Integrate C.Elegans Body Model

configs/celegans_demo.yaml

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+defaults:
+  - stac: stac_celegans
+  - model: celegans
+  - _self_

configs/model/celegans.yaml

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+MJCF_PATH: "models/celegans/celegans.xml"
+
+# Tolerance for the optimizations of the full model, limb, and root. 
+# TODO: Re-implement optimizer loops to use these tolerances
+FTOL: 5.0e-03
+ROOT_FTOL: 1.0e-05
+LIMB_FTOL: 1.0e-06
+
+# Number of alternating pose and offset optimization rounds. 
+N_ITERS: 6
+
+KP_NAMES: 
+  - 'cl1' 
+  - 'cl2' 
+  - 'cl3' 
+  - 'cl4' 
+  - 'cl5' 
+  - 'cl6' 
+  - 'cl7' 
+  - 'cl8' 
+  - 'cl9' 
+  - 'cl10' 
+  - 'cl11' 
+  - 'cl12' 
+  - 'cl13' 
+  - 'cl14' 
+  - 'cl15' 
+  - 'cl16' 
+  - 'cl17' 
+  - 'cl18' 
+  - 'cl19' 
+  - 'cl20' 
+  - 'cl21' 
+  - 'cl22' 
+  - 'cl23' 
+  - 'cl24' 
+  - 'cl25' 
+
+# The model sites used to register the keypoints.
+KEYPOINT_MODEL_PAIRS:
+  cl1: torso1_body
+  cl2: torso2_body
+  cl3: torso3_body
+  cl4: torso4_body
+  cl5: torso5_body
+  cl6: torso6_body
+  cl7: torso7_body
+  cl8: torso8_body
+  cl9: torso9_body
+  cl10: torso10_body
+  cl11: torso11_body
+  cl12: torso12_body
+  cl13: torso13_body
+  cl14: torso14_body
+  cl15: torso15_body
+  cl16: torso16_body
+  cl17: torso17_body
+  cl18: torso18_body
+  cl19: torso19_body
+  cl20: torso20_body
+  cl21: torso21_body
+  cl22: torso22_body
+  cl23: torso23_body
+  cl24: torso24_body
+  cl25: torso25_body
+
+# The initial offsets for each keypoint in meters.
+KEYPOINT_INITIAL_OFFSETS:
+  cl1: 0.0 0.0 0.0
+  cl2: 0.0 0.0 0.0
+  cl3: 0.0 0.0 0.0
+  cl4: 0.0 0.0 0.0
+  cl5: 0.0 0.0 0.0
+  cl6: 0.0 0.0 0.0
+  cl7: 0.0 0.0 0.0
+  cl8: 0.0 0.0 0.0
+  cl9: 0.0 0.0 0.0
+  cl10: 0.0 0.0 0.0
+  cl11: 0.0 0.0 0.0
+  cl12: 0.0 0.0 0.0
+  cl13: 0.0 0.0 0.0
+  cl14: 0.0 0.0 0.0 
+  cl15: 0.0 0.0 0.0
+  cl16: 0.0 0.0 0.0
+  cl17: 0.0 0.0 0.0
+  cl18: 0.0 0.0 0.0
+  cl19: 0.0 0.0 0.0
+  cl20: 0.0 0.0 0.0
+  cl21: 0.0 0.0 0.0
+  cl22: 0.0 0.0 0.0
+  cl23: 0.0 0.0 0.0
+  cl24: 0.0 0.0 0.0
+  cl25: 0.0 0.0 0.0
+
+#ROOT_OPTIMIZATION_KEYPOINT: cl13
+
+TRUNK_OPTIMIZATION_KEYPOINTS: []
+#  - "cl7"
+#  - "cl8"
+#  - "cl9"
+#  - "cl10"
+#  - "cl11"
+#  - "cl12"
+#  - "cl14"
+#  - "cl15"
+#  - "cl16"
+#  - "cl17"
+#  - "cl18"
+
+INDIVIDUAL_PART_OPTIMIZATION:
+  "head": [
+    "torso1_body",
+    "torso2_body",
+    "torso3_body",
+    "torso4_body",
+    "torso5_body",
+  ]
+  "abdomen1": [
+    "torso6_body",
+    "torso7_body",
+    "torso8_body",
+    "torso9_body",
+    "torso10_body",
+  ]
+  "abdomen2": [
+    "torso11_body",
+    "torso12_body",
+    "torso13_body",
+    "torso14_body",
+    "torso15_body",
+  ]
+  "abdomen3": [
+    "torso16_body",
+    "torso17_body",
+    "torso18_body",
+    "torso19_body",
+    "torso20_body",
+  ]
+  "tail": [
+    "torso21_body", 
+    "torso22_body", 
+    "torso23_body", 
+    "torso24_body",
+    "torso25_body",
+    ]
+
+KEYPOINT_COLOR_PAIRS:
+  cl1: 0 .5 1 1
+  cl2: 1 0 .3 1
+  cl3: 0 .5 .3 1
+  cl4: .3 0 .3 1
+  cl5: 0.5 0 .3 1
+  cl6: 0 1 .3 1
+  cl7: 0.3 0 1 1
+  cl8: 0 0.5 .3 1
+  cl9: 1 0.5 .3 1
+  cl10: 0.3 0.3 0.3 1
+  cl11: 0.5 0.5 .5 1
+  cl12: 0 0 0 1
+  cl13: 1 1 1 1
+  cl14: 1.0 0.7 0.5 1
+  cl15: 0.7 0.5 1.0 1
+  cl16: 0.5 1.0 0.7 1
+  cl17: 0.5 0.7 1.0 1
+  cl18: 1.0 0.7 0.5 1
+  cl19: 0.7 1.0 .5 1
+  cl20: 0.3 0.5 .7 1
+  cl21: 0.3 0.7 .5 1
+  cl22: 0.5 0.3 .7 1
+  cl23: 0.5 0.7 0.3 1
+  cl24: 0.7 0.3 .5 1
+  cl25: 0.7 0.5 .3 1
+
+# What is the size of the animal you'd like to register, relative to the model?
+SCALE_FACTOR: 1.0 #0.4532
+
+# Multiplier to put the mocap data into the same scale as the data. Eg, if the
+# mocap data is known to be in millimeters and the model is in meters, this is
+# .001
+MOCAP_SCALE_FACTOR: 1.0 #1e-6
+
+# If you have reason to believe that the initial offsets are correct for particular keypoints, 
+# you can regularize those sites using this with M_REG_COEF. 
+SITES_TO_REGULARIZE: []
+# - HandL
+# - HandR
+# - SpineF
+# - SpineL
+# - SpineM
+
+RENDER_FPS: 50
+
+N_SAMPLE_FRAMES: 100
+
+# If you have reason to believe that the initial offsets are correct for particular keypoints, 
+# you can regularize those sites using _SITES_TO_REGULARIZE. 
+M_REG_COEF: 1

configs/stac/stac_celegans.yaml

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+fit_offsets_path: "celegans_fit_offsets.h5"
+ik_only_path: "celegans_ik_only.h5"
+#data_path: "tests/data/test_rodent_mocap_1000_frames.mat"
+
+n_fit_frames: 500
+skip_fit_offsets: False
+skip_ik_only: True
+infer_qvels: True # Infer qvels from stac output
+n_frames_per_clip: 250 # 1 if mocap is one session
+
+mujoco:
+  solver: "newton"
+  iterations: 1
+  ls_iterations: 4