phd-thesis/phd-thesis.org

#+TITLE: PhD Thesis
:DRAWER:
#+SUBTITLE: My subtitle

#+LANGUAGE: en
#+EMAIL: dehaeze.thomas@gmail.com
#+AUTHOR: Dehaeze Thomas

#+STARTUP: overview
#+DATE: {{{time(%Y-%m-%d)}}}

#+LATEX_CLASS: scrreprt
#+LATEX_CLASS_OPTIONS: [a4paper, twoside, 11pt, onecolumn, bibliography=totoc, openright, appendixprefix=true]

#+OPTIONS: num:t toc:nil ':t *:t -:t ::t <:nil author:t date:t tags:nil todo:nil |:t H:2 title:nil

#+SELECT_TAGS: export
#+EXCLUDE_TAGS: noexport

#+BIND: org-latex-bib-compiler "biber"

#+LATEX_HEADER: \input{config.tex}
#+LATEX_HEADER_EXTRA: \input{config_extra.tex}
#+LATEX_HEADER_EXTRA: \addbibresource{ref.bib}

#+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+ :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:

* Build                                                             :noexport:
#+NAME: startblock
#+BEGIN_SRC emacs-lisp :results none
(add-to-list 'org-latex-classes
             '("scrreprt"
               "\\documentclass{scrreprt}"
               ("\\chapter{%s}" . "\\chapter*{%s}")
               ("\\section{%s}" . "\\section*{%s}")
               ("\\subsection{%s}" . "\\subsection*{%s}")
               ("\\subsubsection{%s}" . "\\subsubsection*{%s}")
               ("\\paragraph{%s}" . "\\paragraph*{%s}")
               ))

;; Remove all org comments in the output LaTeX file
(defun delete-org-comments (backend)
  (loop for comment in (reverse (org-element-map (org-element-parse-buffer)
                                    'comment 'identity))
        do
        (setf (buffer-substring (org-element-property :begin comment)
                                (org-element-property :end comment))
              "")))

;; Add to export hook
(add-hook 'org-export-before-processing-hook 'delete-org-comments)

;; Use no package by default
(setq org-latex-packages-alist nil)
(setq org-latex-default-packages-alist nil)

;; Do not include the subtitle inside the title
(setq org-latex-subtitle-separate t)
(setq org-latex-subtitle-format "\\subtitle{%s}")

(setq org-export-before-parsing-hook '(org-ref-glossary-before-parsing
                                       org-ref-acronyms-before-parsing))
#+END_SRC

* Glossary and Acronyms - Tables                                      :ignore:

#+name: glossary
| label | name              | description           |
|-------+-------------------+-----------------------|
| ka    | \ensuremath{k_a}  | Actuator Stiffness in |
| phi   | \ensuremath{\phi} | A woody bush          |

#+name: acronyms
| key  | abbreviation | full form                        |
|------+--------------+----------------------------------|
| mimo | MIMO         | Multiple-Inputs Multiple-Outputs |
| siso | SISO         | Single-Input Single-Output       |
| nass | NASS         | Nano Active Stabilization System |
| lti  | LTI          | Linear Time Invariant            |

* Title Page                                                          :ignore:

#+begin_export latex
\begin{titlepage}
  \vspace*{5cm}
  \makeatletter
  \begin{center}
    \begin{Huge}
      \@title
    \end{Huge}\\[0.1cm]
    %
    \begin{Large}
      \@subtitle
    \end{Large}\\
    %
    \emph{by}\\
    \@author
    %
    \vfill
    A document submitted in partial fulfillment
    of the requirements for the degree of\\
    \emph{Technical Report}\\
    at\\
    \textsc{Miskatonic University}
  \end{center}
  \makeatother
\end{titlepage}

\newpage
\null
\thispagestyle{empty}
\newpage
#+end_export

* Abstract
:PROPERTIES:
:UNNUMBERED: notoc
:END:

* Résumé
:PROPERTIES:
:UNNUMBERED: notoc
:END:

* Acknowledgments
:PROPERTIES:
:UNNUMBERED: notoc
:END:

* Table of Contents                                                   :ignore:

#+begin_export latex
\dominitoc
\tableofcontents

\listoftables
\listoffigures
#+end_export

* Introduction
* Test
\minitoc
** Test
A list:
- acronyms acrshort:nass acrshort:mimo acrshort:lti [[acrfull:siso][Single-Input Single-Output (SISO)]]
- glossary terms gls:ka, gls:phi.
- Bibliography citations: [[cite:&dehaeze21_activ_dampin_rotat_platf_using;&dehaeze21_mechat_approac_devel_nano_activ_stabil_system]].

A definition list:
- this :: means that
- that :: means this

Some Footnote[fn:1]

** blabla
*** sdlfk

*** sldkjf asdf
**** lksdfjasd
**** lksdfjasd
**** lksdfjasd
** blabla
* Source Blocks
\minitoc
** 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

** Figures
#+begin_src matlab
  t = 0:0.01:5; % Time [s]
  x = sin(2*pi*t); % Output Voltage [V]
#+end_src

#+begin_src matlab
  figure;
  plot(t, x);
  xlabel('Time [s]'); ylabel('Voltage [V]');
#+end_src

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

#+name: fig:matlab_fig_example
#+caption: Matlab Figure
#+RESULTS:
[[file:figs/matlab_fig_example.png]]

** Table Result

#+begin_src matlab
  x = 1:10;
  y = x.^2;
#+end_src

#+begin_src matlab :exports results :results value table replace :tangle no :post addhdr(*this*)
  data2orgtable([x', y'], {}, {'$x$', '$y = x^2$'}, ' %.0f ');
#+end_src

#+name: tab:table_name
#+caption: Table caption
#+RESULTS:
| $x$ | $y = x^2$ |
|-----+-----------|
|   1 |         1 |
|   2 |         4 |
|   3 |         9 |
|   4 |        16 |
|   5 |        25 |
|   6 |        36 |
|   7 |        49 |
|   8 |        64 |
|   9 |        81 |
|  10 |       100 |

** Inline Results

Results can be automatically outputed as shown below.

#+begin_src matlab :results value replace
  sqrt(2)
#+end_src

#+RESULTS:
: 1.4142


#+begin_src matlab :results output replace
  y
#+end_src

#+RESULTS:
: y =
:      1     4     9    16    25    36    49    64    81   100

** Caption and Reference

Captions can be added to code blocks.
Moreover, we can link to specific bode blocks (Listing [[lst:matlab_figure]] or [[lst:matlab_svd]]).

#+name: lst:matlab_figure
#+caption: Code to produce a nice contour plot
#+begin_src matlab
  figure;
  [X,Y,Z] = peaks;
  contour(X,Y,Z,20)
#+end_src

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

#+name: fig:matlab_logo
#+caption: Obtained Contour Plot
#+RESULTS:
[[file:figs/matlab_logo.png]]

#+name: lst:matlab_svd
#+caption: Code to compute the Singular Value Decomposition
#+begin_src matlab :results output replace
  A = [1 2; 3 4; 5 6; 7 8]
  [U,S,V] = svd(A)
#+end_src

#+RESULTS:
#+begin_example
A = [1 2; 3 4; 5 6; 7 8]
A =
     1     2
     3     4
     5     6
     7     8
[U,S,V] = svd(A)
U =
        -0.152483233310201         -0.82264747222566        -0.394501022283829        -0.379959133877596
        -0.349918371807964         -0.42137528768458         0.242796545704357         0.800655879510063
        -0.547353510305727       -0.0201031031435029         0.697909975442776        -0.461434357387336
         -0.74478864880349         0.381169081397575        -0.546205498863303        0.0407376117548695
S =
          14.2690954992615                         0
                         0         0.626828232417541
                         0                         0
                         0                         0
V =
        -0.641423027995072         0.767187395072177
        -0.767187395072177        -0.641423027995072
#+end_example

** Source Blocks with Line Numbers

Citation [[cite:&taghirad13_paral;&dehaeze21_activ_dampin_rotat_platf_using]]

The Listing [[lst:matlab_line_numbers]] has line numbers as the =-n= option was used.

Specific lines of codes can be referenced.
For instance, the code used to specify the wanted the vertical label is on line [[(test)]].

#+name: lst:matlab_line_numbers
#+caption: Specify Labels
#+begin_src matlab +n -r
  figure;
  plot(t, x)
  xlabel('Time [s]');
  ylabel('Output [V]'); (ref:test)
#+end_src

Numbering can be continued by using =+n= option as shown below.
#+begin_src matlab +n
  figure;
  plot(t, u)
  xlabel('Time [s]');
  ylabel('Input [V]');
#+end_src

* Images
\minitoc
** Normal Image

Figure [[fig:general_control_names]] shows the results of the Tikz code of listing [[lst:tikz_test]].

#+name: lst:tikz_test
#+caption: Tikz code that is used to generate Figure [[fig:general_control_names]]
#+begin_src latex :file general_control_names.pdf :exports both
  \begin{tikzpicture}

    % Blocs
    \node[block={2.0cm}{2.0cm}] (P) {$P$};
    \node[block={1.5cm}{1.5cm}, below=0.7 of P] (K) {$K$};

    % Input and outputs coordinates
    \coordinate[] (inputw)  at ($(P.south west)!0.75!(P.north west)$);
    \coordinate[] (inputu)  at ($(P.south west)!0.25!(P.north west)$);
    \coordinate[] (outputz) at ($(P.south east)!0.75!(P.north east)$);
    \coordinate[] (outputv) at ($(P.south east)!0.25!(P.north east)$);

    % Connections and labels
    \draw[<-] (inputw) node[above left, align=right]{(weighted)\\exogenous inputs\\$w$} -- ++(-1.5, 0);
    \draw[<-] (inputu) -- ++(-0.8, 0) |- node[left, near start, align=right]{control signals\\$u$} (K.west);

    \draw[->] (outputz) node[above right, align=left]{(weighted)\\exogenous outputs\\$z$} -- ++(1.5, 0);
    \draw[->] (outputv) -- ++(0.8, 0) |- node[right, near start, align=left]{sensed output\\$v$} (K.east);
  \end{tikzpicture}
#+end_src

#+name: fig:general_control_names
#+caption: General Control Configuration
#+RESULTS: lst:tikz_test
[[file:figs/general_control_names.png]]

** Sub Images

Link to subfigure [[fig:general_control_names_1]].

#+name: fig:subfigure
#+caption: Subfigure Caption
#+attr_latex: :environment subfigure :width 0.49\linewidth :align c
| file:figs/general_control_names.png                | file:figs/general_control_names.png                |
| <<fig:general_control_names_1>> sub figure caption | <<fig:general_control_names_2>> sub figure caption |

* Tables
\minitoc

Table [[tab:table_with_equations]] shows a table with some mathematics inside.

#+name: tab:table_with_equations
#+caption: A Simple table with included math
| $N$ | $N^2$ | $N^3$ | $N^4$ | $\sqrt n$ | $\sqrt[4]N$ |
|-----+-------+-------+-------+-----------+-------------|
|   1 |     1 |     1 |     1 |         1 |           1 |
|   2 |     4 |     8 |    16 | 1.4142136 |   1.1892071 |
|   3 |     9 |    27 |    81 | 1.7320508 |   1.3160740 |
#+TBLFM: $2=$1^2::$3=$1^3::$4=$1^4::$5=sqrt($1)::$6=sqrt(sqrt(($1)))

#+name: tab:table_without_head
#+caption: Table without Head
|     | *1* | *2* | *3* | *4* | *5* |
| *1* |   1 |   2 |   3 |   4 |   5 |
| *2* |   2 |   4 |   6 |   8 |  10 |
| *3* |   3 |   6 |   9 |  12 |  15 |
| *4* |   4 |   8 |  12 |  16 |  20 |
| *5* |   5 |  10 |  15 |  20 |  25 |

#+name: tab:table_multiple_heads
#+ATTR_LATEX: :font \footnotesize
#+caption: Table with multiples groups
|                         |        *Classical Control*         |           *Modern Control*           |                            *Robust Control*                             |
| <l>                     |                <c>                 |                 <c>                  |                                   <c>                                   |
|-------------------------+------------------------------------+--------------------------------------+-------------------------------------------------------------------------|
| *Date*                  |               1930-                |                1960-                 |                                  1980-                                  |
|-------------------------+------------------------------------+--------------------------------------+-------------------------------------------------------------------------|
| *Tools*                 |         Transfer Functions         |       State Space formulation        |                               Disk margin                               |
|                         |           Nyquist Plots            |          Riccati Equations           | Systems and Signals Norms ($\mathcal{H}_\infty$, $\mathcal{H}_2$ Norms) |
|                         |             Bode Plots             |                                      |                     Closed Loop Transfer Functions                      |
|                         |       Phase and Gain margins       |                                      |                           Weighting Functions                           |
|-------------------------+------------------------------------+--------------------------------------+-------------------------------------------------------------------------|
| *Control Architectures* | Proportional, Integral, Derivative |         Full State Feedback          |                      General Control Configuration                      |
|                         |            Leads, Lags             |               LQR, LQG               |                                                                         |
|                         |                                    |            Kalman Filters            |                                                                         |
|-------------------------+------------------------------------+--------------------------------------+-------------------------------------------------------------------------|
| *Advantages*            |          Study Stability           |         Automatic Synthesis          |                           Automatic Synthesis                           |
|                         |               Simple               |                 MIMO                 |                                  MIMO                                   |
|                         |              Natural               |         Optimization Problem         |                          Optimization Problem                           |
|                         |                                    |                                      |                          Guaranteed Robustness                          |
|                         |                                    |                                      |                   Easy specification of performances                    |
|-------------------------+------------------------------------+--------------------------------------+-------------------------------------------------------------------------|
| *Disadvantages*         |           Manual Method            |       No Guaranteed Robustness       |                  Required knowledge of specific tools                   |
|                         |             Only SISO              | Difficult Rejection of Perturbations |               Need a reasonably good model of the system                |


* Appendix                                                            :ignore:
#+latex: \appendix

* Mathematical formulas
* Comments on something
* Bibliography                                                        :ignore:
#+latex: \printbibliography[heading=bibintoc,title={Bibliography}]

* List of Publications
:PROPERTIES:
:UNNUMBERED: notoc
:END:

#+begin_export latex
\begin{refsection}[ref.bib]
  % List all papers even if not cited
  \nocite{*}
  % Sort by year
  \newrefcontext[sorting=ynt]
  % Articles
  \printbibliography[keyword={publication},heading={subbibliography},title={Articles},env=mypubs,type={article}]
  % Proceedings
  \printbibliography[keyword={publication},heading={subbibliography},title={In Proceedings},env=mypubs,type={inproceedings}]
\end{refsection}
#+end_export

* Glossary                                                            :ignore:
#+latex: \printglossary[type=\acronymtype]
#+latex: \printglossary

* Footnotes

[fn:1]this is a footnote with citation [[cite:&dehaeze21_mechat_approac_devel_nano_activ_stabil_system]].