main.tex

% Load the kaobook class
\documentclass[
	fontsize=10pt, % Base font size
	twoside=false, % Use different layouts for even and odd pages (in particular, if twoside=true, the margin column will be always on the outside)
	% open=any, % If twoside=true, uncomment this to force new chapters to start on any page, not only on right (odd) pages
	secnumdepth=2, % How deep to number headings. Defaults to 1 (sections)
	numbers=noenddot,
]{kaobook}

% Choose the language
\usepackage[english]{babel} % Load characters and hyphenation
\usepackage[english=british]{csquotes}	% English quotes

% TODO notes
\usepackage{todonotes}

% Change format of vectors to boldface without arrow.
\usepackage{bm}
\renewcommand\vec{\mathbf}

% Load packages for testing
\usepackage{blindtext}
%\usepackage{showframe} % Uncomment to show boxes around the text area, margin, header and footer
%\usepackage{showlabels} % Uncomment to output the content of \label commands to the document where they are used

% Load the bibliography package
\usepackage{kaobiblio}
\addbibresource{library.bib} % Bibliography file

% Load mathematical packages for theorems and related environments
\usepackage{kaotheorems}

% Load the package for hyperreferences
\usepackage{kaorefs}

\hypersetup{
	linkcolor=black
}

% To be able to include Tikz files
% \usepackage{standalone}

% To typeset date and time
\usepackage{datetime2}
\DTMsetstyle{ddmmyyyy}

% For logos on titlepage.
\usepackage{tabularx}

% To typeset units
\usepackage[separate-uncertainty=true]{siunitx}
\DeclareSIUnit\stretch{unit\,stretch}

% To rotate big images sideways
\usepackage{rotating}
% \usepackage{pdflscape}

% To display svg images.
\usepackage[inkscapelatex=false]{svg}
% \newcommand{\kutblokje}[1]{%
% 	\begin{tikzpicture}
	
% 		\node[rectangle,draw] (r) at (0,0) {};
	
% 	\end{tikzpicture}
% }
% \DeclareUnicodeCharacter{25AF}{\kutblokje{}}

% \newcommand{\ie}{i.\,e.\,}
% \newcommand{\Ie}{I.\,e.\,}
% \newcommand{\eg}{e.\,g.\,}
% \newcommand{\Eg}{E.\,g.\,}

% For logos on title page
\newcolumntype{u}{>{\hsize=0.56\hsize}X}
\newcolumntype{v}{>{\hsize=0.44\hsize}X}

% For check/x-marks
\usepackage{pifont}% http://ctan.org/pkg/pifont
\newcommand{\cmark}{\ding{51}}%
\newcommand{\xmark}{\ding{55}}%

\usepackage{fontawesome5}

% For iterating on images in a directory, using foreach.
\usepackage{pgffor}%

\graphicspath{{images/}{./}} % Paths where images are looked for

\makeindex[columns=3, title=Alphabetical Index, intoc] % Make LaTeX produce the files required to compile the index

% To make numbers boldface: \textbf{\num{number...}}
\sisetup{
text-series-to-math = true ,
propagate-math-font = true
}

% https://github.com/fmarotta/kaobook/issues/145#issuecomment-866744813
% \makeatletter
% \RenewDocumentCommand{\chapterstylekao}{}{%
%     \renewcommand*{\chapterformat}{%
%         \mbox{\chapappifchapterprefix{\nobreakspace}\scalebox{2.85}{\thechapter\autodot}}%
%     }%  
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%                 \parbox[b]{0pt}{##2}%
%             }}%
%         \fi%
%     }%  
%     \RedeclareSectionCommand[beforeskip=0cm,afterskip=10\vscale]{chapter}%
%     \setlength{\mtocshift}{-3\vscale}%
% }
% \makeatother
% \RedeclareSectionCommand[\chapterstylekao]{
% 	\RedeclareSectionCommand[
% 	style=part,
% 	innerskip=0pt,
% 	beforeskip=\fill,
% 	afterskip=\fill
% 	]{chapter}
% }

\begin{document}

%----------------------------------------------------------------------------------------
%	BOOK INFORMATION
%----------------------------------------------------------------------------------------

\titlehead{Draft}
\title[Deep learning on higher harmonic generation images for regression and pathology]{Deep learning on higher harmonic generation images for regression and pathology} % {\normalfont\texttt{kaobook}}
\author[SJ]{Siem de Jong}
\date{\today}
\publishers{}

%----------------------------------------------------------------------------------------

\frontmatter % Denotes the start of the pre-document content, uses roman numerals

%----------------------------------------------------------------------------------------
%	OUTPUT TITLE PAGE AND FRONTMATTER
%----------------------------------------------------------------------------------------

\includepdf[pages=-]{images/cover.pdf}

\input{frontbackmatter/titlepage.tex}
\input{frontbackmatter/titleback.tex}

%----------------------------------------------------------------------------------------
%	PREFACE
%----------------------------------------------------------------------------------------

% \input{preface.tex}
\clearpage
\pagelayout{margin}
\input{abstract.tex}

%----------------------------------------------------------------------------------------
%	TABLE OF CONTENTS & LIST OF FIGURES/TABLES
%----------------------------------------------------------------------------------------

\begingroup % Local scope for the following commands

% Define the style for the TOC, LOF, and LOT
%\setstretch{1} % Uncomment to modify line spacing in the ToC
% \hypersetup{linkcolor=blue} % Uncomment to set the colour of links in the ToC
\setlength{\textheight}{230\vscale} % Manually adjust the height of the ToC pages

% Turn on compatibility mode for the etoc package
\etocstandarddisplaystyle % "toc display" as if etoc was not loaded
\etocstandardlines % "toc lines as if etoc was not loaded
\setcounter{tocdepth}{1}

\addtocontents{toc}{\protect\setcounter{tocdepth}{-1}}
\tableofcontents
\addtocontents{toc}{\protect\setcounter{tocdepth}{1}}

\listoffigures % Output the list of figures

% Comment both of the following lines to have the LOF and the LOT on different pages
\let\cleardoublepage\bigskip
\let\clearpage\bigskip

\listoftables % Output the list of tables

\endgroup

%----------------------------------------------------------------------------------------
%	MAIN BODY
%----------------------------------------------------------------------------------------

\mainmatter % Denotes the start of the main document content, resets page numbering and uses arabic numbers
\setchapterstyle{kao} % Choose the default chapter heading style

\pagelayout{wide}
\chapter{General introduction}\label{ch:general_introduction}
\pagelayout{margin} % Restore margins

\input{general_introduction.tex}

% \pagelayout{wide} % No margins
% \addpart{Theory of artificial neural networks}\label{pt:theory}
% \pagelayout{margin} % Restore margins

\pagelayout{wide}
\chapter{Theory of higher harmonic generation and artificial neural networks}\label{ch:theory}
\pagelayout{margin} % Restore margins

\input{ANN/hhg.tex}
\input{ANN/theory.tex}

% \pagelayout{wide} % No margins
% % \addpart[Skinstression]{Strain-stress regression on \\ second harmonic generation images \\ using {\normalfontSkinstression}}
% \addpart[Skinstression]{Developing and validating a strain-stress regression model on second harmonic generation images from old adult skin tissue}
% \pagelayout{margin} % Restore margins

\pagelayout{wide}
\chapter[Skinstression]{Developing and validating a strain-stress regression model on second harmonic generation images from old adult skin tissue}\label{ch:skinstression}
\pagelayout{margin} % Restore margins

\input{skinstression/sections/abstract.tex}
\clearpage
\input{skinstression/sections/introduction.tex}
\input{skinstression/sections/theory.tex}
\input{skinstression/sections/methods.tex}
\input{skinstression/sections/results.tex}
\input{skinstression/sections/discussion.tex}
\input{skinstression/sections/conclusion.tex}
\input{skinstression/sections/supplementary.tex}

\pagelayout{wide} % No margins
\chapter[SCLICOM]{Developing and validating a clinical context aware multi-instance learning model with self-supervised pre-training on higher harmonic generation images of medulloblastoma and pilocytic astrocytoma in children}\label{ch:sclicom}
\pagelayout{margin} % Restore margins


\input{pediatric-brain-tumours/sections/abstract.tex}
\clearpage
\input{pediatric-brain-tumours/sections/introduction.tex}
\input{pediatric-brain-tumours/sections/theory/theory.tex}
\input{pediatric-brain-tumours/sections/methods/methods.tex}
\input{pediatric-brain-tumours/sections/results/results.tex}
\input{pediatric-brain-tumours/sections/discussion/discussion.tex}
\input{pediatric-brain-tumours/sections/conclusion.tex}
\input{pediatric-brain-tumours/sections/supplementary_materials.tex}

\pagelayout{wide} % No margins
\chapter[General discussion and conclusion]{General discussion and conclusion}\label{ch:general_discussion_and_conclusion}
\pagelayout{margin} % Restore margins

\input{general_discussion_and_conclusion.tex}
\addcontentsline{toc}{chapter}{Acknowledgements}
\input{acknowledgements.tex}

% \defbibnote{bibnote}{Here are the references in citation order.\par\bigskip} % Prepend this text to the bibliography
% \printbibliography[heading=bibintoc, title=Bibliography, prenote=bibnote] % Add the bibliography heading to the ToC, set the title of the bibliography and output the bibliography note
\pagelayout{wide}
\printbibheading[title=References, heading=bibintoc]
\pagelayout{margin}
\printbibliography[heading=none] % Add the bibliography heading to the ToC, set the title of the bibliography and output the bibliography note

\appendix % From here onwards, chapters are numbered with letters, as is the appendix convention

\addcontentsline{toc}{part}{Appendix}

\pagelayout{wide}
\chapter{Skinstression}
\pagelayout{margin}

\input{frontbackmatter/appendix-skin.tex}

\pagelayout{wide}
\chapter{SCLICOM}
\pagelayout{margin}

\input{frontbackmatter/appendix-sclicom.tex}


%----------------------------------------------------------------------------------------

\backmatter % Denotes the end of the main document content
\setchapterstyle{plain} % Output plain chapters from this point onwards

%----------------------------------------------------------------------------------------
%	BIBLIOGRAPHY
%----------------------------------------------------------------------------------------

% The bibliography needs to be compiled with biber using your LaTeX editor, or on the command line with 'biber main' from the template directory

% \defbibnote{bibnote}{Here are the references in citation order.\par\bigskip} % Prepend this text to the bibliography
% \printbibliography[heading=bibintoc, title=Bibliography, prenote=bibnote] % Add the bibliography heading to the ToC, set the title of the bibliography and output the bibliography note

%----------------------------------------------------------------------------------------
%	INDEX
%----------------------------------------------------------------------------------------

% The index needs to be compiled on the command line with 'makeindex main' from the template directory

\printindex % Output the index

\end{document}