Amputation model #15

YusseffRuiz · 2023-11-22T10:13:01Z

Crearing a DPR for the amputation model designed for myosuite testing.
Transtibial amputation with the OpenSource Leg project prosthesis.
We are having issues described in the Readme file.

Problems with ankle movement de-attaching from the body.
Problems with initial position in walking environment.

Will upload the Walk environment.

Vittorio-Caggiano · 2023-11-26T14:45:24Z

TP_Model/OSL_TFA_L_Ankle_Modified_cvt3.xml

+        <site name="vas_int_r_vas_int_r-P1" pos="0.029 -0.1924 0.031"/>
+        <site name="vas_int_r_vas_int_r-P2" pos="0.0335 -0.2084 0.0285"/>
+        <site name="med_gas_r_med_gas_r-P1" pos="-0.019 -0.3929 -0.0235"/>
+        <body name="tibia_r">


add default position directly in the body e.g.

Vittorio-Caggiano · 2023-11-26T14:46:38Z

TP_Model/OSL_TFA_L_Ankle_Modified_cvt3.xml

+            </body>
+          </body>
+          <body name="rect_fem_l_rect_fem_l-P3" pos="0 0 -0.001401">
+            <joint name="rect_fem_l_rect_fem_l-P3_x" pos="0 0 0" axis="1 0 0" type="slide" range="0.01558 0.0733"/>


movable muscle attachment sites are tricky to troubleshoot. Better to start with fixed points or to convert them to fixed points

Vittorio-Caggiano · 2023-11-26T14:51:49Z

Thanks @YusseffRuiz. It would be great to integrate this model in myo_sim to be used with the MyoSuite ecosystem.

A few suggestions to better prepare the model:

try first the model without the movable muscle attachment sites. I suggest introducing those only if they are explicitly needed because in my experience they are difficult to tune and control.
insert the default position on joints in the body position rather than in the joint (added a comment here).
have only one converted file (Intermediate converted files are not needed) that we can iterate on. This will be the only one included in the repository.
use example structure from other files e.g. to reuse mesh library or environment
it would be nice to have the model without the amputation to compare policies with and without amputation

Initial position has been added. Translation of bones have been removed. Still having issues with ankle prosthesis attachment.

YusseffRuiz · 2023-12-06T16:02:18Z

Hello Vittorio.
I already modified the initial position and we can see the model standing properly.
I added a motor actuator on the prosthesis ankle movement for adduction/abduction and flexion.

I removed unused files from the conversion and also removed the duplicated Geometry, reusing the mesh files already on the git repository. I only left the prosthesis mesh files.
For the prosthesis geometry, i will create a new mesh file already mixing bones and prosthesis.
I removed the knee translation to avoid this issue, that was causing the whole problem.

I still don't get what are the muscle attachment sites, aren't those the ones involved to move the body?
And the pivot point for the yR and zR_footToAnkle movement seems to be in a different place than where is expected.
Attaching the image as example.

Do you have any input on that last matter?

Vittorio-Caggiano · 2023-12-06T16:14:53Z

@YusseffRuiz thanks for making those changes.
I just checked the new file and I think the issue with the ankle prosthesis is that the rotation axis of the device is centered with an offset (blue joint .. you can enable this view by pressing j on simulate) wrt the motor reference frame

Regarding the muscle attachment sites. If you look at the body rect_fem_l_rect_fem_l-P3 it has 3 degrees of freedom i.e. it moves during the optimization (constrained to knee_angle_l). My suggestion is to transform those into fixed attachment (there is an option in the myoconverter to do so by setting kwargs['treat_as_normal_path_point'] = True https://github.com/MyoHub/myoconverter/blob/cadf38059367a51239e6dc28c9fbe8b8fbd5149f/examples/leg6dof9musc.py#L23 ). It would be easier to test the model and troubleshoot without those.

Vittorio-Caggiano · 2023-12-06T16:23:55Z

TP_Model/OSL_TFA_L_Ankle_Modified_cvt3.xml

+            <body name="Foot">
+              <inertial pos="0.06215 -0.35314 0.04496" quat="0.130389 0.68448 0.215635 0.684096" mass="0.76" diaginertia="0.00184373 0.001789 0.001"/> <!--pos="0.06215 -0.35314 0.04496"-->
+              <joint name="zR_FootToAnkleAssembly" armature="0.0060" pos="0 0 0" axis="0 0 1" range="-0.104 0.19" type="hinge"/> <!--axis="-0.105003 -0.174005 0.979131" range="-0.45 0.6"-->
+              <joint name="yR_FootToAnkleAssembly" armature="0.0060" pos="0 0 0" axis="1 0 0" range="-0.09 0.09" type="hinge"/> <!-- axis="0.787215 -0.174005 -0.120902" range="-0.8727 0.5236" -->


pos value here is where the joint reference location is with respect to the parent body

Newely created model with fixed attachments, modified joint location of the prosthetic ankle and only 22 DoF.

…le joint.

vikashplus · 2023-12-18T00:45:40Z

I gave a quick browse to the model

kinematically it looks great.
dynamics needs a lot of iteration to get things in order. For example
- The joints can be over-extended
- The body falls abruptly to the ground. Joint and inertial properties need attention for passive dynamics to behave better
- Collision geometries are missing.
  None of these are a deal breaker, it depends on what is the use case for the model. That will define to what level we want to hammer all the specifics.

@Vittorio-Caggiano -- thoughts?

Added a model with pedestal and another with no pedestal.

vikashplus · 2023-12-20T04:48:54Z

Hi @YusseffRuiz thanks for attending to the joint limits. It looks great.

I also took a look at the collision geometries -

It seems like the collisions are with the skeletal mesh. This might not be ideal. Depending on the use case, this might be the next area of attention. Please let us know what use case you are going after.

YusseffRuiz · 2023-12-20T17:20:52Z

Thanks Vikash, In this case, the use is to be used in the study of biomechanics with RL.
My work is to create a DRL approach to design a new push-recovery controller for a transtibial prosthesis working with the whole body.
Similar to the work created in the walk environment with myosuite locomotion challenge 2023.

vikashplus · 2023-12-29T18:00:34Z

@YusseffRuiz -- we are in the process of releasing the models that were used in the locomotion challenge. These models and environments have most of what you are looking for. I would recommend using the MyoLeg model as a base for your model, and the corresponding envs too.

We are still finalizing the release. You can follow along the progress here - https://github.com/MyoHub/myosuite/pull/128/files to get a headstart :)

Once the staged release goes through, I'll hop on here to help you get this model ready and kicking :)

Changing the type of xml files to match actual myoleg code. Created a new assets and chain file. Modified stl files to meshes folder.

… from the foot.

vikashplus · 2024-01-17T14:28:54Z

@YusseffRuiz --- I gave the recent edits a quick browse. It's generally heading in the right direction. Great progress. Let us know if we can help in anyway.

Added a 1 DoF and 2 DoF prostheses. Modified the README file. Modified main README file to add information about the new TP human model and what is the name to use it.

…Model

updated readme with correct image name

…Model

…rrect movement.

vikashplus · 2024-03-26T20:59:46Z

@YusseffRuiz -- do you have the model with the knee as well? I was looking at the full model and I'm very excited about the prospect it presents. Let me know what you have (even just all the meshes will be very helpful) and I can try to help speed things up as much as I can.

YusseffRuiz · 2024-04-02T20:46:03Z

I'm sorry about the delay in my response, last week I was out and unable to provide, I have the meshes for the whole prosthesis with the knee, I will share it over here and I can create a new model with it as well. It has one DoF in Knee and 1 DoF in Ankle.

vikashplus · 2024-04-02T22:29:48Z

Amazing. Share it here I want to get a sense of what it looks like

… the Knee -- Still in development.

Added a new position for the TP model. Adding meshes of Pylon, knee actuator, knee assembly. Modified Muscles to match prosthesis from OSL project.

YusseffRuiz · 2024-04-11T22:34:36Z

Hello @vikashplus, i'm sorry for taking this long, I'm have added in the repository the Model with the Knee Prosthetic Device. In the meshes folder there are the STL files as well, I had to modify the pylon, since the position was not the ideal one, and also to correct the height as it came from the OSL project website.

Please let me know if you have the chance to take a look.
The only problem is that when enabling geometry, it doesn't seems right.

vikashplus · 2024-04-29T08:30:24Z

I took a pass at the model

It seems like the collision geoms need revision. At the moment, here is what collisions look like and everything here collides as meshes which is slow and not as stable as analytics collisions

It seems like something weird is happening to the kinematic chain for the OLS (right side of the image) as well -

Something weird is also happening with the Inertials -

…rosthesis, Creating a new Transfemoral Passive Model with 69 muscles, removing grac med and lat muscles.

…correctly. Meshes modified to match original Model. Updated Passive Leg prosthesis, based on ITESM Project. References will be updated when paper is published.

…Model

Updated a new class

Adding a new foot body to track movement and correct kinematics.

…correctly.

…Model

…correctly.

…s, and dynamics can be same as myoLeg base. Updating initial positions.

…s, and dynamics can be same as myoLeg base. Updating initial positions. Modified to osl to be in right leg, to match behavior.

YusseffRuiz added 2 commits November 22, 2023 04:08

Adding files for TP model

7a93fc9

Adding files for TP model

31966e2

Vittorio-Caggiano reviewed Nov 26, 2023

View reviewed changes

YusseffRuiz added 2 commits December 6, 2023 09:41

modification of the amputation model.

7edc532

Initial position has been added. Translation of bones have been removed. Still having issues with ankle prosthesis attachment.

removing extra Geometry files

044f2b3

Vittorio-Caggiano reviewed Dec 6, 2023

View reviewed changes

YusseffRuiz added 4 commits December 15, 2023 11:24

Updating new Model, with modifications requested.

ce2315e

Newely created model with fixed attachments, modified joint location of the prosthetic ankle and only 22 DoF.

Updating new Model, with modifications requested.

e32df4a

Newely created model with fixed attachments, modified joint location of the prosthetic ankle and only 22 DoF.

updating README.

693af1b

updating mechanical motors actuators in AnkleAssemly, instead of simp…

44480e7

…le joint.

YusseffRuiz added 2 commits December 19, 2023 15:28

modified limits on joints, range of movement limited.

d01db68

Added a model with pedestal and another with no pedestal.

modified limits on joints, range of movement limited.

6a6416c

Added a model with pedestal and another with no pedestal.

Removing the pedestal to provide better walking surface

93eb37a

YusseffRuiz added 4 commits January 12, 2024 18:06

Merge branch 'MyoHub:main' into AmputationModel

410eab0

removing old files.

8ad2aca

Changing the type of xml files to match actual myoleg code. Created a new assets and chain file. Modified stl files to meshes folder.

modified README

d4de1df

modified motor class so it collides with the floor. removing geometry…

b60877f

… from the foot.

YusseffRuiz added 4 commits February 22, 2024 18:19

Merge branch 'MyoHub:main' into AmputationModel

1fadc03

Modified number of xml files to match MyoSuite regular names.

f708b3f

Added a 1 DoF and 2 DoF prostheses. Modified the README file. Modified main README file to add information about the new TP human model and what is the name to use it.

Merge remote-tracking branch 'origin/AmputationModel' into Amputation…

d616a7b

…Model

Update README.md

a90da13

updated readme with correct image name

YusseffRuiz added 3 commits March 18, 2024 21:06

Modified Initial Positions

e5f1f80

Merge remote-tracking branch 'origin/AmputationModel' into Amputation…

092fd22

…Model

Updated position of gaslat and gasmed muscles on left leg to match co…

2a0aca8

…rrect movement.

YusseffRuiz marked this pull request as ready for review April 2, 2024 20:46

YusseffRuiz added 2 commits April 11, 2024 11:07

Adding a new keyPosition for 71musclesModel. Creating a new Model for…

912b7fd

… the Knee -- Still in development.

Creating a new MyoLeg File for a transfemoral prosthesis.

bd2aaff

Added a new position for the TP model. Adding meshes of Pylon, knee actuator, knee assembly. Modified Muscles to match prosthesis from OSL project.

YusseffRuiz added 18 commits May 7, 2024 02:12

Updating Kinematics for Models, Updating mesh Files for Transtibial p…

5a4aa8d

…rosthesis, Creating a new Transfemoral Passive Model with 69 muscles, removing grac med and lat muscles.

Updating Passive Prosthesis mesh

ebe7dfd

Updating Kinematics and meshes for three models. Kinematics and size …

7581f29

…correctly. Meshes modified to match original Model. Updated Passive Leg prosthesis, based on ITESM Project. References will be updated when paper is published.

Merge remote-tracking branch 'origin/AmputationModel' into Amputation…

9adb14b

…Model

Update myoLeg69_TF_Passive_assets.xml

1d9b0e2

Updated a new class

Update myoLeg69_TF_Passive_chain.xml

15dbb88

Adding a new foot body to track movement and correct kinematics.

Update myoLeg71_TP_1Motor_assets.xml

f33d067

Update myoLeg71_TP_1Motor_chain.xml

4cc2882

Update myoLeg_TF_assets.xml

58d5636

Updating Kinematics and meshes for three models. Kinematics and size …

232f6ba

…correctly.

Merge remote-tracking branch 'origin/AmputationModel' into Amputation…

6b44c8b

…Model

Updating Kinematics and meshes for three models. Kinematics and size …

aac1b9a

…correctly.

Updating distances of the mesh files in chains.

b0dfb3f

Updating Files, modifying number of actuators and joints so kinematic…

202d065

…s, and dynamics can be same as myoLeg base. Updating initial positions.

Updating Files, modifying number of actuators and joints so kinematic…

3db81a4

…s, and dynamics can be same as myoLeg base. Updating initial positions. Modified to osl to be in right leg, to match behavior.

Updating meshes and model to have the oslv2

807f557

Updating meshes and model to have the oslv2

21cd52a

Updating meshes and model to have the oslv2

4f7a76c

Vittorio-Caggiano requested a review from elladyr December 15, 2024 12:18

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Amputation model #15

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