Implement tibia knee axis modifications. Straight patella tendon, screw-home knee etc.

[melund]

This PR modifies the knee axis of the tibia. It introduces a new configuration switch BM_LEG_TIBIA_KNEE_AXIS with few options.

The default option is a 20 deg internal rotation offset, which we believe better represents the true knee alignment under loaded. The new rotation ensures that the patella tendon remains perpendicular to the knee axis (i.e. straight) during knee flexion. The previous alignment was based on the unloaded knee joint from the CT scan of the cadaver specimen.

The options are:

1. _TIBIA_KNEE_AXIS_STRAIGHT_PATELLA_TENDON_
2. _TIBIA_KNEE_AXIS_UNLOADED_CT_SCAN_
3. _TIBIA_KNEE_AXIS_SCREWHOME_RHYTHM_

The third option _TIBIA_KNEE_AXIS_SCREWHOME_RHYTHM_ adds an internal rotation rhythm to the knee. A rhythm where tibia internally rotates as a function of knee flexion.

Warning

The screw-home knee rhythm is experimental. Neither the standard functional knee joint axis nor the bony-landmark defined knee joint axis seem to be optimal for the screw-home knee rhythm. So, so a new knee axis may need to be provided to get the screw-home knee working optimally.

1 New rotated tibia:
https://github.com/AnyBody/ammr/assets/1038978/c4d21ced-2d03-4c81-b632-a5353ce82939

2 Old CT tibia position:
https://github.com/AnyBody/ammr/assets/1038978/364cc272-d60b-4eaf-8220-9542e2223352

3: Experimental Screw-home knee:
https://github.com/AnyBody/ammr/assets/1038978/2b845c75-9768-4aa6-83bc-69fb64904fb8

[depierie]

Hey Morten,
while you're restructuring all define statements and joint definitions, I think the knee joint could be adapted further to make it more easily understandable for new users.

Right now BM_LEG_TIBIA_KNEE_AXIS == TIBIA_KNEE_AXIS_STRAIGHT_PATELLA_TENDON controls the tibial axis, while TLEM_JOINT_TYPE_KNEE == JOINT_TYPE_DEFAULT/JOINT_TYPE_BONY_LANDMARK controls the knee femoral axis.

I think KNEE_JOINT_KNEE_TYPE is misleading because it still remains a hinge joint, it doesn't control the TYPE, while renaming it to LEG_FEMUR_KNEE_AXIS could help understanding what it actually does.

There are 2femur*2tibia combinations of knee joint axes, plus the screw_home joint, that the users could choose from, plus the extra fine-tuning control enabled by VarusValgusRotation on the femoral side (which could also be described more in details in the documentation).

I think describing this could help new users understanding what these controls can do. It won't help them knowing what the best settings are for their application, but we could use the upcoming validation paper to suggest a standard one that works reasonably well across activities of daily living.

[melund]

@depierie.

Actually, the KNEE_JOINT_KNEE_TYPE controls the knee-axis for both tibia and femur. It is also the switch we use when the knee is replaced completely. Eventually, I image this switch is used to also add other types of knee joints.

But I agree the BM_LEG_TIBIA_KNEE_AXIS is rather confusing to users of the AMMR. I think we may drop it completely. Right now I only added it to give an option to roll back the change to the tibia internal rotation.

But we just merged #879, which split out TLEM 2.1 into it's own folder. This will allow us to go 'all-in' on updating the TLEM model, and then also update the version number to 2.2.

The rotation of the tibia knee-joint implemented by it self, has one downside. The original functional ankle joint axis hasn't really been designed for that. If we only adjusted the tibia knee axis, the feet would point inwards by around 20 deg.

But luckily we have been working on recreating the ankle complex from the original scans. It makes foot, talus and tibia/fibula fit nicely together. I honestly think a mistake may have been made in the TLEMSafe project when the ankle joint complex was created. But I can not really prove it since we don't have the original data that Twente University used to create the functional axis.

Our work to recreate the ankle joint complex had a small downside which had puzzled us. It created a ankle joint were the feet pointed outward by around 20 degrees. That was hard to justify doing that before, but now I see that may be related to the external rotation of the tibia in the cadaver CT scan. The two rotation basically cancel each other out.

You can see the work when you get here next week. I think we are well underway to create a TLEM 2.2 version, and then we don't need the BM_LEG_TIBIA_KNEE_AXIS switch.

[depierie]

I never really saw any issue with the ankle joint probably because I'm only running MoCap driven simulations, so the foot posiiton was always correct (straight) as determined by the markers, but there was probably some adjustments in ankle, subtalar, and hip rotation angle to make everything match. When I load the model however it does show this internal rotation so I can see that for other applications this can be problematic.

Do you still want me to merge this then, or would you rather wait until you work on the ankle and the tlem 2.2 structure?

[melund]

We will wait a bit, with merging this PR until @divyaksh-chander has finished his update of the ankle joint. It is just around the corner. But I may remove the screw-home knee joint implementation when we do this.

[melund]

I will close this for #882