thesis7.tex

	\documentclass[letterpaper,12pt,titlepage,oneside,final]{book}
	 
	\usepackage{xcolor}
	\definecolor{darkblue}{rgb}{0.0, 0.0, 0.33}
	\definecolor{darkgreen}{rgb}{0.0, 0.33, 0.0}
	 
	\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{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 
	\usepackage{epstopdf}
	
	% 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,letterpaper=true,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=false,          % 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={Improving Spatial Resolution of and Error Estimation for Radical Probe Mass Spectrometry}
	%    pdftitle={uWaterloo\ LaTeX\ Thesis\ Template},    % title: CHANGE THIS TEXT!
	%    pdfauthor={Author},    % author: CHANGE THIS TEXT! and uncomment this line
		pdfauthor={XiaoFei Zhao},    % author: CHANGE THIS TEXT! and uncomment this line
	%    pdfsubject={Subject},  % subject: CHANGE THIS TEXT! and uncomment this line
		pdfsubject={Thesis for completing the MMATH program at the University of Waterloo},  % 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=darkblue,         % color of internal links
	    citecolor=darkgreen,        % 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)
	
	% 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{textcomp}
	\usepackage{graphicx,subcaption}
	
	%======================================================================
	%   L O G I C A L    D O C U M E N T -- the content of your thesis
	%======================================================================
	\include{tex/01_decls}
	\include{tex/02_gloss}
	
	\begin{document}
	
	%----------------------------------------------------------------------
	% FRONT MATERIAL
	%----------------------------------------------------------------------
	\include{tex/03_front} 
	
	%\printmathdefs{}
	
	%----------------------------------------------------------------------
	% MAIN BODY
	%----------------------------------------------------------------------
	
	\include{tex/10_intro}
	\include{tex/21_basic}
	\include{tex/22_basic}
	\include{tex/32_oxlvl}
	\include{tex/31_error}
	\include{tex/33_rpmse}
	\include{tex/80_concl}
	\include{tex/90_appdx}
	
	%======================================================================
	%\chapter[PDF Plots From Matlab]{Matlab Code for Making a PDF Plot}
	%\label{AppendixA}
	%% Tip 4: Example of how to get a shorter chapter title for the Table of Contents 
	%%======================================================================
	%\section{Using the GUI}
	%Properties of Matab plots can be adjusted from the plot window via a graphical interface. Under the Desktop menu in the Figure window, select the Property Editor. You may also want to check the Plot Browser and Figure Palette for more tools. To adjust properties of the axes, look under the Edit menu and select Axes Properties.
	%
	%To set the figure size and to save as PDF or other file formats, click the Export Setup button in the figure Property Editor.
	
	%\section{From the Command Line} 
	%All figure properties can also be manipulated from the command line. Here's an example: 
	%\begin{verbatim}
	%x=[0:0.1:pi];
	%hold on % Plot multiple traces on one figure
	%plot(x,sin(x))
	%plot(x,cos(x),'--r')
	%plot(x,tan(x),'.-g')
	%title('Some Trig Functions Over 0 to \pi') % Note LaTeX markup!
	%legend('{\it sin}(x)','{\it cos}(x)','{\it tan}(x)')
	%hold off
	%set(gca,'Ylim',[-3 3]) % Adjust Y limits of "current axes"
	%set(gcf,'Units','inches') % Set figure size units of "current figure"
	%set(gcf,'Position',[0,0,6,4]) % Set figure width (6 in.) and height (4 in.)
	%cd n:\thesis\plots % Select where to save
	%print -dpdf plot.pdf % Save as PDF
	%\end{verbatim}
	
	%----------------------------------------------------------------------
	% 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{plainnat}
	% 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{tex/99_cited}
	% 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}