'color', colors(1,:));
plot(f, 180/pi*angle(G_d(:,3).*squeeze(freqresp(K(3,3), f, 'Hz'))), 'color', colors(1,:));
plot(f, 180/pi*angle(G_ur(:,1).*squeeze(freqresp(Kb(1,1), f, 'Hz'))), 'color', colors(2,:));
plot(f, 180/pi*angle(G_uh(:,2).*squeeze(freqresp(Kb(2,2), f, 'Hz'))), 'color', colors(2,:));
plot(f, 180/pi*angle(G_d(:,3).*squeeze(freqresp(Kb(3,3), f, 'Hz'))), 'color', colors(2,:));
hold off;
set(gca, 'XScale', 'log'); set(gca, 'YScale', 'lin');
xlabel('Frequency [Hz]'); ylabel('Phase [deg]');
yticks(-360:90:360);

linkaxes([ax1,ax2],'x');
xlim([1, 1e3]);
#+end_src

#+begin_src matlab :tangle no :exports results :results file replace
exportFig('figs/loop_gain_diag_old_new_contr.pdf', 'width', 'full', 'height', 'tall');
#+end_src

#+name: fig:loop_gain_diag_old_new_contr
#+caption: Loop gain
#+RESULTS:
[[file:figs/loop_gain_diag_old_new_contr.png]]

Compare Sensitivity functions
#+begin_src matlab :exports none
%% Sensitivity function
figure;
tiledlayout(1, 1, 'TileSpacing', 'Compact', 'Padding', 'None');

hold on;
plot(f, 1./abs(1 + G_d(:,3).*squeeze(freqresp(K(1,1), f, 'Hz'))), 'DisplayName', 'Old K');
plot(f, 1./abs(1 + G_d(:,3).*squeeze(freqresp(Kb(1,1), f, 'Hz'))), 'DisplayName', 'New K');
hold off;
set(gca, 'XScale', 'log'); set(gca, 'YScale', 'log');
xlabel('Frequency [Hz]'); ylabel('Amplitude');
ylim([1e-2, 1e1]); xlim([1, 1e3]);
legend('location', 'southeast');
#+end_src

#+begin_src matlab :tangle no :exports results :results file replace
exportFig('figs/sensitivity_comp.pdf', 'width', 'full', 'height', 'tall');
#+end_src

#+name: fig:sensitivity_comp
#+caption: Comparison of sensitivity functions
#+RESULTS:
[[file:figs/sensitivity_comp.png]]


#+begin_src matlab
L  = zeros(3, 3, length(f));
Lb = zeros(3, 3, length(f));

for i_f = 1:length(f)
    L(:,:,i_f)  = [G_ur(i_f,:); G_uh(i_f,:); G_d(i_f,:)]*freqresp(K , f(i_f), 'Hz');
    Lb(:,:,i_f) = [G_ur(i_f,:); G_uh(i_f,:); G_d(i_f,:)]*freqresp(Kb, f(i_f), 'Hz');
end
#+end_src

#+begin_src matlab :exports none
%% Compute the Eigenvalues of the loop gain
Ldet  = zeros(3, length(f));
Ldetb = zeros(3, length(f));

% Loop gain
for i_f = 1:length(f)
    Ldet( :, i_f) = eig(squeeze(L( :,:,i_f)));
    Ldetb(:, i_f) = eig(squeeze(Lb(:,:,i_f)));
end
#+end_src

#+begin_src matlab :exports none
%% Plot of the eigenvalues of L in the complex plane
figure;
hold on;
for i = 1:size(Ldet,1)
    plot(real(Ldet(i,:)),  imag(Ldet(i,:)), '.', 'color', colors(1, :));
    plot(real(Ldet(i,:)), -imag(Ldet(i,:)), '.', 'color', colors(1, :));

    plot(real(Ldetb(i,:)),  imag(Ldetb(i,:)), '.', 'color', colors(2, :));
    plot(real(Ldetb(i,:)), -imag(Ldetb(i,:)), '.', 'color', colors(2, :));
end
plot(-1, 0, 'kx', 'HandleVisibility', 'off');
hold off;
set(gca, 'XScale', 'lin'); set(gca, 'YScale', 'lin');
xlabel('Real'); ylabel('Imag');
xlim([-3, 1]); ylim([-2, 2]);
#+end_src

#+begin_src matlab :tangle no :exports results :results file replace
exportFig('figs/loci_loop_gain_comp_controllers.pdf', 'width', 'wide', 'height', 'tall');
#+end_src

#+caption: Root Locus
#+RESULTS:
[[file:figs/loci_loop_gain_comp_controllers.png]]


** Test
#+begin_src matlab
%% Notch
gm = 0.015;
xi = 0.1;
wn = 2*pi*208;

K_notch = (s^2 + 2*gm*xi*wn*s + wn^2)/(s^2 + 2*xi*wn*s + wn^2);
#+end_src

#+begin_src matlab
%% Double integrator
w0 = 2*pi*40;
K_int = (w0^2)/(s^2);
#+end_src

#+begin_src matlab
%% Lead
a = 3;  % Amount of phase lead / width of the phase lead / high frequency gain
K_lead = 1/(sqrt(a))*(1 + s/(w0/sqrt(a)))/(1 + s/(w0*sqrt(a)));
K_lead = K_lead*K_lead;
#+end_src

#+begin_src matlab
%% Low Pass Filter
w0 = 2*pi*120; % Cut-off frequency [rad/s]
xi = 0.3; % Damping Ratio

K_lpf = 1/(1 + 2*xi/w0*s + s^2/w0^2);
#+end_src

#+begin_src matlab
%% Diagonal controller
Kb =  0.8*eye(3)*K_notch*K_int*K_lead*K_lpf;
#+end_src
** New controller - Higher bandwidth

#+begin_src matlab
%% Previously used controller
load('X_tal_cage_PID.mat', 'K');
#+end_src

#+begin_src matlab
%% Current Controller design
% Lead
a  = 8;  % Amount of phase lead / width of the phase lead / high frequency gain
wc = 2*pi*20; % Frequency with the maximum phase lead [rad/s]

% Low Pass Filter
w0 = 2*pi*80; % Cut-off frequency [rad/s]
xi = 0.4; % Damping Ratio

Kb_old = eye(3)*(2*pi*20)^2/(s^2) *1/(sqrt(a))* (1 + s/(wc/sqrt(a)))/(1 + s/(wc*sqrt(a))) * 1/(1 + 2*xi/w0*s + s^2/w0^2);;
#+end_src

#+begin_src matlab
%% Notch
gm = 0.015;
xi = 0.2;
wn = 2*pi*208;

K_notch = (s^2 + 2*gm*xi*wn*s + wn^2)/(s^2 + 2*xi*wn*s + wn^2);
#+end_src

#+begin_src matlab
%% Double integrator
w0 = 2*pi*40;
K_int = (w0^2)/(s^2);
#+end_src

#+begin_src matlab
%% Lead
a = 3;  % Amount of phase lead / width of the phase lead / high frequency gain
w0 = 2*pi*40;
K_lead = 1/(sqrt(a))*(1 + s/(w0/sqrt(a)))/(1 + s/(w0*sqrt(a)));
K_lead = K_lead*K_lead;
#+end_src

#+begin_src matlab
%% Low Pass Filter
w0 = 2*pi*120; % Cut-off frequency [rad/s]
xi = 0.3; % Damping Ratio

K_lpf = 1/(1 + 2*xi/w0*s + s^2/w0^2);
#+end_src

#+begin_src matlab
%% Diagonal controller
Kb =  0.9*eye(3)*K_notch*K_int*K_lead*K_lpf;
#+end_src

#+begin_src matlab :exports none
%% Loop Gain
figure;
tiledlayout(3, 1, 'TileSpacing', 'Compact', 'Padding', 'None');

ax1 = nexttile([2,1]);
hold on;
plot(f, abs(G_ur(:,1).*squeeze(freqresp(K(1,1), f, 'Hz'))), 'DisplayName', 'PID');
plot(f, abs(G_ur(:,1).*squeeze(freqresp(Kb_old(1,1), f, 'Hz'))), 'DisplayName', 'Double Integrator + Lead');
plot(f, abs(G_ur(:,1).*squeeze(freqresp(Kb(1,1), f, 'Hz'))), 'DisplayName', 'Double Integrator + Lead + Notch');
hold off;
set(gca, 'XScale', 'log'); set(gca, 'YScale', 'log');
ylabel('Amplitude'); set(gca, 'XTickLabel',[]);
ylim([1e-3, 1e3]);
legend('location', 'southwest', 'FontSize', 8, 'NumColumns', 1);

ax2 = nexttile;
hold on;
plot(f, 180/pi*angle(G_ur(:,1).*squeeze(freqresp(K(1,1), f, 'Hz'))));
plot(f, 180/pi*angle(G_ur(:,1).*squeeze(freqresp(Kb_old(1,1), f, 'Hz'))));
plot(f, 180/pi*angle(G_ur(:,1).*squeeze(freqresp(Kb(1,1), f, 'Hz'))));
hold off;
set(gca, 'XScale', 'log'); set(gca, 'YScale', 'lin');
xlabel('Frequency [Hz]'); ylabel('Phase [deg]');
yticks(-360:90:360);

linkaxes([ax1,ax2],'x');
xlim([1, 1e3]);
#+end_src

#+begin_src matlab :tangle no :exports results :results file replace
exportFig('figs/loop_gain_compare.pdf', 'width', 'full', 'height', 'tall');
#+end_src

#+name: fig:loop_gain_compare
#+caption: description
#+RESULTS:
[[file:figs/loop_gain_compare.png]]


#+begin_src matlab
L  = zeros(3, 3, length(f));
Lb = zeros(3, 3, length(f));
Lb_new = zeros(3, 3, length(f));

for i_f = 1:length(f)
    L(:,:,i_f)  = [G_ur(i_f,:); G_uh(i_f,:); G_d(i_f,:)]*freqresp(K , f(i_f), 'Hz');
    Lb(:,:,i_f) = [G_ur(i_f,:); G_uh(i_f,:); G_d(i_f,:)]*freqresp(Kb_old, f(i_f), 'Hz');
    Lb_new(:,:,i_f) = [G_ur(i_f,:); G_uh(i_f,:); G_d(i_f,:)]*freqresp(Kb, f(i_f), 'Hz');
end
#+end_src

#+begin_src matlab :exports none
%% Compute the Eigenvalues of the loop gain
Ldet  = zeros(3, length(f));
Ldetb = zeros(3, length(f));
Ldetb_new = zeros(3, length(f));

% Loop gain
for i_f = 1:length(f)
    Ldet( :, i_f) = eig(squeeze(L( :,:,i_f)));
    Ldetb(:, i_f) = eig(squeeze(Lb(:,:,i_f)));
    Ldetb_new(:, i_f) = eig(squeeze(Lb_new(:,:,i_f)));
end
#+end_src

#+begin_src matlab :exports none
%% Plot of the eigenvalues of L in the complex plane
figure;
hold on;
plot(real(Ldet(1,:)),  imag(Ldet(1,:)), '.', 'color', colors(1, :), 'DisplayName', 'PID');
plot(real(Ldet(1,:)), -imag(Ldet(1,:)), '.', 'color', colors(1, :), 'HandleVisibility', 'off');

plot(real(Ldetb(1,:)),  imag(Ldetb(1,:)), '.', 'color', colors(2, :), 'DisplayName', 'Double Integrator + Lead');
plot(real(Ldetb(1,:)), -imag(Ldetb(1,:)), '.', 'color', colors(2, :), 'HandleVisibility', 'off');

plot(real(Ldetb_new(1,:)),  imag(Ldetb_new(1,:)), '.', 'color', colors(3, :), 'DisplayName', 'Double Integrator + Lead + Notch');
plot(real(Ldetb_new(1,:)), -imag(Ldetb_new(1,:)), '.', 'color', colors(3, :), 'HandleVisibility', 'off');
for i = 2:size(Ldet,1)
    plot(real(Ldet(i,:)),  imag(Ldet(i,:)), '.', 'color', colors(1, :), 'HandleVisibility', 'off');
    plot(real(Ldet(i,:)), -imag(Ldet(i,:)), '.', 'color', colors(1, :), 'HandleVisibility', 'off');

    plot(real(Ldetb(i,:)),  imag(Ldetb(i,:)), '.', 'color', colors(2, :), 'HandleVisibility', 'off');
    plot(real(Ldetb(i,:)), -imag(Ldetb(i,:)), '.', 'color', colors(2, :), 'HandleVisibility', 'off');

    plot(real(Ldetb_new(i,:)),  imag(Ldetb_new(i,:)), '.', 'color', colors(3, :), 'HandleVisibility', 'off');
    plot(real(Ldetb_new(i,:)), -imag(Ldetb_new(i,:)), '.', 'color', colors(3, :), 'HandleVisibility', 'off');
end
plot(-1, 0, 'kx', 'HandleVisibility', 'off');
hold off;
set(gca, 'XScale', 'lin'); set(gca, 'YScale', 'lin');
xlabel('Real'); ylabel('Imag');
xlim([-3, 1]); ylim([-2, 2]);
axis square;
legend('location', 'southeast', 'FontSize', 8, 'NumColumns', 1);
#+end_src

#+begin_src matlab :tangle no :exports results :results file replace
exportFig('figs/nyquist_compare.pdf', 'width', 'wide', 'height', 'tall');
#+end_src

#+name: fig:nyquist_compare
#+caption: Nyquist Plot
#+RESULTS:
[[file:figs/nyquist_compare.png]]

#+begin_src matlab :exports none
%% Sensitivity function
figure;
tiledlayout(1, 1, 'TileSpacing', 'Compact', 'Padding', 'None');

hold on;
plot(f, 1./abs(1 + G_d(:,3).*squeeze(freqresp(K(1,1), f, 'Hz'))), 'DisplayName', 'PID');
plot(f, 1./abs(1 + G_d(:,3).*squeeze(freqresp(Kb_old(1,1), f, 'Hz'))), 'DisplayName', '$K_{10Hz}$');
plot(f, 1./abs(1 + G_d(:,3).*squeeze(freqresp(Kb(1,1), f, 'Hz'))), 'DisplayName', '$K_{20Hz}$');
hold off;
set(gca, 'XScale', 'log'); set(gca, 'YScale', 'log');
xlabel('Frequency [Hz]'); ylabel('Sensitivity Magnitude');
ylim([1e-3, 5]); xlim([1, 5e2]);
legend('location', 'southeast');
#+end_src

#+begin_src matlab :tangle no :exports results :results file replace
exportFig('figs/sensitivity_function_compare.pdf', 'width', 'normal', 'height', 'tall');
#+end_src

#+name: fig:sensitivity_function_compare
#+caption: description
#+RESULTS:
[[file:figs/sensitivity_function_compare.png]]



** Added gain
#+begin_src matlab
%% Notch
gm = 0.015;
xi = 0.2;
wn = 2*pi*208;

K_notch = (s^2 + 2*gm*xi*wn*s + wn^2)/(s^2 + 2*xi*wn*s + wn^2);
#+end_src

#+begin_src matlab
%% Double integrator
w0 = 2*pi*40;
K_int = (w0^2)/(s^2);
#+end_src

#+begin_src matlab
%% Lead
a = 3;  % Amount of phase lead / width of the phase lead / high frequency gain
w0 = 2*pi*40;
K_lead = 1/(sqrt(a))*(1 + s/(w0/sqrt(a)))/(1 + s/(w0*sqrt(a)));
K_lead = K_lead*K_lead;
#+end_src

#+begin_src matlab
%% Low Pass Filter
w0 = 2*pi*120; % Cut-off frequency [rad/s]
xi = 0.3; % Damping Ratio

K_lpf = 1/(1 + 2*xi/w0*s + s^2/w0^2);
#+end_src

#+begin_src matlab
gm = 10;
xi = 0.02;
wn = 2*pi*15;

H = (s^2 + 2*gm*xi*wn*s + wn^2)/(s^2 + 2*xi*wn*s + wn^2);
#+end_src

#+begin_src matlab
%% Diagonal controller
Kb_gain =  0.9*eye(3)*H*K_notch*K_int*K_lead*K_lpf;
#+end_src

#+begin_src matlab
Lb_gain = zeros(3, 3, length(f));

for i_f = 1:length(f)
    Lb_gain(:,:,i_f) = [G_ur(i_f,:); G_uh(i_f,:); G_d(i_f,:)]*freqresp(Kb_gain, f(i_f), 'Hz');
end
#+end_src

#+begin_src matlab :exports none
%% Compute the Eigenvalues of the loop gain
Ldetb_gain = zeros(3, length(f));

% Loop gain
for i_f = 1:length(f)
    Ldetb_gain(:, i_f) = eig(squeeze(Lb_gain(:,:,i_f)));
end
#+end_src

#+begin_src matlab :exports none
%% Loop Gain
figure;
tiledlayout(3, 1, 'TileSpacing', 'Compact', 'Padding', 'None');

ax1 = nexttile([2,1]);
hold on;
plot(f, abs(G_ur(:,1).*squeeze(freqresp(Kb(1,1), f, 'Hz'))), 'color', colors(3, :));
plot(f, abs(G_ur(:,1).*squeeze(freqresp(Kb_gain(1,1), f, 'Hz'))), 'color', colors(4, :));
hold off;
set(gca, 'XScale', 'log'); set(gca, 'YScale', 'log');
ylabel('Amplitude'); set(gca, 'XTickLabel',[]);
ylim([1e-4, 1e2]);

ax2 = nexttile;
hold on;
plot(f, 180/pi*angle(G_ur(:,1).*squeeze(freqresp(Kb(1,1), f, 'Hz'))), 'color', colors(3, :));
plot(f, 180/pi*angle(G_ur(:,1).*squeeze(freqresp(Kb_gain(1,1), f, 'Hz'))), 'color', colors(4, :));
hold off;
set(gca, 'XScale', 'log'); set(gca, 'YScale', 'lin');
xlabel('Frequency [Hz]'); ylabel('Phase [deg]');
yticks(-360:90:360);

linkaxes([ax1,ax2],'x');
xlim([1, 1e3]);
#+end_src

#+begin_src matlab :tangle no :exports results :results file replace
exportFig('figs/loop_gain_compare_added_gain.pdf', 'width', 'wide', 'height', 'tall');
#+end_src

#+name: fig:loop_gain_compare_added_gain
#+caption: description
#+RESULTS:
[[file:figs/loop_gain_compare_added_gain.png]]

#+begin_src matlab :exports none
%% Sensitivity function
figure;
tiledlayout(1, 1, 'TileSpacing', 'Compact', 'Padding', 'None');

hold on;
plot(f, 1./abs(1 + G_d(:,3).*squeeze(freqresp(K(1,1), f, 'Hz'))), 'DisplayName', 'Old K');
plot(f, 1./abs(1 + G_d(:,3).*squeeze(freqresp(Kb_old(1,1), f, 'Hz'))), 'DisplayName', 'Act K');
plot(f, 1./abs(1 + G_d(:,3).*squeeze(freqresp(Kb(1,1), f, 'Hz'))), 'DisplayName', 'New K');
plot(f, 1./abs(1 + G_d(:,3).*squeeze(freqresp(Kb_gain(1,1), f, 'Hz'))), 'DisplayName', 'New K');
hold off;
set(gca, 'XScale', 'log'); set(gca, 'YScale', 'log');
xlabel('Frequency [Hz]'); ylabel('Amplitude');
ylim([1e-2, 1e1]); xlim([1, 1e3]);
legend('location', 'southeast');
#+end_src

#+begin_src matlab :tangle no :exports results :results file replace
exportFig('figs/sensitivity_new_gain_compare.pdf', 'width', 'wide', 'height', 'tall');
#+end_src

#+name: fig:sensitivity_new_gain_compare
#+caption: description
#+RESULTS:
[[file:figs/sensitivity_new_gain_compare.png]]

#+begin_src matlab :exports none
%% Plot of the eigenvalues of L in the complex plane
figure;
hold on;
for i = 1:size(Ldet,1)
    plot(real(Ldetb_new(i,:)),  imag(Ldetb_new(i,:)), '.', 'color', colors(3, :));
    plot(real(Ldetb_new(i,:)), -imag(Ldetb_new(i,:)), '.', 'color', colors(3, :));
    plot(real(Ldetb_gain(i,:)),  imag(Ldetb_gain(i,:)), '.', 'color', colors(4, :));
    plot(real(Ldetb_gain(i,:)), -imag(Ldetb_gain(i,:)), '.', 'color', colors(4, :));
end
plot(-1, 0, 'kx', 'HandleVisibility', 'off');
hold off;
set(gca, 'XScale', 'lin'); set(gca, 'YScale', 'lin');
xlabel('Real'); ylabel('Imag');
xlim([-3, 1]); ylim([-2, 2]);
axis square;
#+end_src

#+begin_src matlab :tangle no :exports results :results file replace
exportFig('figs/nyquist_after_gain_frequency.pdf', 'width', 'wide', 'height', 'tall');
#+end_src

#+name: fig:nyquist_after_gain_frequency
#+caption: nyquist plot
#+RESULTS:
[[file:figs/nyquist_after_gain_frequency.png]]


* Noise Budgeting
** Matlab Init                                              :noexport:ignore:
#+begin_src matlab :tangle no :exports none :results silent :noweb yes :var current_dir=(file-name-directory buffer-file-name)
<<matlab-dir>>
#+end_src

#+begin_src matlab :exports none :results silent :noweb yes
<<matlab-init>>
#+end_src

#+begin_src matlab :tangle no :noweb yes
<<m-init-path>>
#+end_src

#+begin_src matlab :eval no :noweb yes
<<m-init-path-tangle>>
#+end_src

#+begin_src matlab :noweb yes
<<m-init-other>>
#+end_src

** No Displacement

|  1 | dz311  |
|  2 | dry311 |
|  3 | drx311 |
|  4 | dz111  |
|  5 | dry111 |
|  6 | drx111 |
|  7 | fjpur  |
|  8 | fjpuh  |
|  9 | fjpd   |
| 10 | bragg  |

#+begin_src matlab
data_10_deg = load('no_mov_10.mat');
data_70_deg = load('no_mov_70.mat');
#+end_src

#+begin_src matlab
data_10_deg = extractDatData('no_mov_10.mat', ...
                             {"dz311", "dry311", "drx311", "dz", "dry", "drx", "fjpur", "fjpuh", "fjpd", "bragg"}, ...
                             [1e-9, 1e-9, 1e-9, 1e-9, 1e-9, 1e-9, 1e-8, 1e-8, 1e-8, pi/180]);
data_10_deg = processMeasData(data_10_deg);
#+end_src

#+begin_src matlab
Ts = 1e-4;
t = Ts*[1:length(data_10_deg.bragg)];
#+end_src

#+begin_src matlab
data_10_deg.dz  = data_10_deg.allValues(:,4) - mean(data_10_deg.allValues(:,4));
data_10_deg.dry = data_10_deg.allValues(:,5) - mean(data_10_deg.allValues(:,5));
data_10_deg.drx = data_10_deg.allValues(:,6) - mean(data_10_deg.allValues(:,6));
#+end_src

#+begin_src matlab
%% Compute motion error in the frame of the fast jack
J_a_111 = [1,  0.14, -0.1525
           1,  0.14,  0.0675
           1, -0.14,  0.0425];

de_111 = [data_10_deg.dz'; data_10_deg.dry'; data_10_deg.drx'];
de_fj = J_a_111*de_111;
data_10_deg.fj_ur = de_fj(1,:)';
data_10_deg.fj_uh = de_fj(2,:)';
data_10_deg.fj_d  = de_fj(3,:)';

de_111 = [data_70_deg.dz'; data_70_deg.dry'; data_70_deg.drx'];
de_fj = J_a_111*de_111;
data_70_deg.fj_ur = de_fj(1,:)';
data_70_deg.fj_uh = de_fj(2,:)';
data_70_deg.fj_d  = de_fj(3,:)';
#+end_src

#+begin_src matlab
win = hanning(ceil(1/Ts));

[pxx_10_ur, f] = pwelch(data_10_deg.fj_ur, win, [], [], 1/Ts);
[pxx_70_ur, ~] = pwelch(data_70_deg.fj_ur, win, [], [], 1/Ts);

[pxx_10_uh, ~] = pwelch(data_10_deg.fj_uh, win, [], [], 1/Ts);
[pxx_70_uh, ~] = pwelch(data_70_deg.fj_uh, win, [], [], 1/Ts);

[pxx_10_d,  ~] = pwelch(data_10_deg.fj_d,  win, [], [], 1/Ts);
[pxx_70_d,  ~] = pwelch(data_70_deg.fj_d,  win, [], [], 1/Ts);
#+end_src

#+begin_src matlab
CPS_10_ur = flip(-cumtrapz(flip(f), flip(pxx_10_ur)));
CPS_10_uh = flip(-cumtrapz(flip(f), flip(pxx_10_uh)));
CPS_10_d  = flip(-cumtrapz(flip(f), flip(pxx_10_d)));

CPS_70_ur = flip(-cumtrapz(flip(f), flip(pxx_70_ur)));
CPS_70_uh = flip(-cumtrapz(flip(f), flip(pxx_70_uh)));
CPS_70_d  = flip(-cumtrapz(flip(f), flip(pxx_70_d)));
#+end_src

#+begin_src matlab
figure;
hold on;
plot(f, sqrt(CPS_10_ur), '-' , 'color', colors(1, :), 'DisplayName', '10 deg - $u_r$')
plot(f, sqrt(CPS_70_ur), '--', 'color', colors(1, :), 'DisplayName', '70 deg - $u_r$')
plot(f, sqrt(CPS_10_uh), '-' , 'color', colors(2, :), 'DisplayName', '10 deg - $u_h$')
plot(f, sqrt(CPS_70_uh), '--', 'color', colors(2, :), 'DisplayName', '70 deg - $u_h$')
plot(f, sqrt(CPS_10_d),  '-' , 'color', colors(3, :), 'DisplayName', '10 deg - $d$')
plot(f, sqrt(CPS_70_d),  '--', 'color', colors(3, :), 'DisplayName', '70 deg - $d$')
hold off;
set(gca, 'XScale', 'log'); set(gca, 'YScale', 'log');
xlabel('Frequency [Hz]'); ylabel('ASD [$\frac{nrad}{\sqrt{Hz}}$]');
legend('location', 'northwest');
xlim([1, 1e3]);
#+end_src

#+begin_src matlab
figure;
hold on;
plot(f, sqrt(pxx_10_ur))
plot(f, sqrt(pxx_70_ur))
hold off;
set(gca, 'XScale', 'log'); set(gca, 'YScale', 'log');
xlabel('Frequency [Hz]'); ylabel('ASD [$\frac{nrad}{\sqrt{Hz}}$]');
legend('location', 'northwest');
xlim([1, 1e3]);
#+end_src

#+begin_src matlab
data_70_deg.dz  = data_70_deg.allValues(:,4) - mean(data_70_deg.allValues(:,4));
data_70_deg.dry = data_70_deg.allValues(:,5) - mean(data_70_deg.allValues(:,5));
data_70_deg.drx = data_70_deg.allValues(:,6) - mean(data_70_deg.allValues(:,6));
#+end_src

#+begin_src matlab
win = hanning(ceil(1/Ts));

[pxx_10_drx, f] = pwelch(data_10_deg.drx, win, [], [], 1/Ts);
[pxx_70_drx, ~] = pwelch(data_70_deg.drx, win, [], [], 1/Ts);

[pxx_10_dry, ~] = pwelch(data_10_deg.dry, win, [], [], 1/Ts);
[pxx_70_dry, ~] = pwelch(data_70_deg.dry, win, [], [], 1/Ts);

[pxx_10_dz,  ~] = pwelch(data_10_deg.dz,  win, [], [], 1/Ts);
[pxx_70_dz,  ~] = pwelch(data_70_deg.dz,  win, [], [], 1/Ts);
#+end_src

#+begin_src matlab
figure;
hold on;
plot(f, sqrt(pxx_10_drx))
plot(f, sqrt(pxx_70_drx))
hold off;
set(gca, 'XScale', 'log'); set(gca, 'YScale', 'log');
xlabel('Frequency [Hz]'); ylabel('ASD [$\frac{nrad}{\sqrt{Hz}}$]');
legend('location', 'northwest');
xlim([1, 1e3]);
#+end_src

#+begin_src matlab
figure;
hold on;
plot(f, sqrt(pxx_10_dry))
plot(f, sqrt(pxx_70_dry))
hold off;
set(gca, 'XScale', 'log'); set(gca, 'YScale', 'log');
xlabel('Frequency [Hz]'); ylabel('ASD [$\frac{nrad}{\sqrt{Hz}}$]');
legend('location', 'northwest');
xlim([1, 1e3]);
#+end_src

#+begin_src matlab
figure;
hold on;
plot(f, sqrt(pxx_10_dz))
plot(f, sqrt(pxx_70_dz))
hold off;
set(gca, 'XScale', 'log'); set(gca, 'YScale', 'log');
xlabel('Frequency [Hz]'); ylabel('ASD [$\frac{nm}{\sqrt{Hz}}$]');
legend('location', 'northwest');
xlim([1, 1e3]);
#+end_src



** Scans

|  1 | dz311  |
|  2 | dry311 |
|  3 | drx311 |
|  4 | dz111  |
|  5 | dry111 |
|  6 | drx111 |
|  7 | fjpur  |
|  8 | fjpuh  |
|  9 | fjpd   |
| 10 | bragg  |

#+begin_src matlab
%% Load Data
data_10_70_deg = extractDatData('thtraj_10_70.mat', ...
                             {"dz311", "dry311", "drx311", "dz", "dry", "drx", "fjur", "fjuh", "fjd", "bragg"}, ...
                             [1e-9, 1e-9, 1e-9, 1e-9, 1e-9, 1e-9, 1e-8, 1e-8, 1e-8, pi/180]);

Ts = 1e-4;
t = Ts*[1:length(data_10_70_deg.bragg)];

%% Actuator Jacobian
J_a_111 = [1,  0.14, -0.0675
           1,  0.14,  0.1525
           1, -0.14,  0.0425];

data_10_70_deg.ddz  = 10.5e-3./(2*cos(data_10_70_deg.bragg)) - data_10_70_deg.dz;

%% Computation of the position of the FJ as measured by the interferometers
error = J_a_111 * [data_10_70_deg.ddz, data_10_70_deg.dry, data_10_70_deg.drx]';

data_10_70_deg.fjur_e = error(1,:)'; % [m]
data_10_70_deg.fjuh_e = error(2,:)'; % [m]
data_10_70_deg.fjd_e  = error(3,:)'; % [m]
#+end_src

#+begin_src matlab
%% Load Data
data_70_10_deg = extractDatData('thtraj_70_10.mat', ...
                             {"dz311", "dry311", "drx311", "dz", "dry", "drx", "fjur", "fjuh", "fjd", "bragg"}, ...
                             [1e-9, 1e-9, 1e-9, 1e-9, 1e-9, 1e-9, 1e-8, 1e-8, 1e-8, pi/180]);
%% Actuator Jacobian
J_a_111 = [1,  0.14, -0.0675
           1,  0.14,  0.1525
           1, -0.14,  0.0425];

data_70_10_deg.ddz  = 10.5e-3./(2*cos(data_70_10_deg.bragg)) - data_70_10_deg.dz;

%% Computation of the position of the FJ as measured by the interferometers
error = J_a_111 * [data_70_10_deg.ddz, data_70_10_deg.dry, data_70_10_deg.drx]';

data_70_10_deg.fjur_e = error(1,:)'; % [m]
data_70_10_deg.fjuh_e = error(2,:)'; % [m]
data_70_10_deg.fjd_e  = error(3,:)'; % [m]
#+end_src

#+begin_src matlab
win = hanning(ceil(1/Ts));

[pxx_10_70_ur, f] = pwelch(data_10_70_deg.fjur_e(t<100), win, [], [], 1/Ts);
[pxx_70_10_ur, ~] = pwelch(data_70_10_deg.fjur_e(t<100), win, [], [], 1/Ts);

[pxx_10_70_uh, ~] = pwelch(data_10_70_deg.fjuh_e(t<100), win, [], [], 1/Ts);
[pxx_70_10_uh, ~] = pwelch(data_70_10_deg.fjuh_e(t<100), win, [], [], 1/Ts);

[pxx_10_70_d,  ~] = pwelch(data_10_70_deg.fjd_e(t<100),  win, [], [], 1/Ts);
[pxx_70_10_d,  ~] = pwelch(data_70_10_deg.fjd_e(t<100),  win, [], [], 1/Ts);
#+end_src

#+begin_src matlab
CPS_10_70_ur = flip(-cumtrapz(flip(f), flip(pxx_10_70_ur)));
CPS_10_70_uh = flip(-cumtrapz(flip(f), flip(pxx_10_70_uh)));
CPS_10_70_d  = flip(-cumtrapz(flip(f), flip(pxx_10_70_d)));

CPS_70_10_ur = flip(-cumtrapz(flip(f), flip(pxx_70_10_ur)));
CPS_70_10_uh = flip(-cumtrapz(flip(f), flip(pxx_70_10_uh)));
CPS_70_10_d  = flip(-cumtrapz(flip(f), flip(pxx_70_10_d)));
#+end_src

#+begin_src matlab :exports none
%% Spectrogram
figure;
hold on;
pspectrum(data_10_70_deg.fjuh_e(t<100), 1e4, 'spectrogram', ...
          'FrequencyResolution', 1e0, ...
          'OverlapPercent',  99, ...
          'FrequencyLimits', [1, 400]);
hold off;
% xlim([0.03, 1.14]); ylim([1, 400]);
% caxis([-160, -130])
title('');
#+end_src

#+begin_src matlab
figure;
hold on;
plot(f, 1e9*sqrt(CPS_10_70_ur))
hold off;
set(gca, 'XScale', 'log'); set(gca, 'YScale', 'log');
xlabel('Frequency [Hz]'); ylabel('ASD [$\frac{nrad}{\sqrt{Hz}}$]');
legend('location', 'northwest');
xlim([1, 1e3]);
#+end_src

#+begin_src matlab
figure;
hold on;
plot(f, sqrt(pxx_10_70_ur))
plot(f, sqrt(pxx_70_10_ur))
hold off;
set(gca, 'XScale', 'log'); set(gca, 'YScale', 'log');
xlabel('Frequency [Hz]'); ylabel('ASD [$\frac{nrad}{\sqrt{Hz}}$]');
legend('location', 'northwest');
xlim([1, 1e3]);
#+end_src

** Noise budgeting - No rotation
First, we look at the position errors when the bragg axis is not moving

#+begin_src matlab
%% Load Measurement Data
ol_data = load('FJPUR_step.mat');
#+end_src

#+begin_src matlab
%% Pre-processing
ol_time = ol_data.time - ol_data.time(1);

ol_drx = ol_data.allValues(ol_time < 45, 6);
ol_dry = ol_data.allValues(ol_time < 45, 5);
ol_dz  = ol_data.allValues(ol_time < 45, 4);

ol_drx = ol_drx - mean(ol_drx);
ol_dry = ol_dry - mean(ol_dry);
ol_dz = ol_dz - mean(ol_dz);

ol_time = ol_time(ol_time < 45);
#+end_src

#+begin_src matlab
figure;
plot(ol_time, ol_drx)
#+end_src

#+begin_src matlab
%% Parameters for Spectral Analysis
Ts = 1e-4;
win = hanning(ceil(1/Ts));
#+end_src

#+begin_src matlab
%% Computation of the PSD
[pxx_ol_drx, f] = pwelch(ol_drx, win, [], [], 1/Ts);
[pxx_ol_dry, ~] = pwelch(ol_dry, win, [], [], 1/Ts);
[pxx_ol_dz,  ~] = pwelch(ol_dz,  win, [], [], 1/Ts);
#+end_src

#+begin_src matlab :exports none
%% Amplitude Spectral Density
figure;
hold on;
plot(f, sqrt(pxx_ol_drx), 'DisplayName', '$R_x$');
plot(f, sqrt(pxx_ol_dry), 'DisplayName', '$R_y$');
plot(f, sqrt(pxx_ol_dz),  'DisplayName', '$D_z$');
hold off;
set(gca, 'XScale', 'log'); set(gca, 'YScale', 'log');
xlabel('Frequency [Hz]'); ylabel('ASD [$\frac{nm,nrad}{\sqrt{Hz}}$]');
legend('location', 'northwest');
xlim([1, 1e3]);
#+end_src

#+begin_src matlab :tangle no :exports results :results file replace
exportFig('figs/noise_budget_no_mov_asd.pdf', 'width', 'wide', 'height', 'normal');
#+end_src

#+name: fig:noise_budget_no_mov_asd
#+caption: Amplitude Spectral Density
#+RESULTS:
[[file:figs/noise_budget_no_mov_asd.png]]

#+begin_src matlab
%% Cumulative Spectral Density
CPS_drx = flip(-cumtrapz(flip(f), flip(pxx_ol_drx)));
CPS_dry = flip(-cumtrapz(flip(f), flip(pxx_ol_dry)));
CPS_dz  = flip(-cumtrapz(flip(f), flip(pxx_ol_dz)));
#+end_src

#+begin_src matlab
%% Cumulative Spectral Density
CPS_drx = cumtrapz(f, pxx_ol_drx);
CPS_dry = cumtrapz(f, pxx_ol_dry);
CPS_dz  = cumtrapz(f, pxx_ol_dz);
#+end_src

#+begin_src matlab :exports none
%% Cumulative Spectral Density
figure;
hold on;
plot(f, sqrt(CPS_drx), 'DisplayName', '$R_x$');
plot(f, sqrt(CPS_dry), 'DisplayName', '$R_y$');
plot(f, sqrt(CPS_dz),  'DisplayName', '$D_z$');
hold off;
set(gca, 'XScale', 'log'); set(gca, 'YScale', 'log');
xlabel('Frequency [Hz]'); ylabel('CAS [nm, nrad rms]');
legend('location', 'northwest');
xlim([1, 1e3]);
#+end_src

#+begin_src matlab :tangle no :exports results :results file replace
exportFig('figs/noise_budget_no_mov_cas.pdf', 'width', 'wide', 'height', 'normal');
#+end_src

#+name: fig:noise_budget_no_mov_cas
#+caption: Cumulative Amplitude Spectrum
#+RESULTS:
[[file:figs/noise_budget_no_mov_cas.png]]


** TODO Noise budgeting - Bragg rotation

* Test Mode C
** Matlab Init                                              :noexport:ignore:
#+begin_src matlab :tangle no :exports none :results silent :noweb yes :var current_dir=(file-name-directory buffer-file-name)
<<matlab-dir>>
#+end_src

#+begin_src matlab :exports none :results silent :noweb yes
<<matlab-init>>
#+end_src

#+begin_src matlab :tangle no :noweb yes
<<m-init-path>>
#+end_src

#+begin_src matlab :eval no :noweb yes
<<m-init-path-tangle>>
#+end_src

#+begin_src matlab :noweb yes
<<m-init-other>>
#+end_src

** Mode B and Mode C
#+begin_src matlab
data_B = extractDatData(sprintf("/home/thomas/mnt/data_id21/22Jan/blc13491/id21/test_regul_220119/%s","lut_const_fj_vel_19012022_1450.dat"), ...
                             {"bragg", "dz", "dry", "drx", "fjur", "fjuh", "fjd"}, ...
                             [pi/180, 1e-9, 1e-9, 1e-9, 1e-8, 1e-8, 1e-8]);
data_B = processMeasData(data_B);
#+end_src

#+begin_src matlab
data_C = extractDatData(sprintf("/home/thomas/mnt/data_id21/22Jan/blc13491/id21/test_regul_220119/%s","lut_const_fj_vel_19012022_1454.dat"), ...
                             {"bragg", "dz", "dry", "drx", "fjur", "fjuh", "fjd"}, ...
                             [pi/180, 1e-9, 1e-9, 1e-9, 1e-8, 1e-8, 1e-8]);
data_C = processMeasData(data_C);
#+end_src

#+begin_src matlab
figure;
hold on;
plot(180/pi*data_B.bragg, 1e9*data_B.drx)
hold off;
xlabel('Bragg Angle [deg]'); ylabel('DRX [nrad]');
#+end_src

#+begin_src matlab
figure;
hold on;
plot(180/pi*data_B.bragg, 1e9*data_B.fjur_e_filt)
plot(180/pi*data_C.bragg, 1e9*data_C.fjur_e_filt)
hold off;
xlabel('Bragg Angle [deg]'); ylabel('FJUR Error [nm]');
#+end_src

#+begin_src matlab
figure;
hold on;
plot(180/pi*data_B.bragg, 1e9*data_B.fjur_e)
plot(180/pi*data_C.bragg, 1e9*data_C.fjur_e)
hold off;
xlabel('Bragg Angle [deg]'); ylabel('FJUR Error [nm]');
#+end_src

#+begin_src matlab
%% FIR Filter
Fs = 1e4; % Sampling Frequency [Hz]
fir_order = 5000; % Filter's order
delay = fir_order/2; % Delay induced by the filter
B_fir = firls(5000, ... % Filter's order
              [0 5/(Fs/2)  10/(Fs/2) 1], ... % Frequencies [Hz]
              [1 1          0        0]); % Wanted Magnitudes
#+end_src

#+begin_src matlab
%% Filtering all measured Fast Jack Position using the FIR filter
data_B.drx_filter = filter(B_fir, 1, data_B.drx);
data_B.drx_filter(1:end-delay) = data_B.drx_filter(delay+1:end);

data_C.drx_filter = filter(B_fir, 1, data_C.drx);
data_C.drx_filter(1:end-delay) = data_C.drx_filter(delay+1:end);
#+end_src

#+begin_src matlab
figure;
hold on;
plot(180/pi*data_B.bragg, 1e9*data_B.drx_filter)
plot(180/pi*data_C.bragg, 1e9*data_C.drx_filter)
hold off;
xlabel('Bragg Angle [deg]'); ylabel('DRX [nrad]');
#+end_src

#+begin_src matlab
Ts = 1e-4;
win = hanning(ceil(1/Ts));

[pxx_B_drx, f] = pwelch(data_B.drx, win, [], [], 1/Ts);
[pxx_C_drx, ~] = pwelch(data_C.drx, win, [], [], 1/Ts);
#+end_src

#+begin_src matlab :exports none
%% Estimation of Sensitivity function
figure;
hold on;
plot(f, sqrt(pxx_B_drx), 'DisplayName', 'B');
plot(f, sqrt(pxx_C_drx), 'DisplayName', 'C');
hold off;
set(gca, 'XScale', 'log'); set(gca, 'YScale', 'log');
xlabel('Frequency [Hz]'); ylabel('ASD');
legend('location', 'northwest');
#+end_src

#+begin_src matlab :exports none
%% Estimation of Sensitivity function
figure;
plot(f, sqrt(pxx_C_drx)./sqrt(pxx_B_drx), 'k-');
set(gca, 'XScale', 'log'); set(gca, 'YScale', 'log');
xlabel('Frequency [Hz]'); ylabel('Sensitivity Function');
legend('location', 'northwest');
#+end_src

* Export numerator and denominator
** Matlab Init                                              :noexport:ignore:
#+begin_src matlab :tangle no :exports none :results silent :noweb yes :var current_dir=(file-name-directory buffer-file-name)
<<matlab-dir>>
#+end_src

#+begin_src matlab :exports none :results silent :noweb yes
<<matlab-init>>
#+end_src

#+begin_src matlab :tangle no :noweb yes
<<m-init-path>>
#+end_src

#+begin_src matlab :eval no :noweb yes
<<m-init-path-tangle>>
#+end_src

#+begin_src matlab :noweb yes
<<m-init-other>>
#+end_src

** Export
#+begin_src matlab
K_order = 10;
#+end_src

#+begin_src matlab
load('X_tal_cage_PID.mat', 'K');
K_order = order(K(1,1));
Kz = c2d(K(1,1)*(1 + s/2/pi/2e3)^(9-K_order)/(1 + s/2/pi/2e3)^(9-K_order), 1e-4);
[num, den] = tfdata(Kz, 'v');

formatSpec = '%.18e %.18e %.18e %.18e %.18e %.18e %.18e %.18e %.18e %.18e\n';
fileID = fopen('X_tal_cage_PID.dat', 'w');
fprintf(fileID, formatSpec, [num; den]');
fclose(fileID);
#+end_src

#+begin_src matlab
load('X_tal_cage_PID_20Hz.mat', 'K');
K_order = order(K(1,1));
Kz = c2d(K(1,1)*(1 + s/2/pi/2e3)^(9-K_order)/(1 + s/2/pi/2e3)^(9-K_order), 1e-4);
[num, den] = tfdata(Kz, 'v');

formatSpec = '%.18e %.18e %.18e %.18e %.18e %.18e %.18e %.18e %.18e %.18e\n';
fileID = fopen('X_tal_cage_PID_20Hz.dat', 'w');
fprintf(fileID, formatSpec, [num; den]');
fclose(fileID);
#+end_src

#+begin_src matlab
load('X_tal_cage_PID_40Hz.mat', 'K');
K_order = order(K(1,1));
Kz = c2d(K(1,1)*(1 + s/2/pi/2e3)^(9-K_order)/(1 + s/2/pi/2e3)^(9-K_order), 1e-4);
[num, den] = tfdata(Kz, 'v');

formatSpec = '%.18e %.18e %.18e %.18e %.18e %.18e %.18e %.18e %.18e %.18e\n';
fileID = fopen('X_tal_cage_PID_40Hz.dat', 'w');
fprintf(fileID, formatSpec, [num; den]');
fclose(fileID);
#+end_src

** Verify
#+begin_src matlab
K_data = importdata('X_tal_cage_PID_20Hz.dat');
K = tf(K_data(1,:), K_data(2,:), 1e-4)
#+end_src

* Helping Functions                                                 :noexport:
** Initialize Path
#+NAME: m-init-path
#+BEGIN_SRC matlab
%% Path for functions, data and scripts
addpath('./matlab/mat/'); % Path for data
addpath('./matlab/src/'); % Path for functions
addpath('./matlab/');     % Path for scripts
#+END_SRC

#+NAME: m-init-path-tangle
#+BEGIN_SRC matlab
%% Path for functions, data and scripts
addpath('./mat/'); % Path for data
addpath('./src/'); % Path for functions
#+END_SRC

** Initialize Simscape Model
#+NAME: m-init-simscape
#+begin_src matlab
#+end_src

** Initialize other elements
#+NAME: m-init-other
#+BEGIN_SRC matlab
%% Colors for the figures
colors = colororder;

%% Frequency Vector
freqs = logspace(0, 3, 1000);
#+END_SRC

** =extractDatData=
:PROPERTIES:
:header-args:matlab+: :tangle matlab/src/extractDatData.m
:header-args:matlab+: :comments none :mkdirp yes :eval no
:END:
<<sec:extractDatData>>

*** Function Description
#+begin_src matlab
function [data_struct] = extractDatData(dat_file, names, scale)
% extractDatData -
%
% Syntax: extractDatData(data_file, lut_file, args)
%
% Inputs:
%    - data_file - Where to load the .mat file
%    - lut_file - Where to save the .dat file
#+end_src

*** Load Data
#+begin_src matlab
%% Load Data
data_array = importdata(dat_file);
#+end_src

#+begin_src matlab
%% Initialize Struct
data_struct = struct();
#+end_src

#+begin_src matlab
%% Populate Struct
for i = 1:length(names)
      data_struct.(names{i}) = scale(i)*data_array(:,i);
end
#+end_src

#+begin_src matlab
%% Add Time
data_struct.time = 1e-4*[1:1:length(data_struct.(names{1}))];
#+end_src

** =processMeasData=
:PROPERTIES:
:header-args:matlab+: :tangle matlab/src/processMeasData.m
:header-args:matlab+: :comments none :mkdirp yes :eval no
:END:
<<sec:processMeasData>>

*** Function Description
#+begin_src matlab
function [data] = processMeasData(data, args)
% processMeasData -
%
% Syntax: processMeasData(data_file, lut_file, args)
%
% Inputs:
%    - data
#+end_src

*** Optional Parameters
#+begin_src matlab
arguments
    data
    args.fir_order (1,1) double {mustBeNumericOrLogical} = 5000
end
#+end_src

*** Process Data
#+begin_src matlab
%% Actuator Jacobian
J_a_111 = [1,  0.14, -0.0675
           1,  0.14,  0.1525
           1, -0.14,  0.0425];
#+end_src

#+begin_src matlab
%% FIR Filter
Fs = 1e4; % Sampling Frequency [Hz]
fir_order = args.fir_order; % Filter's order
delay = fir_order/2; % Delay induced by the filter
B_fir = firls(args.fir_order, ... % Filter's order
              [0 25/(Fs/2)  34/(Fs/2) 1], ... % Frequencies [Hz]
              [1 1          0          0]); % Wanted Magnitudes
#+end_src

#+begin_src matlab
data.ddz  = 10.5e-3./(2*cos(data.bragg)) - data.dz;

%% Computation of the position of the FJ as measured by the interferometers
error = J_a_111 * [data.ddz, data.dry, data.drx]';

data.fjur_e = error(1,:)'; % [m]
data.fjuh_e = error(2,:)'; % [m]
data.fjd_e  = error(3,:)'; % [m]

%% Filtering all measured Fast Jack Position using the FIR filter
data.fjur_e_filt = filter(B_fir, 1, data.fjur_e);
data.fjuh_e_filt = filter(B_fir, 1, data.fjuh_e);
data.fjd_e_filt  = filter(B_fir, 1, data.fjd_e);

%% Compensation of the delay introduced by the FIR filter
data.fjur_e_filt(1:end-delay) = data.fjur_e_filt(delay+1:end);
data.fjuh_e_filt(1:end-delay) = data.fjuh_e_filt(delay+1:end);
data.fjd_e_filt( 1:end-delay) = data.fjd_e_filt( delay+1:end);
#+end_src

#+begin_src matlab
%% Re-sample data to have same data points in FJUR
[data.fjur_e_resampl, data.fjur_resampl] = resample(data.fjur_e_filt, data.fjur, 1/100e-9);
[data.fjuh_e_resampl, data.fjuh_resampl] = resample(data.fjuh_e_filt, data.fjuh, 1/100e-9);
[data.fjd_e_resampl,  data.fjd_resampl]  = resample(data.fjd_e_filt,  data.fjd,  1/100e-9);
#+end_src

* Bibliography                                                        :ignore:
#+latex: \printbibliography