"Generate physical skeleton" creates wrong bone positions

[MrMinimal]

Godot version

3.3.4.stable.official

System information

Windows 10

Issue description

I have a detailed asset, which I wanted to contribute to the Asset Store.
It has a weight painted armature/rig, which I wanted to import into Godot.

Using GLTF, the model has a skeleton, in which all bones have their correct position.
When generating the physical skeleton though, the resulting physical bones are all out of place.

Blender 2.93

Godot 3.3.4.stable.official

Steps to reproduce

1. Open the project - the default scene contains the offset bones.

To recreate yourself with this project

1. Open Blender file
2. Export to gltf
3. Open gltf file in Godot
4. Select Skeleton from hierarchy
5. Press Button "Skeleton"
6. Select "Create physical skeleton"
7. Hide "mira" mesh in hirarchy to see the skeleton and the generated bones

To recreate yourself from scratch:

1. Open Blender
2. Add->Armature->Human(Meta-Rig)
3. Add->Mesh->Cube
4. Select Armature, select cube
5. Ctrl+P, select "With automatic weights"
6. Export to GLTF
7. Open in Godot
8. Select Skeleton from hierarchy
9. Press Button "Skeleton"
10. Select "Create physical skeleton"
11. Hide "cube" mesh in hirarchy to see the skeleton and the generated bones

Minimal reproduction project

Project (sorry, bigger than 100 MB):
https://drive.google.com/file/d/1hL__pWpMKldgO745Uzs5g78lT5TlNctn/view?usp=sharing

[MrMinimal]

My guess is, the axis which is used to offset the physical bone from the skeleton bone origin is wrong.
Should be the bone's local Z axis, not its local Y axis.
https://user-images.githubusercontent.com/8739690/136189585-7e22d5a9-d064-4f54-b1eb-27018444c604.mp4

[rcorre]

Here's a more minimal example

example.zip

Here, "Create Physical Skeleton" did not create bones for LowerLeg.L/LowerLeg.R at all (those bones can be selected from the PhysicalBone dropdown though).

[Calinou]

I can confirm this on 3.x 3e7e701:

@rcorre Could you test #53515 locally to see if it resolves this issue?

[rcorre]

BTW, just realized the lower legs didn't generate because the upper legs were not parented to the hip bone. That might be a bug, but normally I wouldn't have more than 1 parent-less bone, so it might not be a big deal. After fixing that:

[rcorre]

With #53515, the generated bones are now positioned correctly, however it still skips the lower/upper arms (even after fixing the parenting in blender):

That seems like an unrelated issue so I'll open a separate ticket.

[tavurth]

This seems to be related to this PR which was merged to master 2 years ago but maybe never got backported:

#36008

[rcorre]

The bones are generated in the correct positions on main for the example I posted, so #36008 may have fixed it.

[tavurth]

The bones are generated in the correct positions on main

Yep a backport of #36008 will fix this issue, if you'd like to take it first feel free!

[akien-mga]

Fixed in 3.5 by #48327.