1.1 --- a/thesis/cortex.org	Sun Mar 30 00:53:14 2014 -0400
     1.2 +++ b/thesis/cortex.org	Sun Mar 30 01:07:19 2014 -0400
     1.3 @@ -641,11 +641,11 @@
     1.4     #+ATTR_LaTeX: :width 10cm
     1.5     [[./images/empty-sense-nodes.png]]
     1.6  
     1.7 -** COMMENT Bodies are composed of segments connected by joints
     1.8 +** Bodies are composed of segments connected by joints
     1.9  
    1.10     Blender is a general purpose animation tool, which has been used in
    1.11     the past to create high quality movies such as Sintel
    1.12 -   \cite{sintel}. Though Blender can model and render even complicated
    1.13 +   \cite{blender}. Though Blender can model and render even complicated
    1.14     things like water, it is crucual to keep models that are meant to
    1.15     be simulated as creatures simple. =Bullet=, which =CORTEX= uses
    1.16     though jMonkeyEngine3, is a rigid-body physics system. This offers
    1.17 @@ -957,7 +957,7 @@
    1.18      #+ATTR_LaTeX: :width 15cm
    1.19      [[./images/physical-hand.png]]
    1.20  
    1.21 -** COMMENT Eyes reuse standard video game components
    1.22 +** Eyes reuse standard video game components
    1.23  
    1.24     Vision is one of the most important senses for humans, so I need to
    1.25     build a simulated sense of vision for my AI. I will do this with
    1.26 @@ -991,9 +991,9 @@
    1.27      #+caption: =ViewPorts= are cameras in the world. During each frame, 
    1.28      #+caption: the =RenderManager= records a snapshot of what each view 
    1.29      #+caption: is currently seeing; these snapshots are =FrameBuffer= objects.
    1.30 -    #+name: name
    1.31 +    #+name: rendermanagers
    1.32      #+ATTR_LaTeX: :width 10cm
    1.33 -    [[../images/diagram_rendermanager2.png]]
    1.34 +    [[./images/diagram_rendermanager2.png]]
    1.35  
    1.36      Each =ViewPort= can have any number of attached =SceneProcessor=
    1.37      objects, which are called every time a new frame is rendered. A
    1.38 @@ -1165,6 +1165,7 @@
    1.39      #+caption: information from the simulation.
    1.40      #+name: vision-kernel
    1.41      #+begin_listing clojure
    1.42 +    #+BEGIN_SRC clojure
    1.43  (defn vision-kernel
    1.44    "Returns a list of functions, each of which will return a color
    1.45     channel's worth of visual information when called inside a running
    1.46 @@ -1205,6 +1206,7 @@
    1.47                     (.getRGB @vision-image x y))))))
    1.48              register-eye!)))
    1.49           retinal-map))))
    1.50 +    #+END_SRC
    1.51      #+end_listing
    1.52  
    1.53      Note that since each of the functions generated by =vision-kernel=
    1.54 @@ -1224,6 +1226,7 @@
    1.55      #+caption: eyes.
    1.56      #+name: vision!
    1.57      #+begin_listing clojure
    1.58 +    #+BEGIN_SRC clojure
    1.59  (defn vision!
    1.60    "Returns a list of functions, each of which returns visual sensory
    1.61     data when called inside a running simulation."
    1.62 @@ -1232,6 +1235,7 @@
    1.63     concat 
    1.64     (for [eye (eyes creature)]
    1.65       (vision-kernel creature eye))))
    1.66 +    #+END_SRC
    1.67      #+end_listing
    1.68  
    1.69      #+caption: Simulated vision with a test creature and the 
    1.70 @@ -1254,7 +1258,7 @@
    1.71      community and is now (in modified form) part of a system for
    1.72      capturing in-game video to a file.
    1.73  
    1.74 -** COMMENT Hearing is hard; =CORTEX= does it right
    1.75 +** Hearing is hard; =CORTEX= does it right
    1.76     
    1.77     At the end of this section I will have simulated ears that work the
    1.78     same way as the simulated eyes in the last section. I will be able to
    1.79 @@ -1375,6 +1379,7 @@
    1.80      #+caption: listeners via context copying/switching.
    1.81      #+name: sync-openal-sources
    1.82      #+begin_listing C
    1.83 +    #+BEGIN_SRC C
    1.84  void syncSources(ALsource *masterSource, ALsource *slaveSource, 
    1.85  		 ALCcontext *masterCtx, ALCcontext *slaveCtx){
    1.86    ALuint master = masterSource->source;
    1.87 @@ -1438,6 +1443,7 @@
    1.88    // Restore whatever context was previously active.
    1.89    alcMakeContextCurrent(current);
    1.90  }
    1.91 +    #+END_SRC
    1.92      #+end_listing
    1.93  
    1.94      With this special context-switching device, and some ugly JNI
    1.95 @@ -1449,6 +1455,7 @@
    1.96      #+caption: all sensory data to a continuation function.
    1.97      #+name: add-ear
    1.98      #+begin_listing clojure
    1.99 +    #+BEGIN_SRC clojure
   1.100  (defn add-ear!  
   1.101    "Create a Listener centered on the current position of 'ear 
   1.102     which follows the closest physical node in 'creature and 
   1.103 @@ -1464,8 +1471,8 @@
   1.104      (update-listener-velocity! target lis)
   1.105      (.addListener audio-renderer lis)
   1.106      (.registerSoundProcessor audio-renderer lis sp)))
   1.107 +    #+END_SRC
   1.108      #+end_listing
   1.109 -
   1.110      
   1.111      The =Send= device, unlike most of the other devices in =OpenAL=,
   1.112      does not render sound unless asked. This enables the system to
   1.113 @@ -1478,6 +1485,7 @@
   1.114      #+caption: Program to enable arbitrary hearing in =CORTEX=
   1.115      #+name: hearing
   1.116      #+begin_listing clojure
   1.117 +#+BEGIN_SRC clojure
   1.118  (defn hearing-kernel
   1.119    "Returns a function which returns auditory sensory data when called
   1.120     inside a running simulation."
   1.121 @@ -1504,6 +1512,7 @@
   1.122    [#^Node creature]
   1.123    (for [ear (ears creature)]
   1.124      (hearing-kernel creature ear)))
   1.125 +    #+END_SRC
   1.126      #+end_listing
   1.127  
   1.128      Armed with these functions, =CORTEX= is able to test possibly the
   1.129 @@ -1515,6 +1524,7 @@
   1.130      #+caption: goes over a threshold.
   1.131      #+name: sound-test
   1.132      #+begin_listing java
   1.133 +    #+BEGIN_SRC java
   1.134  /**
   1.135   * Respond to sound!  This is the brain of an AI entity that 
   1.136   * hears its surroundings and reacts to them.
   1.137 @@ -1539,6 +1549,7 @@
   1.138      else {
   1.139  	entity.getMaterial().setColor("Color", ColorRGBA.Gray);
   1.140      }
   1.141 +    #+END_SRC
   1.142      #+end_listing
   1.143  
   1.144      #+caption: First ever simulation of multiple listerners in =CORTEX=.
   1.145 @@ -2358,7 +2369,7 @@
   1.146     #+ATTR_LaTeX: :width 16cm
   1.147     [[./images/integration.png]]
   1.148  
   1.149 -** COMMENT =CORTEX= enables many possiblities for further research
   1.150 +** =CORTEX= enables many possiblities for further research
   1.151  
   1.152     Often times, the hardest part of building a system involving
   1.153     creatures is dealing with physics and graphics. =CORTEX= removes