\documentclass[dissertation,appendmultiple,altchapter]{MSUstyle}
%  Created by Seth Humphries 
%  Update and maintained by Prof. Mark Owkes mark.owkes@me.montana.edu
%
%  For latest changes pull from the bitbucket repository
% 
%%    Copyright (c) 2007-2012 Seth D. Humphries
%%    This work is licensed under the Creative Commons
%%    Attribution-Noncommercial-Share Alike 3.0 License. To view a copy
%%    of this license, visit http://creativecommons.org/licenses/by-nc-sa/3.0/;
%%    or, (b) send a letter to Creative Commons, 171 2nd Street, Suite
%%    300, San Francisco, California, 94105, USA. 
%
% The default options are as follows:
%   \documentclass[12pt,letterpaper,oneside,openright,%
%       doublespaced,normalmargins,dissertation,final,numreset,altchapter]{MSUstyle}
%
% default options do not need to be entered. Defaults will generate a document 
% that conforms to the MSU division of graduate education's (DGE)
% guidelines. 
%
% use \documentclass[thesis]{MSUstyle} to adjustment the front matter according to DGE style rules that
% are different for a thesis than for a dissertation.
%
% options 10pt, singlespaced, and draft allow you to require less number of pages for editing
%
% option altchapter provides numbered chapter and section titles
%
% option appendmultiple is required if you have multiple appendices

% ========================= %
%         Packages          %
% ========================= %
% Order of packages matters %
\usepackage[final]{graphicx} %for the \includegraphics command and figures put [final] before ...
%%    {graphix} if you want figures to show up even while in draft mode
%\usepackage{subcaption}    % to be able to have multiple plots in one figure
\usepackage{subfig} %added by TLR, use in place of subcaption
\usepackage{color} % for changing text color in chapters \textcolor{red}{red text read here}. 
\usepackage{varioref}  % for \vref{figure} which shows up like ``figure 4 on page 6'' 
\usepackage{rotating}  % to rotate figures and captions

\usepackage{pdflscape}		%command to rotate a page into landscape mode
\usepackage{setspace}		%\vspace command
\usepackage{mathrsfs}			%a fancy script for fourier and hilbert transform symbols
\usepackage{mathtools}
\usepackage{verbatim}			%add the \comment option

\usepackage[final]{listings} %used for formatting code
\usepackage[pdftex,hidelinks]{hyperref}
%\usepackage{cite} %compresses the citations so \cite{ref1,ref2,ref3,ref4} is printed as [1-4] instead of [1,2,3,4]
\usepackage{natbib} %Added By TLR, use in place of cite
\usepackage{chapterbib}

\usepackage{tikz} % used for creating figures
\usetikzlibrary{calc}
\usetikzlibrary{patterns}
\usetikzlibrary{positioning}
\usetikzlibrary{decorations.markings}
\usetikzlibrary{decorations.pathmorphing}
\usetikzlibrary{arrows}

\usepackage{latexsym}
\usepackage{bm,array}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage{amsmath}
\usepackage{afterpage}
\usepackage{fancyhdr}
\usepackage{lipsum} % Generates random text

%added by TLR:
\usepackage{placeins}
\usepackage{media9}





\lfoot{}\cfoot{}\rfoot{}  %clear footers
\lhead{}\chead{}\rhead{}  %clear headers
\renewcommand{\headrulewidth}{0pt} %Do not print a line below the header

\usepackage{attachfile} %used to attach files into final pdf, must be included after pdftex package

% Style of code listings (Change as needed)
\lstset{%set Code listings styles
	language=Matlab, % program language for keywords and comments styles
	basicstyle=\small, %font size and style
	identifierstyle=\color{red}, %variable name style
	stringstyle=\ttfamily, %string style
	keywordstyle=\color{blue}\bfseries, %language keyword style
	commentstyle=\color{black}\itshape, %commentstyle
	breaklines=true,  % sets automatic line breaking
	breakatwhitespace=false,   %break line not just at whitespaces
}


% ======================= %
%  User defined commands  %
% ======================= %
\newcommand{\msix}{\textit{MOSES-06} } %MOSES-06 shortcut
\newcommand{\mfifteen}{\textit{MOSES-15} } %MOSES-15 shortcut
\newcommand{\ims}{\mathcal{I}_{m}} %MOSES-06 shortcut
\newcommand{\im}{\mathcal{I}_{-1}} %MOSES-06 shortcut
\newcommand{\iz}{\mathcal{I}_{0}} %MOSES-06 shortcut
\newcommand{\ip}{\mathcal{I}_{+1}} %MOSES-06 shortcut
\newcommand{\hell}{He\,\textsc{ii}\,304\,\AA}


% =============================== %
%  Definitions: Change as needed  %
% =============================== %
\name{Thomas Ludwell Rust} %PUT your FULL name here
\DocTitle{\texorpdfstring{Explosive Events in the Quiet Sun: Extreme Ultraviolet Imaging Spectroscopy Instrumentation and Observations}{Explosive Events in the Quiet Sun: Extreme Ultraviolet Imaging Spectroscopy Instrumentation and Observations}} 
\OWNwebpage{http://solar.physics.montana.edu/rust/} %your personal webpage
\degreetitle{Physics} %may be different than department... ie MS in Electrical Engineering is not Elect. and Com. Engnr degree.
\department{Physics}
\committeechair{Dr. Charles C. Kankelborg}
\departmentchair{Dr. Yves Idzerda}
\graduatedean{Dr. Karlene A. Hoo}
\submitdate{July 2017} 
\copyrightyear{2017} %add one to year if document submitted in Dec.
\draftver{1.0} %versioning for use with draft option

% put searchable words you want internet search engines to find here
\keys{solar, \textit{MOSES}, transition region, EUV, explosive event, spectroscopy, tomography, point spread function, wavelet } 
 
\bibfiles{apjl_ee_bib,MOSESI_PSFS,noise_model,moses_inversion_bib,introduction} %your .bib file(s), files containing bibliographic 

%  Configuration of hyperref package
\hypersetup{%
	baseurl={\OWNwebpage}, %baseurl is url that is in pdf document properties
% 	bookmarks=true, %show bookmarks when opening pdf
	citecolor=black, %citations show up black
	colorlinks=true, %use colored links
	draft=false, % prevents hyperref from draft mode...keeps bookmarks and hyperlinks in draft mode
	filecolor=black, %included file links are black text
	linkcolor=black, %the colored links are black for an ETD but can be otherwise
	pdfauthor={\name}, %pdf document maker is you
	pdfcreator={\name \ by \ PDFLaTex}, %pdf document maker is you
	pdfdisplaydoctitle=true, % make display title the same as the document title instead of the filename
	pdffitwindow=true, %fits one page into the open pdf reader window
	pdfkeywords={\keys}, %searchable keywords
	pdfsubject={\degreetype \ for \name}, %the \  is to give a space
	pdftitle={\DocTitle}, %pdf document title is now ETD title
	plainpages=false, %use hyperlinks in pages, gets rid of a lot of warnings too
	urlcolor=black %website links are black text
}%

% ================================ %
%         Actual Document          %
% ================================ %
\begin{document}
\bibliographystyle{aasjournal} % Use a style you and your adviser like
%\bibliographystyle{abbrv}
%\algorithmspagetrue %uncomment this line if you desire a `list of algorithms' page.

\begin{preliminary} %preliminary take care of all the front matter...before your text
  %\begin{dedication} 
   % \input{dedication} % dedication page (not necessary)
  %\end{dedication}

  %\begin{acknowledgements}
   % \input{acknow} % acknowledgements page
  %\end{acknowledgements}

  % Contents pages 
  \contents

  \begin{abstract}
    \input{abstract} % abstract page
  \end{abstract}
\end{preliminary}
%% end making front matter

\part{\msix Observations of the Quiet Sun}
\input{Introduction4}
\input{MOSES_Science_Introduction_5.tex}
\input{MOSES_Inversions3.tex}
\input{MOSES_data_inversion.tex}
%\input{MOSES_Inversions3_2.tex}


\part{\mfifteen Optical Testing and Integration}
\input{MOSES2_Optical_IT_Introduction.tex}
\input{MOSES2_Optical_Testing2.tex}
\input{MOSES2_Alignment_and_Focus3.tex}
\input{Optical_Modeling.tex}



% End matter
\begin{postliminary}
  \Appendtrue  %comment out or remove if you do not have an appendix
  \references  %do not change this
\end{postliminary}


\appendix % put appendix chapters here.
\input{MOVIES.tex}
\input{The_Wavelet_Transform.tex}
\input{Noise_Modeling.tex}
\input{MOSESI_PSFS.tex}% the option appendmultiple is required in your document class if you have multiple appendices!
% \include{appendixb}

\end{document}
% do not put anything after this

