Add all .pdf figures. Update some analysis

.gitignore

@@ -1,7 +1,6 @@
 auto/
 *.tex
 
-**/figs/*.pdf
 **/figs/*.svg
 **/figs/*.tex
 

index.org

@@ -14,6 +14,10 @@
 #+HTML_HEAD: <script type="text/javascript" src="./js/jquery.stickytableheaders.min.js"></script>
 #+HTML_HEAD: <script type="text/javascript" src="./js/readtheorg.js"></script>
 
+#+LATEX_CLASS: scrreprt
+#+LATEX_CLASS_OPTIONS: []
+#+LATEX_HEADER: \usepackage{minted}
+
 #+PROPERTY: header-args:latex  :headers '("\\usepackage{tikz}" "\\usepackage{import}" "\\import{/home/thomas/Cloud/These/LaTeX/}{config.tex}")
 #+PROPERTY: header-args:latex+ :imagemagick t :fit yes
 #+PROPERTY: header-args:latex+ :iminoptions -scale 100% -density 150
@@ -2631,6 +2635,25 @@ This corresponds to a measurement error of the Attocube equals to (in [m])
   The DAC noise use for the Cercalo does not limit the performance of the system.
 #+end_important
 
+* Plant Uncertainty
+** 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
+
+** Coprime Factorization
+#+begin_src matlab
+  load('mat/plant.mat', 'sys', 'Gi', 'Zc', 'Ga', 'Gc', 'Gn', 'Gd');
+#+end_src
+
+#+begin_src matlab
+  [fact, Ml, Nl] = lncf(Gc*Gi);
+#+end_src
+
 * Plant Scaling
 <<sec:plant_scaling>>
 ** Introduction                                                     :ignore:
@@ -3292,6 +3315,16 @@ First, we get the mean value as measured by the interferometer for each value of
   Unvm = mean(reshape(uv.Unv, [fs floor(length(uv.t)/fs)]),2);
 #+end_src
 
+And we can compute the RMS value of the non-repeatable part:
+#+begin_src matlab :exports results :results value table replace :tangle no :post addhdr(*this*)
+  data2orgtable([rms(1e9*(uh.Va - repmat(Vahm, length(uh.t)/length(Vahm),1))), rms(1e9*(uv.Va - repmat(Vavm, length(uv.t)/length(Vavm),1)))], {}, {'Va - Horizontal [nm rms]', 'Va - Vertical [nm rms]'}, ' %.1f ');
+#+end_src
+
+#+RESULTS:
+| Va - Horizontal [nm rms] | Va - Vertical [nm rms] |
+|--------------------------+------------------------|
+|                     19.6 |                   13.9 |
+
 #+begin_src matlab :exports none
   figure;
   ax1 = subplot(1, 2, 1);
@@ -3347,3 +3380,72 @@ First, we get the mean value as measured by the interferometer for each value of
 #+NAME: fig:repeat_plot_subtract_mean
 #+CAPTION: Repeatability of the measurement after subtracting the mean value ([[./figs/repeat_plot_subtract_mean.png][png]], [[./figs/repeat_plot_subtract_mean.pdf][pdf]])
 [[file:figs/repeat_plot_subtract_mean.png]]
+
+** Analysis of the non-repeatable contributions
+Let's know try to determine where does the non-repeatability comes from.
+
+From the 4QD signal, we can compute the angle error of the beam and thus determine the corresponding displacement measured by the attocube.
+
+We then take the non-repeatable part of this displacement and we compare that with the total non-repeatability.
+
+We also plot the displacement measured during the huddle test.
+
+All the signals are shown on Fig. [[]].
+
+#+begin_src matlab :exports none
+  Vphm = mean(reshape(uh.Vph/freqresp(Gd(1,1), 0), [fs floor(length(uh.t)/fs)]),2);
+  Unhm = mean(reshape(uh.Unh, [fs floor(length(uh.t)/fs)]),2);
+
+  Vpvm = mean(reshape(uv.Vpv/freqresp(Gd(2,2), 0), [fs floor(length(uv.t)/fs)]),2);
+  Unvm = mean(reshape(uv.Unv, [fs floor(length(uv.t)/fs)]),2);
+#+end_src
+
+
+#+begin_src matlab :exports none
+  % =Vaheq= is the equivalent measurement error in [m] due to error angle of the Sercalo.
+  Vaheq = uh.Vph/freqresp(Gd(1,1), 0) - repmat(Vphm, length(uh.t)/length(Vphm),1);
+  Vaveq = uv.Vpv/freqresp(Gd(2,2), 0) - repmat(Vpvm, length(uv.t)/length(Vpvm),1);
+
+  Vaheq = sign(Vaheq).*Vaheq.^2;
+  Vaveq = sign(Vaveq).*Vaveq.^2;
+#+end_src
+
+#+begin_src matlab :exports none
+  ht = load('./mat/data_huddle_test_3.mat', 't', 'Va');
+#+end_src
+
+#+begin_src matlab :exports none
+  htm = 1e9*ht.Va(1:length(Vaheq)) - repmat(mean(1e9*ht.Va(1:length(Vaheq))), length(uh.t)/length(Vaheq),1);
+#+end_src
+
+#+begin_src matlab :exports none
+  figure;
+  ax1 = subplot(1, 2, 1);
+  hold on;
+  plot(uh.Unh, 1e9*(uh.Va - repmat(Vahm, length(uh.t)/length(Vahm),1)));
+  plot(uh.Unh, 1e9*ht.Va(1:length(Vaheq))-mean(1e9*ht.Va(1:length(Vaheq))));
+  plot(uh.Unh, 1e9*Vaheq);
+  hold off;
+  xlabel('$V_{n,h}$ [V]'); ylabel('$V_a$ [nm]');
+
+  ax2 = subplot(1, 2, 2);
+  hold on;
+  plot(uv.Unv, 1e9*(uv.Va - repmat(Vavm, length(uv.t)/length(Vavm),1)), 'DisplayName', 'Measured Non-Repeatability');
+  plot(uv.Unv, 1e9*ht.Va(1:length(Vaveq))-mean(1e9*ht.Va(1:length(Vaveq))), 'DisplayName', 'Huddle Test');
+  plot(uv.Unv, 1e9*Vaveq, 'DisplayName', 'Due to Sercalo Angle Error');
+  hold off;
+  xlabel('$V_{n,v}$ [V]'); ylabel('$V_a$ [nm]');
+  legend('location', 'northeast');
+
+  linkaxes([ax1,ax2],'xy');
+  ylim([-100 100]);
+#+end_src
+
+#+HEADER: :tangle no :exports results :results none :noweb yes
+#+begin_src matlab :var filepath="figs/non-repeatability-parts.pdf" :var figsize="full-tall" :post pdf2svg(file=*this*, ext="png")
+  <<plt-matlab>>
+#+end_src
+
+#+NAME: fig:non-repeatability-parts
+#+CAPTION: Non repeatabilities ([[./figs/non-repeatability-parts.png][png]], [[./figs/non-repeatability-parts.pdf][pdf]])
+[[file:figs/non-repeatability-parts.png]]