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1 #+title: Simulated Muscles
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2 #+author: Robert McIntyre
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3 #+email: rlm@mit.edu
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4 #+description: muscles for a simulated creature
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5 #+keywords: simulation, jMonkeyEngine3, clojure
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6 #+SETUPFILE: ../../aurellem/org/setup.org
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7 #+INCLUDE: ../../aurellem/org/level-0.org
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8
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9
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10 * Muscles
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11
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12 Surprisingly enough, terrestrial creatures only move by using torque
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13 applied about their joints. There's not a single straight line of
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14 force in the human body at all! (A straight line of force would
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15 correspond to some sort of jet or rocket propulsion.)
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16
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17 In humans, muscles are composed of muscle fibers which can contract to
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18 exert force. The muscle fibers which compose a muscle are partitioned
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19 into discrete groups which are each controlled by a single alpha motor
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20 neuron. A single alpha motor neuron might control as little as three
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21 or as many as one thousand muscle fibers. When the alpha motor neuron
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22 is engaged by the spinal cord, it activates all of the muscle fibers
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23 to which it is attached. The spinal cord generally engages the alpha
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24 motor neurons which control few muscle fibers before the motor neurons
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25 which control many muscle fibers. This recruitment strategy allows
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26 for precise movements at low strength. The collection of all motor
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27 neurons that control a muscle is called the motor pool. The brain
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28 essentially says "activate 30% of the motor pool" and the spinal cord
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29 recruits motor neurons until 30% are activated. Since the
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30 distribution of power among motor neurons is unequal and recruitment
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31 goes from weakest to strongest, the first 30% of the motor pool might
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32 be 5% of the strength of the muscle.
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33
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34 My simulated muscles follow a similar design: Each muscle is defined
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35 by a 1-D array of numbers (the "motor pool"). Each entry in the array
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36 represents a motor neuron which controls a number of muscle fibers
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37 equal to the value of the entry. Each muscle has a scalar strength
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38 factor which determines the total force the muscle can exert when all
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39 motor neurons are activated. The effector function for a muscle takes
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40 a number to index into the motor pool, and then "activates" all the
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41 motor neurons whose index is lower or equal to the number. Each
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42 motor-neuron will apply force in proportion to its value in the array.
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43 Lower values cause less force. The lower values can be put at the
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44 "beginning" of the 1-D array to simulate the layout of actual human
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45 muscles, which are capable of more precise movements when exerting
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46 less force. Or, the motor pool can simulate more exotic recruitment
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47 strategies which do not correspond to human muscles.
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48
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49 This 1D array is defined in an image file for ease of
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50 creation/visualization. Here is an example muscle profile image.
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51
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52 #+caption: A muscle profile image that describes the strengths of each motor neuron in a muscle. White is weakest and dark red is strongest. This particular pattern has weaker motor neurons at the beginning, just like human muscle.
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53 [[../images/basic-muscle.png]]
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54
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55 * Blender Meta-data
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56
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57 In blender, each muscle is an empty node whose top level parent is
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58 named "muscles", just like eyes, ears, and joints.
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59
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60 These functions define the expected meta-data for a muscle node.
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61
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62 #+name: muscle-meta-data
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63 #+begin_src clojure
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64 (in-ns 'cortex.movement)
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65
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66 (def
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67 ^{:doc "Return the children of the creature's \"muscles\" node."
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68 :arglists '([creature])}
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69 muscles
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70 (sense-nodes "muscles"))
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71
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72
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73 (defn muscle-profile-image
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74 "Get the muscle-profile image from the node's blender meta-data."
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75 [#^Node muscle]
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76 (if-let [image (meta-data muscle "muscle")]
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77 (load-image image)))
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78
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79 (defn muscle-strength
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80 "Return the strength of this muscle, or 1 if it is not defined."
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81 [#^Node muscle]
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82 (if-let [strength (meta-data muscle "strength")]
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83 strength 1))
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84
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85 (defn motor-pool
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86 "Return a vector where each entry is the strength of the \"motor
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87 neuron\" at that part in the muscle."
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88 [#^Node muscle]
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89 (let [profile (muscle-profile-image muscle)]
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90 (vec
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91 (let [width (.getWidth profile)]
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92 (for [x (range width)]
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93 (- 255
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94 (bit-and
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95 0x0000FF
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96 (.getRGB profile x 0))))))))
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97 #+end_src
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98
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99 Of note here is =motor-pool= which interprets the muscle-profile
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100 image in a way that allows me to use gradients between white and red,
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101 instead of shades of gray as I've been using for all the other
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102 senses. This is purely an aesthetic touch.
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103
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104 * Creating Muscles
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105 #+name: muscle-kernel
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106 #+begin_src clojure
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107 (in-ns 'cortex.movement)
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108
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109 (defn movement-kernel
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110 "Returns a function which when called with a integer value inside a
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111 running simulation will cause movement in the creature according
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112 to the muscle's position and strength profile. Each function
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113 returns the amount of force applied / max force."
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114 [#^Node creature #^Node muscle]
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115 (let [target (closest-node creature muscle)
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116 axis
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117 (.mult (.getWorldRotation muscle) Vector3f/UNIT_Y)
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118 strength (muscle-strength muscle)
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119
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120 pool (motor-pool muscle)
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121 pool-integral (reductions + pool)
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122 forces
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123 (vec (map #(float (* strength (/ % (last pool-integral))))
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124 pool-integral))
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125 control (.getControl target RigidBodyControl)]
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126 ;;(println-repl (.getName target) axis)
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127 (fn [n]
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128 (let [pool-index (max 0 (min n (dec (count pool))))
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129 force (forces pool-index)]
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130 (.applyTorque control (.mult axis force))
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131 (float (/ force strength))))))
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132
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133 (defn movement!
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134 "Endow the creature with the power of movement. Returns a sequence
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135 of functions, each of which accept an integer value and will
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136 activate their corresponding muscle."
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137 [#^Node creature]
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138 (for [muscle (muscles creature)]
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139 (movement-kernel creature muscle)))
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140 #+end_src
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141
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142 =movement-kernel= creates a function that will move the nearest
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143 physical object to the muscle node. The muscle exerts a rotational
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144 force dependent on it's orientation to the object in the blender
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145 file. The function returned by =movement-kernel= is also a sense
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146 function: it returns the percent of the total muscle strength that is
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147 currently being employed. This is analogous to muscle tension in
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148 humans and completes the sense of proprioception begun in the last
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149 post.
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150
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151 * Visualizing Muscle Tension
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152 Muscle exertion is a percent of a total, so the visualization is just a
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153 simple percent bar.
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154
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155 #+name: visualization
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156 #+begin_src clojure
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157 (defn movement-display-kernel
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158 "Display muscle exertion data as a bar filling up with red."
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159 [exertion]
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160 (let [height 20
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161 width 300
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162 image (BufferedImage. width height
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163 BufferedImage/TYPE_INT_RGB)
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164 fill (min (int (* width exertion)) width)]
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165 (dorun
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166 (for [x (range fill)
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167 y (range height)]
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168 (.setRGB image x y 0xFF0000)))
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169 image))
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170
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171 (defn view-movement
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172 "Creates a function which accepts a list of muscle-exertion data and
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173 displays each element of the list to the screen."
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174 []
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175 (view-sense movement-display-kernel))
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176 #+end_src
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177
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178 * Adding Touch to the Worm
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179
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180 To the worm, I add two new nodes which describe a single muscle.
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181
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182 #+attr_html: width=755
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183 #+caption: The node highlighted in orange is the parent node of all muscles in the worm. The arrow highlighted in yellow represents the creature's single muscle, which moves the top segment. The other nodes which are not highlighted are joints, eyes, and ears.
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184 [[../images/worm-with-muscle.png]]
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185
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186 #+name: test-movement
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187 #+begin_src clojure
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188 (in-ns 'cortex.test.movement)
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189
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190 (defn test-worm-movement
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191 "Testing movement:
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192 You should see the worm suspended in mid air and a display on the
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193 right which shows the current relative power being exerted by the
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194 muscle. As you increase muscle strength, the bar should fill with
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195 red, and the worm's upper segment should move.
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196
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197 Keys:
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198 h : increase muscle exertion
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199 n : decrease muscle exertion"
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200 ([] (test-worm-movement false))
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201 ([record?]
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202 (let [creature (doto (worm) (body!))
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203
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204 muscle-exertion (atom 0)
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205 muscles (movement! creature)
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206 muscle-display (view-movement)]
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207 (.setMass
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208 (.getControl (.getChild creature "worm-11") RigidBodyControl)
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209 (float 0))
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210 (world
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211 (nodify [creature (floor)])
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212 (merge standard-debug-controls
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213 {"key-h"
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214 (fn [_ value]
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215 (if value
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216 (swap! muscle-exertion (partial + 20))))
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217 "key-n"
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218 (fn [_ value]
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219 (if value
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220 (swap! muscle-exertion (fn [v] (- v 20)))))})
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221 (fn [world]
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222
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223 (let [timer (RatchetTimer. 60)]
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224 (.setTimer world timer)
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225 (display-dilated-time world timer))
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226 (if record?
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rlm@261
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227 (Capture/captureVideo
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228 world
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229 (File. "/home/r/proj/cortex/render/worm-muscles/main-view")))
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230 (light-up-everything world)
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231 (enable-debug world)
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232 (set-gravity world (Vector3f. 0 0 0))
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233 (.setLocation (.getCamera world)
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234 (Vector3f. -4.912815, 2.004171, 0.15710819))
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235 (.setRotation (.getCamera world)
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236 (Quaternion. 0.13828252, 0.65516764,
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237 -0.12370994, 0.7323449)))
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rlm@261
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238 (fn [world tpf]
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239 (muscle-display
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240 (map #(% @muscle-exertion) muscles)
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241 (if record?
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242 (File. "/home/r/proj/cortex/render/worm-muscles/muscles"))))))))
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rlm@261
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243 #+end_src
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244
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245 #+results: test-movement
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246 : #'cortex.test.movement/test-worm-movement
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247
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248 * Video Demonstration
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249
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250 #+begin_html
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251 <div class="figure">
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252 <center>
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253 <video controls="controls" width="550">
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254 <source src="../video/worm-muscles.ogg" type="video/ogg"
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255 preload="none" poster="../images/aurellem-1280x480.png" />
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256 </video>
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rlm@309
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257 <br> <a href="http://youtu.be/8Rp4jEGMDWU"> YouTube </a>
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rlm@261
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258 </center>
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rlm@261
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259 <p>The worm is now able to move. The bar in the lower right displays
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260 the power output of the muscle . Each jump causes 20 more motor neurons to
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261 be recruited. Notice that the power output increases non-linearly
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262 with motor neuron recruitment, similar to a human muscle.</p>
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rlm@261
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263 </div>
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rlm@261
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264 #+end_html
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265
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266 ** Making the Worm Muscles Video
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267 #+name: magick7
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268 #+begin_src clojure
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rlm@261
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269 (ns cortex.video.magick7
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rlm@261
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270 (:import java.io.File)
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rlm@316
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271 (:use clojure.java.shell))
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272
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273 (defn images [path]
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274 (sort (rest (file-seq (File. path)))))
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275
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276 (def base "/home/r/proj/cortex/render/worm-muscles/")
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277
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rlm@261
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278 (defn pics [file]
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279 (images (str base file)))
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280
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281 (defn combine-images []
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rlm@261
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282 (let [main-view (pics "main-view")
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283 muscles (pics "muscles/0")
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284 targets (map
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285 #(File. (str base "out/" (format "%07d.png" %)))
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286 (range 0 (count main-view)))]
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rlm@261
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287 (dorun
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rlm@261
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288 (pmap
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289 (comp
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290 (fn [[ main-view muscles target]]
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291 (println target)
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rlm@261
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292 (sh "convert"
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293 main-view
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294 muscles "-geometry" "+320+440" "-composite"
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295 target))
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296 (fn [& args] (map #(.getCanonicalPath %) args)))
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297 main-view muscles targets))))
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rlm@261
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298 #+end_src
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299
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300 #+begin_src sh :results silent
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301 cd ~/proj/cortex/render/worm-muscles
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302 ffmpeg -r 60 -i out/%07d.png -b:v 9000k -c:v libtheora worm-muscles.ogg
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rlm@261
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303 #+end_src
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304
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rlm@260
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305 * Headers
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rlm@260
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306 #+name: muscle-header
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rlm@260
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307 #+begin_src clojure
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rlm@260
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308 (ns cortex.movement
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rlm@260
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309 "Give simulated creatures defined in special blender files the power
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310 to move around in a simulated environment."
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rlm@260
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311 {:author "Robert McIntyre"}
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rlm@260
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312 (:use (cortex world util sense body))
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rlm@260
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313 (:import java.awt.image.BufferedImage)
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rlm@260
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314 (:import com.jme3.scene.Node)
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315 (:import com.jme3.math.Vector3f)
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316 (:import com.jme3.bullet.control.RigidBodyControl))
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rlm@260
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317 #+end_src
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318
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rlm@261
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319 #+name: test-header
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rlm@261
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320 #+begin_src clojure
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rlm@261
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321 (ns cortex.test.movement
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322 (:use (cortex world util sense body movement))
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rlm@261
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323 (:use cortex.test.body)
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rlm@261
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324 (:import java.io.File)
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325 (:import java.awt.image.BufferedImage)
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326 (:import com.jme3.scene.Node)
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rlm@283
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327 (:import (com.jme3.math Quaternion Vector3f))
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rlm@341
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328 (:import (com.aurellem.capture Capture RatchetTimer IsoTimer))
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rlm@261
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329 (:import com.jme3.bullet.control.RigidBodyControl))
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rlm@261
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330 #+end_src
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331
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rlm@341
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332 #+results: test-header
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rlm@341
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333 : com.jme3.bullet.control.RigidBodyControl
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334
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rlm@261
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335 * Source Listing
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rlm@261
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336 - [[../src/cortex/movement.clj][cortex.movement]]
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rlm@261
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337 - [[../src/cortex/test/movement.clj][cortex.test.movement]]
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rlm@261
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338 - [[../src/cortex/video/magick7.clj][cortex.video.magick7]]
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rlm@261
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339 #+html: <ul> <li> <a href="../org/movement.org">This org file</a> </li> </ul>
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340 - [[http://hg.bortreb.com ][source-repository]]
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rlm@158
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341
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rlm@158
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342 * COMMENT code generation
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rlm@158
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343 #+begin_src clojure :tangle ../src/cortex/movement.clj
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rlm@261
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344 <<muscle-header>>
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rlm@261
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345 <<muscle-meta-data>>
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rlm@261
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346 <<muscle-kernel>>
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rlm@261
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347 <<visualization>>
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rlm@158
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348 #+end_src
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rlm@261
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349
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rlm@261
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350 #+begin_src clojure :tangle ../src/cortex/test/movement.clj
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rlm@261
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351 <<test-header>>
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rlm@261
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352 <<test-movement>>
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rlm@261
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353 #+end_src
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rlm@261
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354
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rlm@261
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355 #+begin_src clojure :tangle ../src/cortex/video/magick7.clj
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rlm@261
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356 <<magick7>>
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rlm@261
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357 #+end_src
|
