1.1 --- a/org/proprioception.org	Mon Feb 13 23:45:38 2012 -0700
     1.2 +++ b/org/proprioception.org	Tue Feb 14 00:37:42 2012 -0700
     1.3 @@ -6,23 +6,46 @@
     1.4  #+SETUPFILE: ../../aurellem/org/setup.org
     1.5  #+INCLUDE: ../../aurellem/org/level-0.org
     1.6  
     1.7 -#+name: proprioception
     1.8 +* Proprioception
     1.9 +
    1.10 +Close your eyes, and touch your nose with your right index finger. How
    1.11 +did you do it? You could not see your hand, and neither your hand nor
    1.12 +your nose could use the sense of touch to guide the path of your hand.
    1.13 +There are no sound cues, and Taste and Smell certainly don't provide
    1.14 +any help. You know where your hand is without your other senses
    1.15 +because of Proprioception.
    1.16 +
    1.17 +Humans can sometimes loose this sense through viral infections or
    1.18 +damage to the spinal cord or brain, and when they do, they loose the
    1.19 +ability to control their own bodies without looking directly at the
    1.20 +parts they want to move. In [[http://en.wikipedia.org/wiki/The_Man_Who_Mistook_His_Wife_for_a_Hat][The Man Who Mistook His Wife for a Hat]],
    1.21 +a woman named Christina looses this sense and has to learn how to move
    1.22 +by carefully watching her arms and legs. She describes proprioception
    1.23 +as the "eyes of the body, the way the body sees itself". 
    1.24 +
    1.25 +Proprioception in humans is mediated by [[http://en.wikipedia.org/wiki/Articular_capsule][joint capsules]], [[http://en.wikipedia.org/wiki/Muscle_spindle][muscle
    1.26 +spindles]], and the [[http://en.wikipedia.org/wiki/Golgi_tendon_organ][Golgi tendon organs]]. These measure the relative
    1.27 +positions of each pody part by monitoring muscle strain and length.
    1.28 +
    1.29 +It's clear that this is a vital sense for fulid, graceful
    1.30 +movement. It's also particurally easy to implement in jMonkeyEngine.
    1.31 +
    1.32 +My simulated proprioception calculates the relative angles of each
    1.33 +joint from the rest position defined in the blender file. This
    1.34 +simulates the muscle-spindles and joint capsules.  I will deal with
    1.35 +Golgi tendon organs, which calculate muscle strain, in the [[./movement.org][next post]].
    1.36 +
    1.37 +* Helper Functions
    1.38 +
    1.39 +
    1.40 +#+name: helpers
    1.41  #+begin_src clojure
    1.42 -(ns cortex.proprioception
    1.43 -  "Simulate the sense of proprioception (ability to detect the
    1.44 -  relative positions of body parts with repsect to other body parts)
    1.45 -  in jMonkeyEngine3. Reads specially prepared blender files to
    1.46 -  automatically generate proprioceptive senses."
    1.47 -  (:use (cortex world util sense body))
    1.48 -  (:use clojure.contrib.def)
    1.49 -  (:import com.jme3.scene.Node)
    1.50 -  (:import java.awt.image.BufferedImage)
    1.51 -  (:import (com.jme3.math Vector3f Quaternion)))
    1.52 +(in-ns 'cortex.proprioception)
    1.53  
    1.54  (defn right-handed?
    1.55    "true iff the three vectors form a right handed coordinate
    1.56 -  system. The three vectors do not have to be normalized or
    1.57 -  orthogonal."
    1.58 +   system. The three vectors do not have to be normalized or
    1.59 +   orthogonal."
    1.60    [vec1 vec2 vec3]
    1.61    (< 0 (.dot (.cross vec1 vec2) vec3)))
    1.62  
    1.63 @@ -34,8 +57,11 @@
    1.64    (let [angle (.angleBetween vec1 vec2)]
    1.65      (if (right-handed? vec1 vec2 axis)
    1.66        angle (- (* 2 Math/PI) angle))))
    1.67 +#+end_src
    1.68  
    1.69 -(defn proprioception-fn
    1.70 +#+name: proprioception
    1.71 +#+begin_src clojure
    1.72 +(defn proprioception-kernel
    1.73    "Returns a function which returns proprioceptive sensory data when
    1.74    called inside a running simulation."
    1.75    [#^Node parts #^Node joint]
    1.76 @@ -80,18 +106,21 @@
    1.77     that joint."
    1.78    [#^Node creature]
    1.79    ;; extract the body's joints
    1.80 -  (let [senses (map (partial proprioception-fn creature)
    1.81 +  (let [senses (map (partial proprioception-kernel creature)
    1.82                      (joints creature))]
    1.83      (fn []
    1.84        (map #(%) senses))))
    1.85 +#+end_src
    1.86  
    1.87 +#+name: visualize
    1.88 +#+begin_src clojure 
    1.89 +(in-ns 'cortex.proprioception)
    1.90  
    1.91  (defn draw-sprite [image sprite x y color ]
    1.92    (dorun
    1.93     (for [[u v] sprite]
    1.94       (.setRGB image (+ u x) (+ v y) color))))
    1.95  
    1.96 -
    1.97  (defn view-angle
    1.98    "create a debug view of an angle"
    1.99    [color]
   1.100 @@ -143,15 +172,24 @@
   1.101     display each element of the list to the screen as an image."
   1.102    []
   1.103    (view-sense proprioception-display-kernel))
   1.104 -  
   1.105 -  
   1.106 +#+end_src
   1.107  
   1.108 +#+name: proprioception-header
   1.109 +#+begin_src clojure
   1.110 +(ns cortex.proprioception
   1.111 +  "Simulate the sense of proprioception (ability to detect the
   1.112 +  relative positions of body parts with repsect to other body parts)
   1.113 +  in jMonkeyEngine3. Reads specially prepared blender files to
   1.114 +  automatically generate proprioceptive senses."
   1.115 +  (:use (cortex world util sense body))
   1.116 +  (:use clojure.contrib.def)
   1.117 +  (:import com.jme3.scene.Node)
   1.118 +  (:import java.awt.image.BufferedImage)
   1.119 +  (:import (com.jme3.math Vector3f Quaternion)))
   1.120  #+end_src
   1.121  
   1.122  #+name: test-body
   1.123  #+begin_src clojure
   1.124 -
   1.125 -
   1.126  (defn test-proprioception
   1.127    "Testing proprioception:
   1.128     You should see two foating bars, and a printout of pitch, yaw, and
   1.129 @@ -246,5 +284,8 @@
   1.130  
   1.131  * COMMENT generate source
   1.132  #+begin_src clojure :tangle ../src/cortex/proprioception.clj
   1.133 +<<proprioception-header>>
   1.134 +<<helpers>>
   1.135  <<proprioception>>
   1.136 +<<visualize>>
   1.137  #+end_src