1.1 --- a/thesis/Makefile	Fri Mar 21 15:43:15 2014 -0400
     1.2 +++ b/thesis/Makefile	Fri Mar 21 20:56:56 2014 -0400
     1.3 @@ -5,7 +5,7 @@
     1.4  all:
     1.5  	./weave-thesis.sh cortex
     1.6  	rsync -avz --delete /home/r/proj/cortex/thesis "r@aurellem.org:~"
     1.7 -	ssh r@aurellem.org cd "~/thesis; $(INVOKE_LATEX) $(INVOKE_LATEX)"
     1.8 +	ssh r@aurellem.org cd "~/thesis; $(INVOKE_LATEX)"
     1.9  	scp "r@aurellem.org:/home/r/thesis/$(THESIS_NAME).pdf" .
    1.10  
    1.11  

     2.1 --- a/thesis/aux/org/first-chapter.org	Fri Mar 21 15:43:15 2014 -0400
     2.2 +++ b/thesis/aux/org/first-chapter.org	Fri Mar 21 20:56:56 2014 -0400
     2.3 @@ -9,7 +9,6 @@
     2.4  #+OPTIONS: toc:nil, num:nil
     2.5  
     2.6  * Artificial Imagination
     2.7 -
     2.8    Imagine watching a video of someone skateboarding. When you watch
     2.9    the video, you can imagine yourself skateboarding, and your
    2.10    knowledge of the human body and its dynamics guides your
    2.11 @@ -41,6 +40,10 @@
    2.12     not only other humans, but entities ranging from animals to cartoon
    2.13     characters to [[http://www.youtube.com/watch?v=0jz4HcwTQmU][single dots]] on a screen!
    2.14  
    2.15 +# and can infer intention from the actions of not only other humans,
    2.16 +# but also animals, cartoon characters, and even abstract moving dots
    2.17 +# on a screen!
    2.18 +
    2.19     Another kind of imagination is /predictive/ imagination: you
    2.20     construct scenes in your mind that are not entirely related to
    2.21     whatever you are observing, but instead are predictions of the

     3.1 --- a/thesis/cortex.bib	Fri Mar 21 15:43:15 2014 -0400
     3.2 +++ b/thesis/cortex.bib	Fri Mar 21 20:56:56 2014 -0400
     3.3 @@ -8,4 +8,23 @@
     3.4  ADDRESS = {Berlin},
     3.5  YEAR = {1977},
     3.6  MRCLASS = {76.41 (86.41)},
     3.7 +NOTE = {\why{This is a cool paper that really helped me out. It's
     3.8 +                  related to the thesis because they talk about
     3.9 +                  manifolds and other types of pure, unrefined
    3.10 +                  bullshit.}}
    3.11  }
    3.12 +@incollection {Tappert78,
    3.13 +AUTHOR = {Tappert, Fred D.},
    3.14 +TITLE = {The parabolic approximation method},
    3.15 +BOOKTITLE = {Wave propagation and underwater acoustics ({W}orkshop,
    3.16 +              {M}ystic, {C}onn., 1974)},
    3.17 +PAGES = {224--287. Lecture Notes in Phys., Vol. 70},
    3.18 +PUBLISHER = {Springer},
    3.19 +ADDRESS = {Berlin},
    3.20 +YEAR = {1977},
    3.21 +MRCLASS = {76.41 (86.41)},
    3.22 +NOTE = {\why{This is a cool paper that really helped me out. It's
    3.23 +                  related to the thesis because they talk about
    3.24 +                  manifolds and other types of pure, unrefined
    3.25 +                  bullshit.}}
    3.26 +}

     4.1 --- a/thesis/cortex.org	Fri Mar 21 15:43:15 2014 -0400
     4.2 +++ b/thesis/cortex.org	Fri Mar 21 20:56:56 2014 -0400
     4.3 @@ -43,16 +43,10 @@
     4.4     [[./images/cat-drinking.jpg]]
     4.5  
     4.6  
     4.7 -This is a basic test for the vision system.  It only tests the
     4.8 -vision-pipeline and does not deal with loading eyes from a blender
     4.9 -file. The code creates two videos of the same rotating cube from
    4.10 -different angles. 
    4.11 -
    4.12 -
    4.13 +#+begin_listing
    4.14 +\caption{This is a basic test for the vision system. It only tests the vision-pipeline and does not deal with loading eyes from a blender file. The code creates two videos of the same rotating cube from different angles.}
    4.15  #+name: test-1
    4.16  #+begin_src clojure
    4.17 -(in-ns 'cortex.test.vision)
    4.18 -
    4.19  (defn test-pipeline
    4.20    "Testing vision:
    4.21     Tests the vision system by creating two views of the same rotating
    4.22 @@ -97,6 +91,10 @@
    4.23          (fn [world tpf]
    4.24            (.rotate candy (* tpf 0.2) 0 0))))))
    4.25  #+end_src
    4.26 +#+end_listing
    4.27  
    4.28 +- This is test1 \cite{Tappert77}.
    4.29  
    4.30 -- This is test1 \cite{Tappert77}.
    4.31 \ No newline at end of file
    4.32 +\cite{Tappert77}
    4.33 +lol
    4.34 +\citet{Tappert77}
    4.35 \ No newline at end of file

     5.1 --- a/thesis/cortex.tex	Fri Mar 21 15:43:15 2014 -0400
     5.2 +++ b/thesis/cortex.tex	Fri Mar 21 20:56:56 2014 -0400
     5.3 @@ -42,15 +42,9 @@
     5.4  \end{figure}
     5.5  
     5.6  
     5.7 -This is a basic test for the vision system.  It only tests the
     5.8 -vision-pipeline and does not deal with loading eyes from a blender
     5.9 -file. The code creates two videos of the same rotating cube from
    5.10 -different angles. 
    5.11 -
    5.12 -
    5.13 +\begin{listing}
    5.14 +\caption{This is a basic test for the vision system. It only tests the vision-pipeline and does not deal with loading eyes from a blender file. The code creates two videos of the same rotating cube from different angles.}
    5.15  \begin{clojurecode}
    5.16 -(in-ns 'cortex.test.vision)
    5.17 -
    5.18  (defn test-pipeline
    5.19    "Testing vision:
    5.20     Tests the vision system by creating two views of the same rotating
    5.21 @@ -95,8 +89,12 @@
    5.22          (fn [world tpf]
    5.23            (.rotate candy (* tpf 0.2) 0 0))))))
    5.24  \end{clojurecode}
    5.25 -
    5.26 +\end{listing}
    5.27  
    5.28  \begin{itemize}
    5.29  \item This is test1 \cite{Tappert77}.
    5.30  \end{itemize}
    5.31 +
    5.32 +\cite{Tappert77}
    5.33 +lol
    5.34 +\citet{Tappert77}

     6.1 --- a/thesis/cover.tex	Fri Mar 21 15:43:15 2014 -0400
     6.2 +++ b/thesis/cover.tex	Fri Mar 21 20:56:56 2014 -0400
     6.3 @@ -46,8 +46,11 @@
     6.4  % layout of your title page with your thesis advisor and/or the MIT 
     6.5  % Libraries before printing your final copy.
     6.6  \title{CORTEX : A Virtual World for Sensate AI}
     6.7 +\author{Robert Louis M\raisebox{\depth}{\small \underline{\underline{c}}}Intyre}
     6.8 +%\author{Robert McIntyre}
     6.9  
    6.10 -\author{Robert McIntyre}
    6.11 +
    6.12 +
    6.13  % If you wish to list your previous degrees on the cover page, use the 
    6.14  % previous degrees command:
    6.15  %       \prevdegrees{A.A., Harvard University (1985)}
    6.16 @@ -124,12 +127,12 @@
    6.17  % \input{abstract}
    6.18  % \end{abstractpage}
    6.19  
    6.20 -\cleardoublepage
    6.21 +%% \cleardoublepage
    6.22  
    6.23 -\section*{Acknowledgments}
    6.24 +%% \section*{Acknowledgments}
    6.25  
    6.26 -This is the acknowledgements section.  You should replace this with your
    6.27 -own acknowledgements.
    6.28 +%% This is the acknowledgements section.  You should replace this with your
    6.29 +%% own acknowledgements.
    6.30  
    6.31  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
    6.32  % -*-latex-*-

     7.1 --- a/thesis/rlm-cortex-meng.tex	Fri Mar 21 15:43:15 2014 -0400
     7.2 +++ b/thesis/rlm-cortex-meng.tex	Fri Mar 21 20:56:56 2014 -0400
     7.3 @@ -25,7 +25,7 @@
     7.4  %% Page Intentionally Left Blank'', use the ``leftblank'' option, as
     7.5  %% above. 
     7.6  
     7.7 -\documentclass[12pt,twoside]{mitthesis}
     7.8 +\documentclass[12pt,twoside,singlespace]{mitthesis}
     7.9  \usepackage[utf8]{inputenc}
    7.10  \usepackage[T1]{fontenc}
    7.11  \usepackage{fixltx2e}
    7.12 @@ -41,19 +41,29 @@
    7.13  \usepackage{wasysym}
    7.14  \usepackage{amssymb}
    7.15  \usepackage{hyperref}
    7.16 +\usepackage{natbib}
    7.17 +\usepackage{libertine}
    7.18 +\usepackage{inconsolata}
    7.19 +
    7.20 +\renewcommand{\thesection}{\arabic{section}}
    7.21  
    7.22  %%%%% better source code display
    7.23  \usepackage{minted}
    7.24  
    7.25 +%% dyl fonts
    7.26 +
    7.27  % \usemintedstyle{friendly}
    7.28  % \usemintedstyle{perldoc}
    7.29  %\definecolor{bg}{rgb}{0.95,0.95,0.95}
    7.30 -\definecolor{bg}{rgb}{0.95,0.95,0.95}
    7.31 +\definecolor{bg}{rgb}{0.625,0,0}
    7.32  \usemintedstyle{default}
    7.33 +\newcommand{\why}[1]{\\ \par{\footnotesize #1}}
    7.34 +%\setmonofont[Scale=0.9,BoldFont={Inconsolata Bold}]{Inconsolata}
    7.35  
    7.36 -
    7.37 -%\newminted{clojure}{fontsize=\scriptsize,bgcolor=bg}
    7.38 -\newminted{clojure}{fontsize=\scriptsize}
    7.39 +%\usepackage[gray]{xcolor}
    7.40 +\newminted{clojure}{fontsize=\footnotesize}
    7.41 +%\newminted{clojure}{fontsize=\footnotesize,bgcolor=bg}
    7.42 +%\newminted{clojure}{fontsize=\scriptsize}
    7.43  
    7.44  %\usepackage{lgrind}
    7.45  \pagestyle{plain}
    7.46 @@ -66,13 +76,20 @@
    7.47  % applicable.
    7.48  % \include{signature}
    7.49  \pagestyle{plain}
    7.50 -\include{contents}
    7.51 +\tableofcontents
    7.52 +%\newpage
    7.53 +%\listoffigures
    7.54 +%\newpage
    7.55 +%\listoftables
    7.56  \include{cortex}
    7.57 +\nocite{*}
    7.58  %\include{chap2}
    7.59  \appendix
    7.60  \begin{singlespace}
    7.61  \bibliography{cortex}
    7.62 -\bibliographystyle{plain}
    7.63 +%\bibliographystyle{agsm}
    7.64 +%\bibliographystyle{apa}
    7.65 +\bibliographystyle{plainnat}
    7.66  \end{singlespace}
    7.67  \end{document}
    7.68