main_phd.tex

%%%%%%%%%%%%%%%%%%%% book.tex %%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% sample root file for the chapters of your "monograph"
%
% Use this file as a template for your own input.
%
%%%%%%%%%%%%%%%% Springer-Verlag %%%%%%%%%%%%%%%%%%%%%%%%%%
%https://www.mathstat.dal.ca/~selinger/pdfa/

% RECOMMENDED %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\documentclass[12pt,graybox,envcountchap ]{th_template}

\usepackage[
a4paper,
vmargin=2.5cm,
hmargin=3cm
]{geometry}

\usepackage[greek.polutonikogreek,english,silent]{babel}
%\usepackage[no-math, silent]{fontspec}
\usepackage[silent]{fontspec}


%\newfontfamily\unicodefont{Tex Gyre TermesX}
%\setmainfont{Tex Gyre TermesX}
%\setmainfont{TeX Gyre Termes}
%\fontencoding{OT1}\fontfamily{ptm}\selectfont
\babelfont[english]{rm}[Language=Default]{Tex Gyre TermesX}
%\babelfont[english]{rm}[Language=Default,Script=Latin]{TeXGyreTermesX-Regular.otf}

%\babelfont[english]{rm}{Tex Gyre Schola}
%\babelfont[english]{rm}{Tex Gyre TermesX}
%\babelfont{rm}{lmroman10-regular.otf}
%\babelfont{rm}{Times New Roman}
%\babelfont[greek.polutonikogreek]{rm}{Linux Libertine O}
\babelfont[greek.polutonikogreek]{rm}{CMU Serif}
%\usepackage{empheq}

%\usepackage{unicode-math}
%\setmathrmfont{TeX Gyre Termes Math}%[version=Termes]
% choose options for [] as required from the list
% in the Reference Guide
% PACKAGES %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\usepackage{type1cm}        % activate if the above 3 fonts are
                            % not available on your system
%
\usepackage{makeidx}         % allows index generation
\usepackage{graphicx}        % standard LaTeX graphics tool
                             % when including figure files
\usepackage{ifpdf}           % shoose graphic format
\usepackage{multicol}        % used for the two-column index
\usepackage[bottom]{footmisc}% places footnotes at page bottom

% Using natbib we need to fix manually the months in bib file (they are written numerically)
%\usepackage{natbib}		     % used for the spbasic bibliography style
%\setcitestyle{numbers,open={[},close={]}}

% Use biber to fix month format from mendeley files
% Use customized ieee format without urls (changes commented in ieee.bbx)
% IEEE formating is suggested by the university
\usepackage[backend=biber,style=ieee, citestyle=numeric-comp]{biblatex}
\addbibresource{Thesis_refs.bib}

%\usepackage{newtxtext}       %
\usepackage{mathtools}
\usepackage{newtxmath}       % selects Times Roman as basic font
\usepackage{soul}            % Highlight pending changes
\usepackage{float}           % Handle figure positioning
\usepackage{placeins}        % Avoid a figure from being displayed in a different section

\usepackage[left]{lineno}
%\linenumbers

\usepackage[final]{pdfpages} % To insert the UC3M cover

\usepackage[symbols,acronym,nonumberlist,toc]{glossaries-extra} % To use acronyms
\setabbreviationstyle[acronym]{long-short} % Define acronym on first use, then always use short version
%\preto\chapter{\glsresetall} % Define acronyms at every chapter
\usepackage{glossary-superragged} %To sort acronyms alphabetically
\usepackage{glossary-longragged}

\usepackage[a-1b]{pdfx}    %To create the right output pdf file
\usepackage[]{hyperref}    %To create the right output pdf file
\usepackage{verbatim}
%% WARNING! Output.xmpdata must be included in the folder


\usepackage{siunitx}    % to use SI units
\sisetup{detect-all}
%\sisetup{mode = text}
%\sisetup{math-rm = \symup}
\sisetup{per-mode = symbol}
%\newcommand*\unit[1]{& \left[\text{#1}\right]}
\newcommand*\unit[1]{& \left[#1\right]}
 \sisetup{math-micro=\text{µ},text-micro=µ}
 \DeclareSIUnit \phts {photons}
  \DeclareSIUnit \particles {particles}


%To use greek typing
\usepackage{setspace}
\usepackage{csquotes}
\usepackage{booktabs}

\usepackage{tabularx}


\usepackage{epigraph}
\setlength\epigraphwidth{.6\textwidth}
\setlength\epigraphrule{0pt}
\renewcommand{\epigraphsize}{\footnotesize}

\hypersetup{
    colorlinks,
    linkcolor={black},
    citecolor={black},
    urlcolor={black}
}

% CONFIGURE UNITS MODE
\sisetup{
    quotient-mode = fraction,
    fraction-function=\nicefrac
}

\makeatletter
\providecommand\add@text{}
\newcommand\tagaddtext[1]{%
  \gdef\add@text{#1\gdef\add@text{}}}%
\renewcommand\tagform@[1]{%
  \maketag@@@{\llap{\add@text\quad}(\ignorespaces#1\unskip\@@italiccorr)}%
}
\makeatother

% CONFIGURE FIGURE POSITIONING %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\let\Oldsection\section
\renewcommand{\section}{\FloatBarrier\Oldsection}

\let\Oldsubsection\subsection
\renewcommand{\subsection}{\FloatBarrier\Oldsubsection}

\let\Oldsubsubsection\subsubsection
\renewcommand{\subsubsection}{\FloatBarrier\Oldsubsubsection}
% CONFIGURE GLOSSARY %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Acronyms
\loadglsentries{acronyms}
\makeglossaries
\renewcommand*{\acronymname}{Acronyms}
\renewcommand*{\glspostdescription}{} % remove trailing dot
\renewcommand{\glsnamefont}[1]{\textbf{#1}}

\glssetcategoryattribute{acronym}{glossname}{firstuc}
\glssetcategoryattribute{acronym}{glossdesc}{title}

%Print the glosary
\newcommand{\printacronyms}{\printglossary[style=super, type=acronym]}
\renewcommand{\printsymbols}{\printglossary[type=symbols,style=altlongragged4col,nogroupskip]}
% CONFIGURE GRAPHIC SOURCES %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Paths for figures
\graphicspath{{figures/pdf/}}
%\graphicspath{{figures/jpeg_60_80/}}
%Choose prefered graphic format (to speedup compilation if neeeded)
\ifpdf
  \DeclareGraphicsExtensions{.pdf,.png,.jpg}
\else
  \DeclareGraphicsExtensions{.eps}
\fi

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%Paper debug stuff
\usepackage{xcolor}
\definecolor{ref}{rgb}{0.2, 0.8, 0.2}
\newcommand{\cita}[1]{\textcolor{ref}{[#1]}}
\newcommand{\rev}[1]{\textcolor{red}{[#1]}}
\newcommand{\sideref}[1]{\marginpar{\scriptsize\textcolor{ref}{[#1]}}}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%beginning of document
% see the list of further useful packages
% in the Reference Guide

\makeindex             % used for the subject index
                       % please use the style svind.ist with
                       % your makeindex program

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\begin{document}
%\selectlanguage{english}
%% UC3M cover

\includepdf[pages=-]{chapters/PhD_Cover_front.pdf}
\includepdf[pages=-]{chapters/template_UC3M_new_amarcos.pdf}


%\author{Author name(s)}
%\title{Book title}
%\subtitle{-- Monograph --}
%\maketitle

\frontmatter%%%%%%%%%%%%%%%%%%

\include{chapters/quotation}

%\include{foreword}
%\include{preface}
%\include{acknowledgements}

%%     CONTENTS
\tableofcontents
\listoffigures

% This lines work best
%\setglossarystyle{super}
\printacronyms
\printsymbols

%%      CHAPTERS
\mainmatter%%%%%%%%%%%%%%%%%%%%%
\include{chapters/abstract}
\include{chapters/motivation}

\include{chapters/1_near_infrared_theory}
%\include{chapters/2_optical_imaging_review}
%\resetlinenumber
%\include{chapters/3_assessment_nir_imaging}
%\resetlinenumber
%\include{chapters/4_monte_carlo_spim}
%\include{chapters/5_opt_spim}
%\include{chapters/6_OPT_opaque_samples}
\include{chapters/conclusions}
\include{chapters/future}


\backmatter%%%%%%%%%%%%%%%%%%%%%

%%     BIBLIOGRAPHY
\include{chapters/references}
\includepdf[pages=-]{chapters/PhD_Cover_back.pdf}

\end{document}