custom.tex

% !TEX TS-program = pdflatex
% !TEX root = Tesis.tex
%-------------------------------------------------------------
% Change custom title font
%-------------------------------------------------------------
%
\addbibresource[label=referencias]{referencias.bib}
\addbibresource[label=ownpubs]{FJMM_Publications.bib}

%-------------------------------------------------------------
%% Solve geometry problems with B5paper. 
%-------------------------------------------------------------
\usepackage{geometry}
  \geometry{
  	twoside,
  	includehead,
  	includefoot,
  	right=20mm,
  	left=20mm,
  	bottom=10mm, % space from bottomn to footer (space from text to bottom = footskip + bottom)
  	bindingoffset=3mm, % For printing 
  	top=10mm,    % space from top to text
  }
  \geometry{
  	paper=b5paper
  }

  % Chapter thumbs
  \usepackage[
  % if not commented these are defaults
  thumblink=rule, 
  linefill=dots,
  height=auto,             
  minheight={47pt}, 
  width={15mm},            % reduce for space to text body; default=auto
  distance={3mm},          % default = 2mm
  topthumbmargin={3cm},    % more space to top, to avoid clash with pagenumber of chapter; default = auto
  bottomthumbmargin={auto},
  eventxtindent={10pt},    % default = 5pt
  oddtxtexdent={10pt},      % default = 5pt
  evenmarkindent={0pt},      % use for pdf
  %evenmarkindent={15.5mm},     % use for print; default = 0pt, 210mm(a4) - 176 (b5) / 2 = 17.5mm - 2mm for cutting = 15.5mm for B5
  oddmarkexdent={0pt},       % use for pdf
  %oddmarkexdent={15.5mm},      % use for print; default = 0pt
  evenprintvoffset={0pt}, 
  nophantomsection=false, 
  ignorehoffset=true,
  ignorevoffset=true,
  final=true,
  hidethumbs=false
  ]{thumbs}

%-------------------------------------------------------------
% Include acronyms
%-------------------------------------------------------------
\PassOptionsToPackage{printonlyused,smaller}{acronym} 
\usepackage{acronym} % nice macros for handling all acronyms in the thesis
%\renewcommand{\bflabel}[1]{{#1}\hfill} % fix the list of acronyms --> no longer working
%\renewcommand*{\acsfont}[1]{\textsc{#1}} 
\renewcommand*{\aclabelfont}[1]{\acsfont{#1}}
\newcommand{\tableheadline}[1]{\multicolumn{1}{c}{\spacedlowsmallcaps{#1}}}

%-------------------------------------------------------------
% Math operators
%-------------------------------------------------------------
\DeclareMathOperator*{\argmax}{arg\,max}
\DeclareMathOperator*{\argmin}{arg\,min}

%-------------------------------------------------------------
% Custom Commands and Environments
%-------------------------------------------------------------
\newcommand{\myfloatalign}{\centering} % to be used with each float for alignment

\newenvironment{bigtable}[1][]{%
	\begin{sidewaystable}[htbp]\myfloatalign}
		{\end{sidewaystable}}

\newenvironment{bigfigure}[1][]{%
	\begin{sidewaysfigure}[htbp]\myfloatalign}
		{\end{sidewaysfigure}}


% ********************************************************************
% Setup, finetuning, and useful commands
% ********************************************************************
\newcounter{dummy} % necessary for correct hyperlinks (to index, bib, etc.)
\newlength{\abcd} % for ab..z string length calculation
\providecommand{\mLyX}{L\kern-.1667em\lower.25em\hbox{Y}\kern-.125emX\@}
\newcommand{\ie}{i.\,e.}
\newcommand{\Ie}{I.\,e.}
\newcommand{\eg}{e.\,g.}
\newcommand{\Eg}{E.\,g.} 
\newcommand{\vdlndat}{{\large\textsc{vdln-dat}}}
\newcommand{\vdlvdat}{{\large\textsc{vdlv-dat}}}
\newcommand{\ppmidat}{{\large\textsc{ppmi-dat}}}
\newcommand{\aimsmri}{{\large\textsc{aims-mri}}}
\newcommand{\adnimri}{{\large\textsc{adni-mri}}}
\newcommand{\adnipet}{{\large\textsc{adni-pet}}}
\newcommand{\vdlnhmpao}{{\large\textsc{vdln-hmpao}}}
\newcommand{\lon}{{\large\textsc{lon}}}
\newcommand{\cam}{{\large\textsc{cam}}}
\newcommand{\all}{{\large\textsc{all}}}
%\newcommand{\datscan}{{\Large\textsc{d}}{\normalsize a}{\Large\textsc{tscan}}}

\hyphenation{A-na-to-mi-cal io-flu-pane lan-gua-ge Wi-lliams me-ta-bo-lic pipe-line}

%\hypersetup{hidelinks} % Uncomment for print version. 
\usepackage{gillius2}

% ********************************************************************
% Custom hack for no-cite bibliographies (copied from authortitle.bbx/authoryear.bbx)
% ********************************************************************
\defbibenvironment{nolabelbib}
{\list
	{}
	{\setlength{\leftmargin}{\bibhang}%
		\setlength{\itemindent}{-\leftmargin}%
		\setlength{\itemsep}{\bibitemsep}%
		\setlength{\parsep}{\bibparsep}}}
{\endlist}
{\item}

\DeclareFieldFormat{doi}{%
	\newline
	\mkbibacro{DOI}\addcolon\space
	\ifhyperref
	{\href{http://dx.doi.org/#1}{\nolinkurl{#1}}}
	{\nolinkurl{#1}}}