westernthesis.tex

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% University of Western Ontario Thesis Template
% 1. Initial version by: Justin Quinn Veenstra, 2010 with thanks to Mr. (soon to be Dr.) Will Robertson.
% 2. Adapted by: Dr. John Stuart Haberl Baxter, 2018 for his thesis.
% 3. Dr. Baxter's thesis converted to generic template by: Dr. Jonathan C. Lau, 2018.


\documentclass[hidelinks,12pt,oneside]{report}
%% Decomment next line to use PostScript fonts
%%\UsePackage{times}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%                                                                    %%
%%                    ***   I M P O R T A N T   ***                   %%
%%                                                                    %%
%% Fill in the following fields with the required information:        %%
%%  - \department{...}  name of the graduate department               %%
%%  - \degree{...}      name of the degree obtained                   %%
%%  - \author{...}      name of the author                            %%
%%  - \title{...}       title of the thesis                           %%
%%  - \gyear{...}       year of graduation                            %%
%%  - \super{...}    supervisor
%%  - \firstname, \middlename, \lastname... there is additional documentation by the actual fields, so I'll leave it at that
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\usepackage{appendix}
\usepackage{graphicx}
\usepackage[fleqn]{amsmath}
\usepackage[byname]{smartref}
\usepackage[]{amssymb}
\usepackage[font=small]{caption}
\usepackage[font=small]{subcaption}
\usepackage{setspace}
\usepackage{enumitem}
\usepackage{lmodern}
\newlength\longest
%\usepackage{lineno}%comment out for hardcopy
\usepackage{units}
\usepackage{txfonts}
\usepackage{tocloft}
\usepackage{tabularx}
\usepackage{longtable}
%\usepackage[sectionbib]{chapterbib}

\usepackage{hyperref} %comment out for hardcopy
\usepackage{txfonts}
\usepackage{tocloft}
\usepackage{color}
\usepackage{pdfpages}


\makeatletter
\numberwithin{figure}{chapter}
\newenvironment{acknowledgements}%
{\clearemptydoublepage
 \begin{center}
  \section*{Acknowledgements}
 \end{center}
 \begingroup
}{\newpage\endgroup}


\usepackage[boxruled,algochapter]{algorithm2e}

\DeclareMathOperator*{\argmin}{\operatorname{argmin}}
\DeclareMathOperator*{\Proj}{\operatorname{Proj}}
\DeclareMathOperator*{\dvg}{\operatorname{div}}

\newenvironment{dedication}%
{\clearemptydoublepage 
 \begin{center}
  \section*{Dedication}
 \end{center}
 \begingroup
}{\newpage\endgroup}

\newenvironment{preliminary}%
{\pagestyle{plain}\pagenumbering{roman}}%
{\pagenumbering{arabic}}

\addtoreflist{chapter}
\newtheorem{theorem}{Theorem}[section]
\newtheorem{lemma}[theorem]{Lemma}
\newtheorem{proposition}[theorem]{Proposition}
\newtheorem{corollary}[theorem]{Corollary}
\newtheorem{axiom}{Axiom}

\newenvironment{proof}[1][Proof]{\begin{trivlist}
\item[\hskip \labelsep {\bfseries #1}]}{\end{trivlist}}
\newenvironment{definition}[1][Definition]{\begin{trivlist}
\item[\hskip \labelsep {\bfseries #1}]}{\end{trivlist}}
\newenvironment{example}[1][Example]{\begin{trivlist}
\item[\hskip \labelsep {\bfseries #1}]}{\end{trivlist}}
\newenvironment{remark}[1][Remark]{\begin{trivlist}
\item[\hskip \labelsep {\bfseries #1}]}{\end{trivlist}}

\newcommand{\qed}{\nobreak \ifvmode \relax \else
      \ifdim\lastskip<1.5em \hskip-\lastskip
      \hskip1.5em plus0em minus0.5em \fi \nobreak
      \vrule height0.75em width0.5em depth0.25em\fi}

% Default values for title page.

%% To produce output with the desired line spacing, the argument of
%% \spacing should be multiplied by 5/6 = 0.8333, so that 1 1/2 spaced
%% corresponds to \spacing{1.5} and double spaced is \spacing{1.66}.
\def\normalspacing{1.66} % default line spacing


%% Define the "thesis" page style.
\if@twoside % If two-sided printing.
\def\ps@thesis{\let\@mkboth\markboth
   \def\@oddfoot{}
   \let\@evenfoot\@oddfoot
   \def\@oddhead{
      {\sc\rightmark} \hfil \rm\thepage
      }
   \def\@evenhead{
      \rm\thepage \hfil {\sc\leftmark}
      }
   \def\chaptermark##1{\markboth{\ifnum \c@secnumdepth >\m@ne
      Chapter \ \thechapter. \ \fi ##1}{}}
   \def\sectionmark##1{\markright{\ifnum \c@secnumdepth >\z@
      \thesection. \ \fi ##1}}}
\else % If one-sided printing.
\def\ps@thesis{\let\@mkboth\markboth
   \def\@oddfoot{}
   \def\@oddhead{
      {\sc\rightmark} \hfil \rm\thepage
      }
   \def\chaptermark##1{\markright{\ifnum \c@secnumdepth >\m@ne
      Chapter\ \thechapter. \ \fi ##1}}}
\fi

\if@twoside % If two-sided printing.
\def\ps@appendix{\let\@mkboth\markboth
   \def\@oddfoot{}
   \let\@evenfoot\@oddfoot
   \def\@oddhead{
      {\sc\rightmark} \hfil \rm\thepage
      }
   \def\@evenhead{
      \rm\thepage \hfil {\sc\leftmark}
      }
   \def\chaptermark##1{\markboth{\ifnum \c@secnumdepth >\m@ne
      Appendix \ \thechapter. \ \fi ##1}{}}
   \def\sectionmark##1{\markright{\ifnum \c@secnumdepth >\z@
      \thesection. \ \fi ##1}}}
\else % If one-sided printing.
\def\ps@thesis{\let\@mkboth\markboth
   \def\@oddfoot{}
   \def\@oddhead{
      {\sc\rightmark} \hfil \rm\thepage
      }
   \def\chaptermark##1{\markright{\ifnum \c@secnumdepth >\m@ne
      Chapter\ \thechapter. \ \fi ##1}}}
\fi

\pagestyle{thesis}
% Set up page layout.
\setlength{\textheight}{9in} % Height of the main body of the text
\setlength{\topmargin}{-.5in} % .5" margin on top of page
\setlength{\headsep}{.5in}  % space between header and top of body
\addtolength{\headsep}{-\headheight} % See The LaTeX Companion, p 85
\setlength{\footskip}{.5in}  % space between footer and bottom of body
\setlength{\textwidth}{6.25in} % width of the body of the text
\setlength{\oddsidemargin}{.25in} % 1.25" margin on the left for odd pages
\setlength{\evensidemargin}{0in} % 1.25"  margin on the right for even pages

% Marginal notes
\setlength{\marginparwidth}{.75in} % width of marginal notes
\setlength{\marginparsep}{.125in} % space between marginal notes and text

% Make each page fill up the entire page. comment this out if you
% prefer. 
\flushbottom

\setcounter{tocdepth}{3} % Number the subsubsections 
\def\normalspacing{1.66} % default line spacing

\newcommand\isco[1]{%
  \edef\@tempa{#1}%
  \def\@tempb{}%
  \ifx\@tempa\@tempb
	\else \\\underline{Co-Supervisor:}\vspace{0.35in}\\\dots\dots\dots\dots\dots\dots\dots\\{#1}\\
  \fi
}

\newcommand\isjoint[1]{%
  \edef\@tempa{#1}%
  \def\@tempb{}%
  \ifx\@tempa\@tempb
	\else \\\underline{Joint Supervisor:}\vspace{0.35in}\\\dots\dots\dots\dots\dots\dots\dots\\{#1}\\
  \fi
}

\newcommand\isalt[1]{%
  \edef\@tempa{#1}%
  \def\@tempb{}%
  \ifx\@tempa\@tempb
	\else \\\underline{Alternate Supervisor:}\vspace{0.35in}\\\dots\dots\dots\dots\dots\dots\dots\\{#1}\\
  \fi
}

\newcommand\isdefinedsig[1]{%
  \edef\@tempa{#1}%
  \def\@tempb{}%
  \ifx\@tempa\@tempb
	\else \\ \dots\dots\dots\dots\dots\dots\dots\\{#1}\\
  \fi
}
\newcommand\isdefinedspinetitle[1]{%
  \edef\@tempa{#1}%
  \def\@tempb{}%
  \ifx\@tempa\@tempb
	\else (Spine title: #1)\\
  \fi
}
\newcommand\coauthor[1]{%
  \edef\@tempa{#1}%
  \def\@tempb{}%
  \ifx\@tempa\@tempb
	\else \newpage \Large Co-Authorship Statement\normalsize\\\indent\\#1\\
  \fi
}

\newcommand\acknowlege[1]{%
  \edef\@tempa{#1}%
  \def\@tempb{}%
  \ifx\@tempa\@tempb
	\else \newpage \Large Acknowledgements\normalsize\\\indent\\#1\newpage
  \fi
}

%\renewcommand{\appendixtocname}{\Huge \textbf{List of Appendices} \normalsize}
\newcommand{\blank}{\hspace{-2mm}}
\newcommand{\super}{Dr. Supervisor1} %supervisor
\newcommand{\superj}{Dr. Supervisor2} %joint supervisor, if there is one, leave blank if not (lbin)... only one of the three.
\newcommand{\superc}{} %co-supervisor, if there is one, leave blank if not (lbin)
\newcommand{\supera}{} %alternate supervisor, if there is one, leave blank if not (lbin)
\newcommand{\scoa}{Dr. Committee1}  %member of supervisory committee
\newcommand{\scob}{Dr. Committee2}  %member of supervisory committee
\newcommand{\scoc}{Dr. Committee3}  %member of supervisory committee
\newcommand{\sct}{}  %other member of supervisory committee (lbin)
\newcommand{\examo}{Dr. Examiner1}  %examining committee (up to four, if less leave blank)
\newcommand{\examt}{Dr. Examiner2}
\newcommand{\examth}{Dr. Examiner3}
\newcommand{\examf}{Dr. Examiner4}
\newcommand{\department}{Department of []}
\newcommand{\degree}{Doctor of Philosophy}
\newcommand{\firstname}{Firstname}
\newcommand{\middlename}{Middleinitial}
\newcommand{\lastname}{Lastname}
%\renewcommand{\author}[1]{\ifx\empty#1\else\gdef\@author{#1}\fi} 
\newcommand{\authorname}{{\firstname} {\middlename} {\lastname}}
\newcommand{\titl}{Thesis Title}
\newcommand{\spinetitle}{}%only if the above is more than 60 characters
\newcommand{\thesisformat}{Integrated Article} %or Monograph
\newcommand{\gyear}{\number\year}
\newcommand{\makecoauthor}{}
\newcommand{\makeacknowlege} {
%Type in acknowlegements here
}
\newcommand{\listappendixname}{List of Appendices}
\newlistof{myappendices}{app}{\listappendixname}
\newcommand{\myappendices}[1]{%
\addcontentsline{app}{myappendices}{#1}\par}

\renewcommand{\maketitle}
{\begin{titlepage}
   \setcounter{page}{1}
   %% Set the line spacing to 1 for the title page.
   %\begin{spacing}{1} 
   \begin{large}
   \begin{center}
      \mbox{}
      \vfill
      {\MakeUppercase{\titl}}\\
      \isdefinedspinetitle{\spinetitle}
      (Thesis format: \thesisformat)\\
      \vfill
      by \\
      \vfill
      {\firstname{} \middlename } \underline{\lastname}\\
      \vfill
      Graduate Program in {\department}\\
      \vfill
		A thesis submitted in partial fulfillment\\
		of the requirements for the degree of\\
		\degree\\
		\vfill
		The School of Graduate and Postdoctoral Studies\\
		The University of Western Ontario\\
		London, Ontario, Canada\\
		\vfill
      {\copyright} {\authorname} {\gyear}  \\
      \vspace*{.2in}
   \end{center}
   \end{large}
%   \end{spacing}
   \end{titlepage}

}%\maketitle

\newcommand{\makecert}{
   \setcounter{page}{2}
\vfill
\begin{center}
\large
THE UNIVERSITY OF WESTERN ONTARIO\\
School of Graduate and Postdoctoral Studies\\
\vfill
\textbf{CERTIFICATE OF EXAMINATION}
\end{center}

\vfill
\begin{table}[ht]
\begin{minipage}[t]{0.5\linewidth} %tabular instead?
\begin{tabular}{l}
\underline{Supervisor:}\vspace{0.35in}
\isdefinedsig{\super}
\isco{\superc}
\isjoint{\superj}
\isalt{\supera}
\\
%\underline{Supervisory Committee:}\vspace{0.35in}
%\isdefinedsig{\scoa}\vspace{0.15in}
%\isdefinedsig{\scob}\vspace{0.15in}
%\isdefinedsig{\scoc}\vspace{0.15in}
%\isdefinedsig{\sct}
\end{tabular}
\vfill
\end{minipage}
\hspace{0.5in}
\begin{minipage}[t]{0.5\linewidth}
\begin{tabular}{l}
\underline{Examiners:} \\\vspace{.5cm}
\isdefinedsig{\examo}\\
\isdefinedsig{\examt}\\
\isdefinedsig{\examth}\\
\isdefinedsig{\examf}
\end{tabular}
\vfill
\end{minipage}
\vfill
\end{table}
\vfill
\begin{center}
The thesis by \\ \vfill
\textbf{\firstname{} \middlename{} \underline{\lastname}}\\
\vfill
entitled:\\\vfill
\textbf{\titl}\\\vfill
is accepted in partial fulfillment of the \\
requirements for the degree of\\
\degree\\
\end{center}
\begin{table}[ht]
\begin{minipage}[t]{0.5\linewidth}
\begin{tabular}{l}
\dots\dots\dots\dots\dots\\
Date
\end{tabular}
\end{minipage}
\hspace{0.5in}
\begin{minipage}[t]{0.5\linewidth}
\begin{tabular}{l}
\dots\dots\dots\dots\dots\dots\dots\dots\dots\dots\\
Chair of the Thesis Examination Board
\end{tabular}
\end{minipage}
\end{table}

}

\makeatother
\begin{document}


%% ***   NOTE   ***
%% You should put all of your '\newcommand', '\newenvironment', and
%% '\newtheorem's (in other words, all the global definitions that you
%% will need throughout your thesis) in a separate file and use
%% "\input{filename}" to input it here.


%% This sets the page style and numbering for preliminary sections.
\begin{preliminary}

%% This generates the title page from the information given above.
\maketitle
%\addcontentsline{toc}{chapter}{Certificate of Examination}
%\makecert
\newpage


%\addcontentsline{toc}{chapter}{Co-Authorship Statement}
%\coauthor{\makecoauthor}  %comment this out if none
%\newpage
%\addcontentsline{toc}{chapter}{Acknowlegements}
%\acknowlege{\makeacknowlege}	%as above
\setcounter{page}{2}
\addcontentsline{toc}{chapter}{Abstract}
\Large\begin{center}\textbf{Abstract}\end{center}\normalsize
%%  ***  Put your Abstract here.   ***
%% (150 words for M.Sc. and 350 words for Ph.D.)
\input{abstract}

\vfill
\noindent\textbf{Keywords:} keyword 1, keyword 2, keyword 3.
\newpage




\clearpage

\thispagestyle{empty}
\null\vfill
{
	\settowidth\longest{\Large\itshape Planning to write is not writing. Outlining, researching,}
	\centering
	\hspace{3cm}\parbox{\longest}{%
		\raggedright{\Large\itshape%
      Planning to write is not writing. Outlining, researching, talking to people about what you’re doing, none of that is writing. Writing is writing.\par\bigskip
		}   
		\raggedleft\MakeUppercase{E. L. Doctorow}\par%
		\raggedleft\MakeUppercase{\textit{Some book}}\par%
}}

\vfill\vfill

\newpage


\addcontentsline{toc}{chapter}{Acknowledgments}
\Large\begin{center}\textbf{Acknowledgments}\end{center}\normalsize
\input{acknowledgements}
\vfill
\newpage
\singlespacing

%%  ***  Put your Abstract here.   ***
%% (150 words for M.Sc. and 350 words for Ph.D.)
\tableofcontents\newpage
\newpage
\addcontentsline{toc}{chapter}{List of Figures}
\listoffigures
\newpage
\addcontentsline{toc}{chapter}{List of Algorithms}
\listofalgorithms
\addtocontents{loa}{\def\string\figurename{Algorithm}}
\newpage
\addcontentsline{toc}{chapter}{List of Tables}
\listoftables
\newpage
\addcontentsline{toc}{chapter}{List of Appendices}
\listofmyappendices\newpage

\addcontentsline{toc}{chapter}{List of Abbreviations, Symbols, and Nomenclature}
\Large \textbf{List of Abbreviations, Symbols, and Nomenclature} \normalsize

\begin{tabular}{lcl}
\\
\multicolumn{3}{l}{\textbf{Terminology}}\\
CNR & & Contrast-to-noise ratio \\
SNR & \, & Signal-to-noise ratio \\
\\
\multicolumn{3}{l}{\textbf{Medical Imaging Terminology}}\\
CT & \, & Computed Tomography \\
MRI & \, & Magnetic Resonance Imaging \\
QSM & \, & Quantitative Susceptibility Mapping \\
\\
\multicolumn{3}{l}{\textbf{Terms Introduced by this Thesis}}\\
$\mathbb{ABC}$ && ABC \\
DEF & \, & DEF \\
\end{tabular}

\newpage
	
\clearpage

\addcontentsline{toc}{chapter}{Preface}
\Large\begin{center}\textbf{Preface}\end{center}\normalsize
\onehalfspacing
\input{preface}

\newpage

\end{preliminary}
%% End of the preliminary sections: reset page style and numbering.

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%                                                                    %%
%%                    ***   I M P O R T A N T   ***                   %%
%%                                                                    %%
%% Put your Chapters here; the easiest way to do this is to keep each %%
%% chapter in a separate file and \include all the files right here.  %%
%% Note that each chapter file should start with the line             %%
%% "\chapter{ChapterName}".  Note that using "\include" instead of    %%
%% "\input" makes each chapter start on a new page.                   %%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\onehalfspacing
\input{chapter_intro}
\input{chapter_example}
\input{chapter_conc}

%Appendices.
\begin{appendices}
%\pagestyle{appendix}
\input{app_example}
\input{app_ethics}
\input{app_copyright}
\end{appendices}
\newpage
\singlespacing

%% This adds a line for the Bibliography in the Table of Contents.
\addcontentsline{toc}{chapter}{Bibliography}
%% ***   Set the bibliography style.   ***
\bibliographystyle{plain} % (change according to your preference)
%%% ***   Set the bibliography file.   ***
\bibliography{westernthesis}{}
%% ***   NOTE   ***
%% If you don't use bibliography files, comment out the previous line
%% and use \begin{thebibliography}...\end{thebibliography}.  (In that
%% case, you should probably put the bibliography in a separate file
%% and \include or \input it here).


%CV only relevant stuff... not full CV.
\include{curriculum_vitae}

\end{document}