Musculoskeletal dog creation #402

vittorione94 · 2023-06-12T16:29:19Z

As per title

…F root rather than 7DOF; modified joint angles limits

…cted

…anged scale in muscles model

…aults

yuvaltassa

Looking good.

The Euler-angle free joint is a deal breaker though. We have to undo this and fix the underlying issue.

yuvaltassa · 2023-06-14T22:14:41Z

dm_control/locomotion/walkers/assets/dog_v2/add_markers.py

+def add_markers(model):
+  bodies = model.find_all('body')
+
+  TOT_MARKERS = 0


What is TOT? TOTAL? maybe rename for clarity?

yuvaltassa · 2023-06-14T22:16:58Z

dm_control/locomotion/walkers/assets/dog_v2/add_torque_actuators.py

@@ -58,11 +58,19 @@ def add_motors(physics, model, lumbar_joints, cervical_joints, caudal_joints):
  all_spinal_joints = []
  for region in spinal_joints.values():
    all_spinal_joints.extend(region)
-  root_joint = model.find('joint', 'root')
+
+  # root_joint = model.find('joint', 'root')


I'm not happy about the free joint -> euler angle decision. Why did you need this again? This will definitely become a problem for large rotations (e.g. rolling on the floor).

I think we should understand whatever the underlying cause was and fix it, rather than do this.

yuvaltassa · 2023-06-14T22:17:47Z

dm_control/locomotion/walkers/assets/dog_v2/add_wrapping_geoms.py

+    Ca_1.add('site', name='Ca_1_wrapping_forward', pos=[0, 0, -0.05], dclass='wrapping')
+    Ca_1.add('site', name='Ca_1_wrapping_backward', pos=[0, 0, 0.05], dclass='wrapping')
+
+    # L_1 = model.find('body', 'L_1')


Either delete the commented code or add an option to activate it that is off by defaults

yuvaltassa · 2023-06-14T22:18:56Z

dm_control/locomotion/walkers/assets/dog_v2/build_torso.py

@@ -54,7 +54,20 @@ def create_torso(
  sternum = [m for m in bones if 'Sternum' in m]
  torso_bones = thoracic_spine + ribs + sternum  # + ['Xiphoid_cartilage']
  torso = parent.add('body', name='torso')
-  torso.add('freejoint', name='root')
+  # torso.add('freejoint', name='root')


See my other comment.

yuvaltassa · 2023-06-14T22:19:35Z

dm_control/locomotion/walkers/assets/dog_v2/create_skin.py

@@ -23,7 +23,7 @@
 from scipy import spatial


-def create(model, skin_msh):
+def create(model, mesh_file, name_mesh, asset_dir, tex_coords=True, transform=True):
  """Create and add skin in the dog model.

  Args:


Please fix the docstring

yuvaltassa · 2023-06-14T22:24:53Z

dm_control/locomotion/walkers/assets/dog_v2/dog.xml

+      <site name="marker_torso_8" class="marker" rgba="1 0.5 0 0.5" size="0.01 0.01 0.01" pos="0.05 0.09 -0.02"/>
+    </body>
+    <body name="marker_0" mocap="true">
+      <site name="marker_0" class="marker" rgba="0 1 0 0.5" size="0.01 0.01 0.01"/>


rgba="0 1 0 0.5" size="0.01 0.01 0.01"

Please put all repeated values into default classes

yuvaltassa · 2023-06-14T22:25:49Z

dm_control/locomotion/walkers/assets/dog_v2/dog_base.xml

@@ -3,23 +3,24 @@

  <option timestep="0.005" noslip_iterations="4"/>

-  <size njmax="900" nconmax="300" nkey="1"/>
+  <size njmax="900" nconmax="900" nkey="1"/>


Don't use this, use memory

https://mujoco.readthedocs.io/en/latest/modeling.html#memory-allocation

yuvaltassa · 2023-06-14T22:28:01Z

dm_control/locomotion/walkers/assets/dog_v2/muscles.py

+         'm_tranversus_abdominis_R']
+
+to_skip = [
+               # 'm_serratus_dorsalis_caudalis_L1',


bunch of comments and commented-out lines in this file.

either delete or explain why they are here like

# uncomment the lines below for serratus muscles

or whatever.

Also for other comments and commented lines in this file.

yuvaltassa · 2023-06-14T22:31:18Z

dm_control/locomotion/walkers/assets/dog_v2/utils.py

+    return ' '.join(['%8g' % num for num in array])
+
+
+def calculate_transformation(element):


Please add docstrings to this and all other nontrivial functions in this file

yuvaltassa · 2023-06-14T22:32:13Z

dm_control/mjcf/schema.xml

@@ -904,6 +904,7 @@
            <attribute name="inflate" type="float"/>
            <attribute name="material" type="reference"/>
            <attribute name="rgba" type="array" array_type="float" array_size="4"/>
+            <attribute name="group" type="int"/>


Really?! Here?
Please submit this as a separate PR 🙂

Oh yes this must've slipped in my branch to get it work, I'll create a separate PR.

lqh20

Nice work! As far as I can tell the logic looks good but I added a bunch of small style comments. In general more comments and doc strings would be great as well.

lqh20 · 2023-10-13T16:31:15Z

dm_control/locomotion/walkers/assets/dog_v2/utils.py

+
+import numpy as np
+
+from scipy.spatial.transform import Rotation as Rot


Does dm_control.utils.transformations work for this instead?

lqh20 · 2023-10-16T09:57:05Z

dm_control/locomotion/walkers/assets/dog_v2/add_markers.py

+
+"""Add markers to the dog model, used for motion capture tracking."""
+
+markers_per_body = {


This is quite minor but generally file level constant should be in all caps. I also prefer making constants immutable if possible (so in particular, tuples rather than lists).

lqh20 · 2023-10-16T09:57:40Z

dm_control/locomotion/walkers/assets/dog_v2/add_markers.py

+    marker_body = model.worldbody.add('body', name="marker_" + str(i), mocap=True)
+    marker_body.add('site', name="marker_" + str(i), dclass="mocap_marker")
+
+  print("TOT_MARKERS:", TOTAL_MARKERS)


nit: Maybe make this a little more informative.

lqh20 · 2023-10-16T09:59:40Z

dm_control/locomotion/walkers/assets/dog_v2/add_muscles.py

+from os.path import isfile, join
+
+import numpy as np
+from scipy.spatial.transform import Rotation as Rot


Not sure this is essential but consider whether we need the scipy dependency here or whether the dm_control utils offer the same.

lqh20 · 2023-10-16T10:00:08Z

dm_control/locomotion/walkers/assets/dog_v2/add_muscles.py

+
+from utils import array_to_string, slices2paths
+
+muscle_legs = extensors_back + extensors_front + \


nit: prefer constants in all caps.

lqh20 · 2023-10-16T10:32:42Z

dm_control/locomotion/walkers/assets/dog_v2/build_torso.py

@@ -55,6 +55,7 @@ def create_torso(
  torso_bones = thoracic_spine + ribs + sternum  # + ['Xiphoid_cartilage']
  torso = parent.add('body', name='torso')
  torso.add('freejoint', name='root')
+


revert this change.

lqh20 · 2023-10-16T10:33:18Z

dm_control/locomotion/walkers/assets/dog_v2/create_skin.py

      'geom',
-      name='skinmesh',
-      mesh='skin_msh',
+      name=name_mesh,


nit: maybe mesh_name is more intuitive?

lqh20 · 2023-10-16T10:34:17Z

dm_control/locomotion/walkers/assets/dog_v2/create_skin.py

-  distance = np.zeros((skin_vertices.shape[0], physics.model.nbody))
-  for i in range(1, physics.model.nbody):
+  distance = np.ones((skin_vertices.shape[0], physics.model.nbody)) * 1e6
+  for i in range(2, physics.model.nbody):


lqh20 · 2023-10-16T10:35:28Z

dm_control/locomotion/walkers/assets/dog_v2/muscles.py

@@ -0,0 +1,232 @@
+lateral = ['m_abdominis_Aponeurosis',


nit: constants in all caps for readability.

lqh20 · 2023-10-16T10:35:53Z

dm_control/locomotion/walkers/assets/dog_v2/utils.py

+    return ' '.join(['%8g' % num for num in array])
+
+
+def calculate_transformation(element):


dm_control/locomotion/walkers/assets/__init__.py

dm_control/locomotion/walkers/assets/dog_v2/add_markers.py

dm_control/locomotion/walkers/assets/dog_v2/utils.py

…th the new muscle model; removed muscles that did not converge because of odd geometries

nimrod-gileadi

There are two main things missing from this PR:

Add dog_v2_test where the model is instantiated and stepped. Look at https://github.com/google-deepmind/dm_control/blob/main/dm_control/locomotion/walkers/cmu_humanoid_test.py
The public API of the module needs to be clear. Are users expected to call add_markers.add_markers, etc.? The test will make it a bit clearer for me how to use the module, but also, you should choose the small number of functions that are to be used by the clients, and import them publically into __init__.py

nimrod-gileadi · 2024-03-18T13:16:11Z

dm_control/locomotion/walkers/assets/dog_v2/add_markers.py

+  Args:
+      model: The model to add markers to.
+
+  Returns:


If the function returns None you don't need to document it. Just drop it (and find any other places where such documentation is added).

vittorione94 added 10 commits May 26, 2023 15:52

new muscle creation files

0950d16

modified schema to support skin groups; modified scripts to use a 6DO…

bde75e2

…F root rather than 7DOF; modified joint angles limits

updated scripts: removed unused imports; now everything works as expe…

ef6b333

…cted

adding markers as part of main script; damping root for stability; ch…

95abf96

…anged scale in muscles model

new lengthrange compute

c92bff7

utils

ce0ed6c

nconmax increased; aded skin.obj file

6c2605a

musculoskeltal dog creation script

2a439a4

modified parameters for general tendon model; fixed a typo in the def…

c8b0fc3

…aults

updated mesh and tendons colours

1f592ed

yuvaltassa reviewed Jun 14, 2023

View reviewed changes

vittorione94 and others added 5 commits June 15, 2023 08:07

removed useless comments; updated doc-strings; rolled back to freejoint

2af6f49

removed skin group from schema.xml

a2293b8

Merge branch 'deepmind:main' into musculoskeletal_dog_creation

c41d84d

Merge branch 'deepmind:main' into musculoskeletal_dog_creation

85d2b1e

Merge branch 'google-deepmind:main' into musculoskeletal_dog_creation

863b1e2

lqh20 reviewed Oct 16, 2023

View reviewed changes

vittorione94 and others added 3 commits October 23, 2023 20:29

Merge branch 'google-deepmind:main' into musculoskeletal_dog_creation

56cfba9

Merge branch 'google-deepmind:main' into musculoskeletal_dog_creation

2dc9e57

fixed code review issues

ffa2358

yuvaltassa requested a review from nimrod-gileadi December 18, 2023 15:27

nimrod-gileadi requested changes Dec 19, 2023

View reviewed changes

vittorione94 and others added 4 commits January 26, 2024 11:17

Merge branch 'google-deepmind:main' into musculoskeletal_dog_creation

34bf5db

Merge branch 'google-deepmind:main' into musculoskeletal_dog_creation

2d4846f

fixed all formatting issues; checked that the model still compiles wi…

99025d6

…th the new muscle model; removed muscles that did not converge because of odd geometries

code formatted with 2 spaces

9140a6a

nimrod-gileadi requested changes Mar 18, 2024

View reviewed changes

vittorione94 and others added 3 commits March 21, 2024 00:24

Merge branch 'google-deepmind:main' into musculoskeletal_dog_creation

2c0db7a

fixed adding markers bug with tuples; updateed directories

c36590f

Merge branch 'google-deepmind:main' into musculoskeletal_dog_creation

757251e

vittorione94 and others added 5 commits April 20, 2024 10:47

updated neck joints ranges

b6d930c

Merge branch 'google-deepmind:main' into musculoskeletal_dog_creation

4cb3465

added dog creation and simulations tests

ea1e5d4

changed asset path from absolute to relative

007c06e

Merge branch 'google-deepmind:main' into musculoskeletal_dog_creation

bf855d6

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Musculoskeletal dog creation #402

Musculoskeletal dog creation #402

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		return ' '.join(['%8g' % num for num in array])


		def calculate_transformation(element):


		import numpy as np

		from scipy.spatial.transform import Rotation as Rot


		"""Add markers to the dog model, used for motion capture tracking."""

		markers_per_body = {


		from utils import array_to_string, slices2paths

		muscle_legs = extensors_back + extensors_front + \

Musculoskeletal dog creation #402

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Musculoskeletal dog creation #402

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vittorione94 commented Jun 12, 2023

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