%! TEX root = main.tex
%\documentclass[chap]{thesis}
\documentclass{thesis}

\input{CrallPramb}
\input{CrallDef}

%\addbibresource{final-bib.bib}
%\defbibheading{secbib}[\bibname]{%
%  \section*{#1}%
%  \markboth{#1}{#1}}

\begin{comment}

https://www.cs.rpi.edu/academics/grad/phd.html
http://gradoffice.rpi.edu/update.do
http://www.rpi.edu/dept/grad/docs/Dissertation%20Checklist.pdf
http://www.rpi.edu/dept/grad/docs/Thesis%20Manual.pdf

http://www.ewp.rpi.edu/hartford/~ernesto/Ancillary-Codes/RPI_Thesis_Templates/Word/manual.pdf

Submit here: http://www.etdadmin.com/cgi-bin/school?siteId=489

    rsync -arvhzP --include='figures*/***' --exclude='*' joncrall@hyrule.cs.rpi.edu:latex/crall-thesis-2017/ ~/latex/crall-thesis-2017
    rsync -arvhzP --include='figures*/***' --exclude='*' joncrall@lev.cs.rpi.edu:latex/crall-thesis-2017/ ~/latex/crall-thesis-2017

    rsync -arvhzP joncrall@hyrule.cs.rpi.edu:latex/crall-thesis-2017/figures5/PZ_Master1/dbstats.tex ~/latex/crall-thesis-2017/figures5/PZ_Master1/dbstats.tex

    rsync -arvhzP --include='figures*/***' --exclude='*' ~/latex/crall-thesis-2017 joncrall@hyrule.cs.rpi.edu:latex/crall-thesis-2017/ 

    rsync -arvhzP ~/latex/crall-thesis-2017/figures2/ joncrall@hyrule.cs.rpi.edu:latex/crall-thesis-2017/figures2
    rsync -arvhzP ~/latex/crall-thesis-2017/figures1/ joncrall@hyrule.cs.rpi.edu:latex/crall-thesis-2017/figures1

    ./texfix.py --fpaths main.tex --outline --asmarkdown --numlines=999 -w --ignoreinputstartswith=def,Crall,header,colordef,figdef
    ./texfix.py --fpaths main.tex --outline --numlines=0 -w --ignoreinputstartswith=def,Crall,header,colordef,figdef
    ./texfix.py --fpaths main.tex --outline --numlines=0 --ignoreinputstartswith=def,Crall,header,colordef,figdef
\end{comment}

\author{Jonathan P. Crall}

\thesistitle{Identifying Individual Animals using Ranking, Verification, and Connectivity}        

\degree{Doctor of Philosophy}        
\department{Computer Science} 
     
\signaturelines{4}     %max number of signature lines is 7        
\thadviser{Dr.\ Charles Stewart}
\memberone{Dr.\ Barbara Cutler}        
\membertwo{Dr.\ Bülent Yener}        
\memberthree{Dr.\ Richard Radke}

\submitdate{June 2017\\(For Graduation August 2017)}        
%\submitdate{June 2016}
%\copyrightyear{2017}   % if omitted, current year is used.        


\begin{document}

\titlepage{}

%\copyrightpage{}         % optional           
\tableofcontents{}        

\listoftables{}          % required if there are tables
\listoffigures{}         % required if there are figures

\input{acknowledgment}
\input{abstract}

\input{def}

\input{figdef1}
\input{figdef2}
\input{figdef3}
\input{figdef4}
\input{figdef5}

\include{chapter1-intro}
\include{chapter2-related-work}
\include{chapter3-matching}
\include{chapter4-pairclf}
\include{chapter5-graphid}
\include{chapter6-conclusion}

%\include{testfile}

%\cleardoublepage
%\phantomsection
%\addcontentsline{toc}{chapter}{BIBLIOGRAPHY}
\specialhead{BIBLIOGRAPHY}

%\bibliographystyle{IEEETran}
\bibliographystyle{ieee}
%\bibliography{,mybibfile}
%\bibliographystyle{IEEEtran}
\bibliography{final-bib}

%\printbibliography


\include{appendix}

\end{document}
% chktex-file 17