[BUG] <anatomical_markers> tag in JMP settings files does not seem to work

[bfregly]

Describe the bug
I tried to use JMP to scale just the two femurs and two humeruses to match the static medial and lateral knee markers and static elbow markers better.

I used the <anatomical_markers> tag to tell JMP that when it scaled the two femurs and two humeruses, it should also scale the marker locations in those body segments.

When I loaded the JMP-scaled model into the OpenSim GUI and ran an IK analysis in the GUI using the static trial marker data, the medial and lateral knee markers on both sides were matched better, and the femurs were scaled to be much shorter. HOWEVER, the marker locations on the femurs were not scaled with the femur bodies (which is what setting <anatomical_markers> to true is supposed to do), and the humeruses were not scaled at all (they were supposed to be scaled).

To Reproduce
Steps to reproduce the behavior:

1. Download the attached zip file, unzip it, and go to the unzipped folder.
2. Run JMP with the provided settings file.
3. Open the resulting model file UF_Subject_1_v2_manual_JMPProximal.osim in the GUI.
4. Run IK in the GUI using the provided settings file with "Preview static pose (no marker movement)" selected.
5. Use File->Preview Experimental Data to load the static marker data.
6. Note how poorly the foot markers are matched due to the excessively shortened femurs.

Expected behavior
I expected to see the medial and lateral knee markers still located over the medial and lateral epicondyles of the femurs, and I expected the two humeruses to be scaled at least a little bit. I also expected the foot markers in the JMP-scaled model to match better than they were with the starting model UF_Subject_1_v2_manual.osim.

Screenshots

Desktop (please complete the following information):

• OS: Windows
• OpenSim Version: 4.5
• MATLAB Version:R2023a
• NMSM Pipeline Version: v1.1

Additional context
Add any other context about the problem here.
JMPBug.zip

[cvhammond]

It seems to be an issue with OpenSim 4.5. The issue does not occur on a run-through w/OpenSim 4.4

[cvhammond]

I was also not able to replicate the issue after downloading and using OpenSim 4.5.

Please provide additional information to replicate the bug

[bfregly]

Please see issue #319 that I just submitted, which provides another example where <anatomical_markers> does not scale marker locations with scaling of bodies.