thesis.tex

% uWaterloo Thesis Template for LaTeX 
% Last Updated May 24, 2011 by Stephen Carr, IST Client Services
% FOR ASSISTANCE, please send mail to rt-IST-CSmathsci@ist.uwaterloo.ca

% Effective October 2006, the University of Waterloo 
% requires electronic thesis submission. See the uWaterloo thesis regulations at
% http://www.grad.uwaterloo.ca/Thesis_Regs/thesistofc.asp.

% DON'T FORGET TO ADD YOUR OWN NAME AND TITLE in the "hyperref" package
% configuration below. THIS INFORMATION GETS EMBEDDED IN THE PDF FINAL PDF DOCUMENT.
% You can view the information if you view Properties of the PDF document.

% Many faculties/departments also require one or more printed
% copies. This template attempts to satisfy both types of output. 
% It is based on the standard "book" document class which provides all necessary 
% sectioning structures and allows multi-part theses.

% DISCLAIMER
% To the best of our knowledge, this template satisfies the current uWaterloo requirements.
% However, it is your responsibility to assure that you have met all 
% requirements of the University and your particular department.
% Many thanks to the feedback from many graduates that assisted the development of this template.

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

% By default, output is produced that is geared toward generating a PDF 
% version optimized for viewing on an electronic display, including 
% hyperlinks within the PDF.
 
% E.g. to process a thesis called "mythesis.tex" based on this template, run:

% pdflatex mythesis	-- first pass of the pdflatex processor
% bibtex mythesis	-- generates bibliography from .bib data file(s) 
% pdflatex mythesis	-- fixes cross-references, bibliographic references, etc
% pdflatex mythesis	-- fixes cross-references, bibliographic references, etc

% If you use the recommended LaTeX editor, Texmaker, you would open the mythesis.tex
% file, then click the pdflatex button. Then run BibTeX (under the Tools menu).
% Then click the pdflatex button two more times. If you have an index as well,
% you'll need to run MakeIndex from the Tools menu as well, before running pdflatex
% the last two times.

% N.B. The "pdftex" program allows graphics in the following formats to be
% included with the "\includegraphics" command: PNG, PDF, JPEG, TIFF
% Tip 1: Generate your figures and photos in the size you want them to appear
% in your thesis, rather than scaling them with \includegraphics options.
% Tip 2: Any drawings you do should be in scalable vector graphic formats:
% SVG, PNG, WMF, EPS and then converted to PNG or PDF, so they are scalable in
% the final PDF as well.
% Tip 3: Photographs should be cropped and compressed so as not to be too large.

% To create a PDF output that is optimized for double-sided printing: 
%
% 1) comment-out the \documentclass statement in the preamble below, and
% un-comment the second \documentclass line.
%
% 2) change the value assigned below to the boolean variable
% "PrintVersion" from "false" to "true".

% --------------------- Start of Document Preamble -----------------------

% Specify the document class, default style attributes, and page dimensions
% For hyperlinked PDF, suitable for viewing on a computer, use this:
\documentclass[letterpaper,12pt,titlepage,oneside,]{book}
\usepackage[utf8]{inputenc}

% For PDF, suitable for double-sided printing, change the PrintVersion variable below
% to "true" and use this \documentclass line instead of the one above:
%\documentclass[letterpaper,12pt,titlepage,openright,twoside,final]{book}

% Some LaTeX commands I define for my own nomenclature.
% If you have to, it's better to change nomenclature once here than in a 
% million places throughout your thesis!
\newcommand{\package}[1]{\textbf{#1}} % package names in bold text
\newcommand{\cmmd}[1]{\textbackslash\texttt{#1}} % command name in tt font 
\newcommand{\href}[1]{#1} % does nothing, but defines the command so the
    % print-optimized version will ignore \href tags (redefined by hyperref pkg).
%\newcommand{\texorpdfstring}[2]{#1} % does nothing, but defines the command
% Anything defined here may be redefined by packages added below...

% This package allows if-then-else control structures.
\usepackage{ifthen}
\newboolean{PrintVersion}
\setboolean{PrintVersion}{false} 
% CHANGE THIS VALUE TO "true" as necessary, to improve printed results for hard copies
% by overriding some options of the hyperref package below.
\usepackage{ifdraft}

%\usepackage{nomencl} % For a nomenclature (optional; available from ctan.org)
\usepackage{amsmath,amssymb,amstext} % Lots of math symbols and environments
\usepackage[pdftex]{graphicx} % For including graphics N.B. pdftex graphics driver

\makeatletter
\def\input@path{{figures/}}
\makeatother
\graphicspath{{figures/}}

% Hyperlinks make it very easy to navigate an electronic document.
% In addition, this is where you should specify the thesis title
% and author as they appear in the properties of the PDF document.
% Use the "hyperref" package 
% N.B. HYPERREF MUST BE THE LAST PACKAGE LOADED; ADD ADDITIONAL PKGS ABOVE
\usepackage[pdftex,pagebackref=true]{hyperref} % with basic options
		% N.B. pagebackref=true provides links back from the References to the body text. This can cause trouble for printing.
\hypersetup{
    plainpages=false,       % needed if Roman numbers in frontpages
    % pdfpagelabels=true,     % adds page number as label in Acrobat's page count
    % bookmarks=true,         % show bookmarks bar?
    unicode=true,          % non-Latin characters in Acrobat’s bookmarks
    pdftoolbar=true,        % show Acrobat’s toolbar?
    pdfmenubar=true,        % show Acrobat’s menu?
    pdffitwindow=false,     % window fit to page when opened
    pdfstartview={FitH},    % fits the width of the page to the window
%    pdftitle={uWaterloo\ LaTeX\ Thesis\ Template},    % title: CHANGE THIS TEXT!
%    pdfauthor={Author},    % author: CHANGE THIS TEXT! and uncomment this line
%    pdfsubject={Subject},  % subject: CHANGE THIS TEXT! and uncomment this line
%    pdfkeywords={keyword1} {key2} {key3}, % list of keywords, and uncomment this line if desired
    pdfnewwindow=true,      % links in new window
    colorlinks=true,        % false: boxed links; true: colored links
    linkcolor=blue,         % color of internal links
    citecolor=green,        % color of links to bibliography
    filecolor=magenta,      % color of file links
    urlcolor=cyan           % color of external links
}
\ifthenelse{\boolean{PrintVersion}}{   % for improved print quality, change some hyperref options
\hypersetup{	% override some previously defined hyperref options
%    colorlinks,%
    citecolor=black,%
    filecolor=black,%
    linkcolor=black,%
    urlcolor=black}
}{} % end of ifthenelse (no else)

\hypersetup{final}
\input{header}

% Setting up the page margins...
% uWaterloo thesis requirements specify a minimum of 1 inch (72pt) margin at the
% top, bottom, and outside page edges and a 1.125 in. (81pt) gutter
% margin (on binding side). While this is not an issue for electronic
% viewing, a PDF may be printed, and so we have the same page layout for
% both printed and electronic versions, we leave the gutter margin in.
% Set margins to minimum permitted by uWaterloo thesis regulations:
\setlength{\marginparwidth}{0pt} % width of margin notes
% N.B. If margin notes are used, you must adjust \textwidth, \marginparwidth
% and \marginparsep so that the space left between the margin notes and page
% edge is less than 15 mm (0.6 in.)
\setlength{\marginparsep}{0pt} % width of space between body text and margin notes
\setlength{\evensidemargin}{0.125in} % Adds 1/8 in. to binding side of all 
% even-numbered pages when the "twoside" printing option is selected
\setlength{\oddsidemargin}{0.125in} % Adds 1/8 in. to the left of all pages
% when "oneside" printing is selected, and to the left of all odd-numbered
% pages when "twoside" printing is selected
\setlength{\textwidth}{6.375in} % assuming US letter paper (8.5 in. x 11 in.) and 
% side margins as above
\raggedbottom

% The following statement specifies the amount of space between
% paragraphs. Other reasonable specifications are \bigskipamount and \smallskipamount.
\setlength{\parskip}{\medskipamount}

% The following statement controls the line spacing.  The default
% spacing corresponds to good typographic conventions and only slight
% changes (e.g., perhaps "1.2"), if any, should be made.
\renewcommand{\baselinestretch}{1} % this is the default line space setting

% By default, each chapter will start on a recto (right-hand side)
% page.  We also force each section of the front pages to start on 
% a recto page by inserting \cleardoublepage commands.
% In many cases, this will require that the verso page be
% blank and, while it should be counted, a page number should not be
% printed.  The following statements ensure a page number is not
% printed on an otherwise blank verso page.
\let\origdoublepage\cleardoublepage
\newcommand{\clearemptydoublepage}{%
  \clearpage{\pagestyle{empty}\origdoublepage}}
\let\cleardoublepage\clearemptydoublepage

%=====
% \usepackage{hyperref}
% \let\Contentsline\contentsline
% \renewcommand\contentsline[3]{\Contentsline{#1}{#2}{}}
%=====

%=====================================================================
%   L O G I C A L    D O C U M E N T -- the content of your thesis
%=====================================================================
\begin{document}

% For a large document, it is a good idea to divide your thesis
% into several files, each one containing one chapter.
% To illustrate this idea, the "front pages" (i.e., title page,
% declaration, borrowers' page, abstract, acknowledgements,
% dedication, table of contents, list of tables, list of figures,
% nomenclature) are contained within the file "uw-ethesis-frontpgs.tex" which is
% included into the document by the following statement.
%----------------------------------------------------------------------
% FRONT MATERIAL
%----------------------------------------------------------------------
\input{thesis-front} 

%----------------------------------------------------------------------
% MAIN BODY
%----------------------------------------------------------------------
% Because this is a short document, and to reduce the number of files
% needed for this template, the chapters are not separate
% documents as suggested above, but you get the idea. If they were
% separate documents, they would each start with the \chapter command, i.e, 
% do not contain \documentclass or \begin{document} and \end{document} commands.
%======================================================================

% For an explanation of the following line,
% see http://tex.stackexchange.com/a/36874/64973 
\setcounter{mtc}{2}

\input{introduction}
\input{preliminaries}
\input{discrimination}
\input{programs}
\input{mes}
\input{ups}
\input{conclusion}

\appendix

% Add a title page before the appendices and a line in the Table of Contents
\chapter*{APPENDICES}
\addcontentsline{toc}{chapter}{APPENDICES}
%======================================================================
\input{matlab_notebook}

%----------------------------------------------------------------------
% END MATERIAL
%----------------------------------------------------------------------

% B I B L I O G R A P H Y
% -----------------------

% The following statement selects the style to use for references.  It controls the sort order of the entries in the bibliography and also the formatting for the in-text labels.
\bibliographystyle{alphaurl}
% This specifies the location of the file containing the bibliographic information.  
% It assumes you're using BibTeX (if not, why not?).
\cleardoublepage % This is needed if the book class is used, to place the anchor in the correct page,
                 % because the bibliography will start on its own page.
                 % Use \clearpage instead if the document class uses the "oneside" argument
\phantomsection  % With hyperref package, enables hyperlinking from the table of contents to bibliography             
% The following statement causes the title "References" to be used for the bibliography section:
\renewcommand*{\bibname}{References}

% Add the References to the Table of Contents
\addcontentsline{toc}{chapter}{\textbf{References}}

\bibliography{thesis}
% Tip 5: You can create multiple .bib files to organize your references. 
% Just list them all in the \bibliogaphy command, separated by commas (no spaces).

% The following statement causes the specified references to be added to the bibliography
% even if they were not cited in the text. The asterisk is a wildcard that causes all 
% entries in the bibliographic database to be included (optional).
\nocite{*}

\end{document}