1.1 --- a/thesis/cortex.org	Sun Mar 30 01:07:19 2014 -0400
     1.2 +++ b/thesis/cortex.org	Sun Mar 30 01:22:23 2014 -0400
     1.3 @@ -247,8 +247,7 @@
     1.4     #+caption: full circle. Imagine how you would replicate this functionality
     1.5     #+caption: using low-level pixel features such as HOG filters!
     1.6     #+name: grand-circle-intro
     1.7 -   #+attr_latex: [htpb]
     1.8 -#+begin_listing clojure
     1.9 +   #+begin_listing clojure
    1.10     #+begin_src clojure
    1.11  (defn grand-circle?
    1.12    "Does the worm form a majestic circle (one end touching the other)?"
    1.13 @@ -1378,8 +1377,8 @@
    1.14      #+caption: Program for extending =OpenAL= to support multiple
    1.15      #+caption: listeners via context copying/switching.
    1.16      #+name: sync-openal-sources
    1.17 -    #+begin_listing C
    1.18 -    #+BEGIN_SRC C
    1.19 +    #+begin_listing c
    1.20 +    #+BEGIN_SRC c
    1.21  void syncSources(ALsource *masterSource, ALsource *slaveSource, 
    1.22  		 ALCcontext *masterCtx, ALCcontext *slaveCtx){
    1.23    ALuint master = masterSource->source;
    1.24 @@ -1560,7 +1559,7 @@
    1.25      #+caption: change color in response to the sound.
    1.26      #+name: sound-cubes.
    1.27      #+ATTR_LaTeX: :width 10cm
    1.28 -    [[./images/aurellem-gray.png]]
    1.29 +    [[./images/java-hearing-test.png]]
    1.30  
    1.31      This system of hearing has also been co-opted by the
    1.32      jMonkeyEngine3 community and is used to record audio for demo
    1.33 @@ -2441,7 +2440,7 @@
    1.34          hard control problems without worrying about physics or
    1.35          senses.
    1.36  
    1.37 -* COMMENT Empathy in a simulated worm
    1.38 +* Empathy in a simulated worm
    1.39  
    1.40    Here I develop a computational model of empathy, using =CORTEX= as a
    1.41    base. Empathy in this context is the ability to observe another
    1.42 @@ -2525,8 +2524,7 @@
    1.43     #+caption: independent and ignores vermopomorphic differences such as 
    1.44     #+caption: worm textures and colors.
    1.45     #+name: curled
    1.46 -   #+attr_latex: [htpb]
    1.47 -#+begin_listing clojure
    1.48 +   #+begin_listing clojure
    1.49     #+begin_src clojure
    1.50  (defn curled?
    1.51    "Is the worm curled up?"
    1.52 @@ -2541,9 +2539,7 @@
    1.53     #+caption: Program for summarizing the touch information in a patch 
    1.54     #+caption: of skin.
    1.55     #+name: touch-summary
    1.56 -   #+attr_latex: [htpb]
    1.57 -
    1.58 -#+begin_listing clojure
    1.59 +   #+begin_listing clojure
    1.60     #+begin_src clojure
    1.61  (defn contact
    1.62    "Determine how much contact a particular worm segment has with
    1.63 @@ -2568,7 +2564,6 @@
    1.64     #+caption: floor. Note that this function contains no references to 
    1.65     #+caption: proprioction at all.
    1.66     #+name: resting
    1.67 -   #+attr_latex: [htpb]
    1.68  #+begin_listing clojure
    1.69     #+begin_src clojure
    1.70  (def worm-segment-bottom (rect-region [8 15] [14 22]))
    1.71 @@ -2588,7 +2583,6 @@
    1.72     #+caption: I am able to both use a previous action predicate (=curled?=)
    1.73     #+caption: as well as the direct tactile experience of the head and tail.
    1.74     #+name: grand-circle
    1.75 -   #+attr_latex: [htpb]
    1.76  #+begin_listing clojure
    1.77     #+begin_src clojure
    1.78  (def worm-segment-bottom-tip (rect-region [15 15] [22 22]))
    1.79 @@ -2619,7 +2613,6 @@
    1.80     #+caption: wiggle but can't. Frustrated wiggling is very visually different 
    1.81     #+caption: from actual wiggling, but this definition gives it to us for free.
    1.82     #+name: wiggling
    1.83 -   #+attr_latex: [htpb]
    1.84  #+begin_listing clojure
    1.85     #+begin_src clojure
    1.86  (defn fft [nums]
    1.87 @@ -2660,7 +2653,6 @@
    1.88     #+caption: Use the action predicates defined earlier to report on 
    1.89     #+caption: what the worm is doing while in simulation.
    1.90     #+name: report-worm-activity
    1.91 -   #+attr_latex: [htpb]
    1.92  #+begin_listing clojure
    1.93     #+begin_src clojure
    1.94  (defn debug-experience
    1.95 @@ -2779,7 +2771,6 @@
    1.96     #+caption: Program to convert an experience vector into a 
    1.97     #+caption: proprioceptively binned lookup function.
    1.98     #+name: bin
    1.99 -   #+attr_latex: [htpb]
   1.100  #+begin_listing clojure
   1.101     #+begin_src clojure
   1.102  (defn bin [digits]
   1.103 @@ -2838,7 +2829,6 @@
   1.104     #+caption: and finding the longest (ie. most coherent) interpretation
   1.105     #+caption: of the data.
   1.106     #+name: longest-thread
   1.107 -   #+attr_latex: [htpb]
   1.108  #+begin_listing clojure
   1.109     #+begin_src clojure
   1.110  (defn longest-thread
   1.111 @@ -2881,7 +2871,6 @@
   1.112     #+caption: Fill in blanks in sensory experience by replicating the most 
   1.113     #+caption: recent experience.
   1.114     #+name: infer-nils
   1.115 -   #+attr_latex: [htpb]
   1.116  #+begin_listing clojure
   1.117     #+begin_src clojure
   1.118  (defn infer-nils
   1.119 @@ -2916,7 +2905,6 @@
   1.120     #+caption: a motor control script that causes the worm to execute a series
   1.121     #+caption: of ``exercices'' that include all the action predicates.
   1.122     #+name: generate-phi-space
   1.123 -   #+attr_latex: [htpb]
   1.124  #+begin_listing clojure 
   1.125     #+begin_src clojure
   1.126  (def do-all-the-things 
   1.127 @@ -2944,7 +2932,6 @@
   1.128     #+caption: Use longest thread and a phi-space generated from a short
   1.129     #+caption: exercise routine to interpret actions during free play.
   1.130     #+name: empathy-debug
   1.131 -   #+attr_latex: [htpb]
   1.132  #+begin_listing clojure
   1.133     #+begin_src clojure
   1.134  (defn init []
   1.135 @@ -2993,7 +2980,6 @@
   1.136     #+caption: Determine how closely empathy approximates actual 
   1.137     #+caption: sensory data.
   1.138     #+name: test-empathy-accuracy
   1.139 -   #+attr_latex: [htpb]
   1.140  #+begin_listing clojure
   1.141     #+begin_src clojure
   1.142  (def worm-action-label
   1.143 @@ -3034,7 +3020,6 @@
   1.144  
   1.145     #+caption: Program to generate \Phi-space using manual training.
   1.146     #+name: manual-phi-space
   1.147 -   #+attr_latex: [htpb]
   1.148     #+begin_listing clojure
   1.149     #+begin_src clojure
   1.150  (defn init-interactive []
   1.151 @@ -3221,7 +3206,7 @@
   1.152     completely scrambled. The cross shape is just for convienence. This
   1.153     example justifies the use of pre-defined touch regions in =EMPATH=.
   1.154  
   1.155 -* COMMENT Contributions
   1.156 +* Contributions
   1.157    
   1.158    In this thesis you have seen the =CORTEX= system, a complete
   1.159    environment for creating simulated creatures. You have seen how to
   1.160 @@ -3260,7 +3245,7 @@
   1.161  #+BEGIN_LaTeX
   1.162  \appendix
   1.163  #+END_LaTeX
   1.164 -* COMMENT Appendix: =CORTEX= User Guide
   1.165 +* Appendix: =CORTEX= User Guide
   1.166  
   1.167    Those who write a thesis should endeavor to make their code not only
   1.168    accessable, but actually useable, as a way to pay back the community
   1.169 @@ -3547,7 +3532,6 @@
   1.170          blender. This function is required before other world building
   1.171          functions are called.
   1.172  	
   1.173 -
   1.174  *** Creature Manipulation / Import
   1.175  
   1.176     - =(body! creature)= :: give the creature a physical body.