1.1 --- a/thesis/cortex.org	Sun Mar 30 00:21:50 2014 -0400
     1.2 +++ b/thesis/cortex.org	Sun Mar 30 00:53:14 2014 -0400
     1.3 @@ -41,7 +41,7 @@
     1.4      [[./images/aurellem-gray.png]]
     1.5  
     1.6  
     1.7 -* COMMENT Empathy and Embodiment as problem solving strategies
     1.8 +* Empathy and Embodiment as problem solving strategies
     1.9    
    1.10    By the end of this thesis, you will have seen a novel approach to
    1.11    interpreting video using embodiment and empathy. You will have also
    1.12 @@ -374,7 +374,7 @@
    1.13    possible, so that =CORTEX= may be used for things I have not
    1.14    forseen.
    1.15  
    1.16 -** COMMENT Simulation or Reality?
    1.17 +** Simulation or Reality?
    1.18     
    1.19     The most important archetictural decision of all is the choice to
    1.20     use a computer-simulated environemnt in the first place! The world
    1.21 @@ -437,7 +437,7 @@
    1.22      doing everything in software is far cheaper than building custom
    1.23      real-time hardware. All you need is a laptop and some patience.
    1.24  
    1.25 -** COMMENT Because of Time, simulation is perferable to reality
    1.26 +** Because of Time, simulation is perferable to reality
    1.27  
    1.28     I envision =CORTEX= being used to support rapid prototyping and
    1.29     iteration of ideas. Even if I could put together a well constructed
    1.30 @@ -460,7 +460,7 @@
    1.31     simulations of very simple creatures in =CORTEX= generally run at
    1.32     40x on my machine!
    1.33  
    1.34 -** COMMENT What is a sense?
    1.35 +** What is a sense?
    1.36     
    1.37     If =CORTEX= is to support a wide variety of senses, it would help
    1.38     to have a better understanding of what a ``sense'' actually is!
    1.39 @@ -538,7 +538,7 @@
    1.40     #+ATTR_LaTeX: :width 10cm
    1.41     [[./images/finger-1.png]]
    1.42  
    1.43 -** COMMENT Video game engines provide ready-made physics and shading
    1.44 +** Video game engines provide ready-made physics and shading
    1.45     
    1.46     I did not need to write my own physics simulation code or shader to
    1.47     build =CORTEX=. Doing so would lead to a system that is impossible
    1.48 @@ -562,7 +562,7 @@
    1.49     from the base system, other researchers can turn to this community
    1.50     for help when doing their research.
    1.51     
    1.52 -** COMMENT =CORTEX= is based on jMonkeyEngine3
    1.53 +** =CORTEX= is based on jMonkeyEngine3
    1.54  
    1.55     While preparing to build =CORTEX= I studied several video game
    1.56     engines to see which would best serve as a base. The top contenders
    1.57 @@ -604,7 +604,7 @@
    1.58     write my code in clojure, an implementation of =LISP= that runs on
    1.59     the JVM.
    1.60  
    1.61 -** COMMENT =CORTEX= uses Blender to create creature models
    1.62 +** =CORTEX= uses Blender to create creature models
    1.63  
    1.64     For the simple worm-like creatures I will use later on in this
    1.65     thesis, I could define a simple API in =CORTEX= that would allow
    1.66 @@ -2049,7 +2049,7 @@
    1.67      #+ATTR_LaTeX: :width 15cm
    1.68      [[./images/touch-cube.png]]
    1.69  
    1.70 -** COMMENT Proprioception is the sense that makes everything ``real''
    1.71 +** Proprioception is the sense that makes everything ``real''
    1.72  
    1.73     Close your eyes, and touch your nose with your right index finger.
    1.74     How did you do it? You could not see your hand, and neither your
    1.75 @@ -2183,7 +2183,7 @@
    1.76      #+ATTR_LaTeX: :width 11cm
    1.77      [[./images/proprio.png]]
    1.78  
    1.79 -** COMMENT Muscles are both effectors and sensors
    1.80 +** Muscles are both effectors and sensors
    1.81  
    1.82     Surprisingly enough, terrestrial creatures only move by using
    1.83     torque applied about their joints. There's not a single straight
    1.84 @@ -2326,7 +2326,7 @@
    1.85      in humans and completes the sense of proprioception begun in the
    1.86      last section.
    1.87      
    1.88 -** COMMENT =CORTEX= brings complex creatures to life!
    1.89 +** =CORTEX= brings complex creatures to life!
    1.90     
    1.91     The ultimate test of =CORTEX= is to create a creature with the full
    1.92     gamut of senses and put it though its paces. 

     2.1 --- a/thesis/rlm-cortex-meng.tex	Sun Mar 30 00:21:50 2014 -0400
     2.2 +++ b/thesis/rlm-cortex-meng.tex	Sun Mar 30 00:53:14 2014 -0400
     2.3 @@ -27,18 +27,20 @@
     2.4  
     2.5  \documentclass[12pt,twoside,singlespace,vi]{mitthesis}
     2.6  %\documentclass[12pt,twoside,vi]{mitthesis}
     2.7 +
     2.8 +%\usepackage{floatrow}
     2.9  \usepackage[utf8]{inputenc}
    2.10  \usepackage[T1]{fontenc}
    2.11 -\usepackage{fixltx2e}
    2.12 -\usepackage{graphicx}
    2.13 -\usepackage{longtable}
    2.14 -\usepackage{float}
    2.15 -\usepackage{wrapfig}
    2.16 -\usepackage{rotating}
    2.17 +%\usepackage{fixltx2e}
    2.18 +%\usepackage{graphicx}
    2.19 +%\usepackage{longtable}
    2.20 +%\usepackage{float}
    2.21 +%\usepackage{wrapfig}
    2.22 +%\usepackage{rotating}
    2.23  \usepackage[normalem]{ulem}
    2.24  \usepackage{mathtools}
    2.25 -\usepackage{amsmath}
    2.26 -\usepackage{textcomp}
    2.27 +%\usepackage{amsmath}
    2.28 +%\usepackage{textcomp}
    2.29  \usepackage{marvosym}
    2.30  \usepackage{wasysym}
    2.31  \usepackage{amssymb}
    2.32 @@ -48,10 +50,13 @@
    2.33  \usepackage{rotating}
    2.34  \usepackage{caption}
    2.35  \usepackage{xcolor}
    2.36 -\usepackage{minted}
    2.37 +\usepackage{minted}    
    2.38  \usepackage[backend=bibtex,style=alphabetic]{biblatex}
    2.39 +%\floatsetup[listing]{style=Plaintop}    
    2.40  
    2.41  
    2.42 +\captionsetup{width=.85\textwidth,font=small}
    2.43 +
    2.44  % Configure minted source code listings.
    2.45  \usemintedstyle{default}
    2.46  \newminted{clojure}{fontsize=\footnotesize}
    2.47 @@ -60,7 +65,7 @@
    2.48  \newenvironment{anchoredListing}{\captionsetup{type=listing}}{}
    2.49  
    2.50  \renewenvironment{listing}{\begin{anchoredListing}}{
    2.51 -    \end{anchoredListing}\ignorespacesafterend
    2.52 +   \end{anchoredListing}
    2.53  }
    2.54  
    2.55  % Remove ugly boxes around hyperlinks