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keenon / AddBiomechanics

A tool to automatically process and share biomechanics data
https://addbiomechanics.org/
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Unable to process SMPL sequence + BSM model using current AddBiomechanics #263

Open yunhanwang1105 opened 5 months ago

yunhanwang1105 commented 5 months ago

Hi. Thank you for building up this platform.

I am following the instructions from SKEL to generate b3d files from SMPL sequence + BSM model using the current AddBiomechanics platform. However, I encountered an error FileNotFoundError: [Errno 2] No such file or directory: '/tmp/tmp53dq25zt/optimized_scale_and_markers.osim'. I will attach the full error message in the end.

To my knowledge, SKEL was said to use the development version of AddBiomechanics. But from what I see, the dev version only supports uploading datasets.

May I kindly ask how can I mitigate this issue with the current AddBiomechanics? Thank you for your support. Best.

Running lowpass filter
ERROR: Unwrapped joint pose is out of bounds at timestep 1185 of 2000. This means that we are trying to lowpass filter a joint angle that has wrapped around (for example, from 2PI back to 0, or from PI to -PI), and in "unwrapping" the joint angle to be continuous with the previous angle has caused it to go past the bound. Error joints are ['pelvis_tilt']
Writing OpenSim results
Writing the OpenSim result files...
Adjusting marker locations on scaled OpenSim file
Scaling OpenSim files: cd /tmp/tmp53dq25zt/ && opensim-cmd run-tool /tmp/tmp53dq25zt/rescaling_setup.xml
[info] Preparing to run ScaleTool.
[info] Processing subject optimized_scale_and_markers...
[info] Step 1: Loading generic model
[info] Updating Model file from 40000 to latest format...
[info] Loaded model FullBodyModel_MuscleActuatedLowerLimb_TorqueActuatedUpperBody from file /tmp/tmp53dq25zt/unscaled_but_with_optimized_markers.osim
[warning] Couldn't find file 'sacrum.vtp'.
[warning] Couldn't find file 'r_femur.vtp'.
[warning] Couldn't find file 'r_fibula.vtp'.
[warning] Couldn't find file 'r_patella.vtp'.
[warning] Couldn't find file 'r_talus.vtp'.
[warning] Couldn't find file 'r_foot.vtp'.
[warning] Couldn't find file 'r_bofoot.vtp'.
[warning] Couldn't find file 'l_femur.vtp'.
[warning] Couldn't find file 'l_fibula.vtp'.
[warning] Couldn't find file 'l_patella.vtp'.
[warning] Couldn't find file 'l_talus.vtp'.
[warning] Couldn't find file 'l_foot.vtp'.
[warning] Couldn't find file 'l_bofoot.vtp'.
[warning] Couldn't find file 'cervical_spine.vtp'.
[warning] Couldn't find file 'lumbar_spine.vtp'.
[warning] Couldn't find file 'thorax.vtp'.
[warning] Couldn't find file 'scapula.vtp'.
[warning] Couldn't find file 'scapula_l.vtp'.
[warning] Couldn't find file 'humerus.vtp'.
[warning] Couldn't find file 'humerus_l.vtp'.
[warning] Couldn't find file 'ulna.vtp'.
[warning] Couldn't find file 'ulna_l.vtp'.
[warning] Couldn't find file 'radius.vtp'.
[warning] Couldn't find file 'radius_l.vtp'.
[warning] Couldn't find file 'lunate.vtp'.
[warning] Couldn't find file 'lunate.vtp'.
[warning] Couldn't find file 'lunate_l.vtp'.
[error] Failed to connect Socket 'parent_frame' of type PhysicalFrame (details: Component 'BLTI' could not find 'tibia_l' of type PhysicalFrame. Make sure a component exists at this path and that it is of the correct type.
    Thrown at Component.h:770 in getComponent().).
    In Object 'BLTI' of type Marker.
    Thrown at Component.cpp:310 in finalizeConnections().
[error] Unable to load the generic model or marker set file.
[error] ScaleTool: No model specified.
[error] ScaleTool: No model specified.
Traceback (most recent call last):
  File "/app/src/../../engine/src/engine.py", line 105, in <module>
    main()
  File "/app/src/../../engine/src/engine.py", line 84, in main
    subject.write_opensim_results(path + output_name,
  File "/engine/src/subject.py", line 1017, in write_opensim_results
    self.scale_osim(
  File "/engine/src/subject.py", line 978, in scale_osim
    shutil.copyfile(tmpdirname + 'optimized_scale_and_markers.osim',
  File "/usr/lib/python3.8/shutil.py", line 264, in copyfile
    with open(src, 'rb') as fsrc, open(dst, 'wb') as fdst:
FileNotFoundError: [Errno 2] No such file or directory: '/tmp/tmp53dq25zt/optimized_scale_and_markers.osim'
exit: 1
davidpagnon commented 4 months ago

I'm interested, too. Maybe related to this? https://github.com/keenon/AddBiomechanics/issues/222