osim model not scaled using Python API (Think it is a path problem)

[EveCharbie]

I get an error message not informative in the Python API (see bellow).
The scaled wholebody_AOT_01.osim model file was created, but I still get an error message and the model was not scaled (it is a copy of the orginal .osim file).
Could someone help me understand?

[info] Processing subject AOT_scaled...
[info] Step 1: Loading generic model
[info] Updating Model file from 40500 to latest format...
[info] Loaded model Whole-body from file /home/charbie/Documents/Programmation/GaitAnalyzer/models/OpenSim_models/wholebody.osim
[info] Step 2: Scaling generic model
[info] Loaded marker file ../models/OpenSim_models/../../data/AOT_01/AOT_01_ManipStim_static.trc (49 markers, 531 frames)
[info] Measurement 'pelvis'
[info] 	pair 0 (RASIS, LASIS): model = 0.256, experimental = 0.255993
[info] 	pair 1 (LPSIS, RPSIS): model = 0.08, experimental = 0.0613892
[info] 	overall scale factor = 0.883668
[info] Measurement 'femur_r'
[info] 	pair 0 (RGT, RLFE): model = 0.395429, experimental = 0.431454
[info] 	pair 1 (RMFE, RLFE): model = 0.105000, experimental = 0.116833
[info] 	pair 2 (RMFE, RGT): model = 0.421769, experimental = 0.471831
[info] 	overall scale factor = 1.10750
[info] Measurement 'tibia_r'
[info] 	pair 0 (RLM, RATT): model = 0.359123, experimental = 0.385987
[info] 	pair 1 (RSPH, RATT): model = 0.33291, experimental = 0.375302
[info] 	pair 2 (RSPH, RLM): model = 0.103663, experimental = 0.0838040
[info] 	overall scale factor = 1.00352
[info] Measurement 'calcn_r'
[info] 	pair 0 (RCAL, RMFH1): model = 0.209521, experimental = 0.204883
[info] 	pair 1 (RMFH5, RCAL): model = 0.168846, experimental = 0.192522
[info] 	overall scale factor = 1.05904
[info] Measurement 'talus_r'
[info] 	pair 0 (RCAL, RSPH): model = 0.104459, experimental = 0.0927381
[info] 	pair 1 (RCAL, RLM): model = 0.0818, experimental = 0.0847098
[info] 	overall scale factor = 0.961683
[info] Measurement 'toes_r'
[info] 	pair 0 (RMFH1, RTT2): model = 0.0745078, experimental = 0.0779936
[info] 	pair 1 (RMFH5, RTT2): model = 0.101941, experimental = 0.0970183
[info] 	overall scale factor = 0.999246
[info] Measurement 'torso'
[info] 	pair 0 (STR, SUP): model = 0.170532, experimental = 0.170508
[info] 	pair 1 (C7, T10): model = 0.222612, experimental = 0.213531
[info] 	pair 2 (T10, STR): model = 0.210238, experimental = 0.222808
[info] 	pair 3 (SUP, C7): model = 0.127236, experimental = 0.145673
[info] 	overall scale factor = 1.04094
[info] Measurement 'head_and_neck'
[info] 	pair 0 (HV, C7): model = 0.253734, experimental = 0.281397
[info] 	pair 1 (LTEMP, RTEMP): model = 0.2, experimental = 0.181464
[info] 	pair 2 (OCC, SEL): model = 0.222072, experimental = 0.235356
[info] 	overall scale factor = 1.02539
[info] Measurement 'humerus_r'
[info] 	pair 0 (RA, RLHE): model = 0.32892, experimental = 0.319013
[info] 	pair 1 (RA, RMHE): model = 0.331216, experimental = 0.34462
[info] 	overall scale factor = 1.00517
[info] Measurement 'ulna_r'
[info] 	pair 0 (RMHE, RUS): model = 0.253226, experimental = 0.285188
[info] 	overall scale factor = 1.12622
[info] Measurement 'radius_r'
[info] 	pair 0 (RLHE, RRS): model = 0.261732, experimental = 0.274362
[info] 	overall scale factor = 1.04826
[info] Measurement 'lunate_r'
[info] 	pair 0 (RUS, RRS): model = 0.0690507, experimental = 0.0779091
[info] 	overall scale factor = 1.12829
[info] Measurement 'hand_r'
[info] 	pair 0 (RRS, RUS): model = 0.0690507, experimental = 0.0779091
[info] 	pair 1 (RHMH5, RHMH2): model = 0.0833136, experimental = 0.0966010
[info] 	pair 2 (RUS, RHMH5): model = 0.0725534, experimental = 0.0934954
[info] 	pair 3 (RRS, RHMH2): model = 0.0915186, experimental = 0.108150
[info] 	overall scale factor = 1.18954
[info] Measurement 'femur_l'
[info] 	pair 0 (LGT, LLFE): model = 0.395429, experimental = 0.393603
[info] 	pair 1 (LLFE, LMFE): model = 0.105000, experimental = 0.120284
[info] 	pair 2 (LMFE, LGT): model = 0.421769, experimental = 0.45211
[info] 	overall scale factor = 1.07096
[info] Measurement 'tibia_l'
[info] 	pair 0 (LLM, LATT): model = 0.360651, experimental = 0.390256
[info] 	pair 1 (LSPH, LATT): model = 0.331555, experimental = 0.365895
[info] 	pair 2 (LSPH, LLM): model = 0.103663, experimental = 0.0870216
[info] 	overall scale factor = 1.00838
[info] Measurement 'talus_l'
[info] 	pair 0 (LCAL, LLM): model = 0.0818, experimental = 0.0818030
[info] 	pair 1 (LCAL, LSPH): model = 0.104459, experimental = 0.101084
[info] 	overall scale factor = 0.983863
[info] Measurement 'calcn_l'
[info] 	pair 0 (LCAL, LMFH1): model = 0.209521, experimental = 0.211055
[info] 	pair 1 (LCAL, LMFH5): model = 0.168846, experimental = 0.184616
[info] 	overall scale factor = 1.05036
[info] Measurement 'toes_l'
[info] 	pair 0 (LMFH1, LTT2): model = 0.0745078, experimental = 0.0826411
[info] 	pair 1 (LMFH5, LTT2): model = 0.101941, experimental = 0.0958655
[info] 	overall scale factor = 1.02478
[info] Measurement 'humerus_l'
[info] 	pair 0 (LA, LLHE): model = 0.32892, experimental = 0.321982
[info] 	pair 1 (LA, LMHE): model = 0.331216, experimental = 0.341333
[info] 	overall scale factor = 1.00473
[info] Measurement 'ulna_l'
[info] 	pair 0 (LMHE, LUS): model = 0.253226, experimental = 0.291053
[info] 	overall scale factor = 1.14938
[info] Measurement 'radius_l'
[info] 	pair 0 (LLHE, LRS): model = 0.254918, experimental = 0.271812
[info] 	overall scale factor = 1.06627
[info] Measurement 'lunate_l'
[info] 	pair 0 (LRS, LUS): model = 0.0692475, experimental = 0.0768925
[info] 	overall scale factor = 1.11040
[info] Measurement 'hand_l'
[info] 	pair 0 (LUS, LRS): model = 0.0692475, experimental = 0.0768925
[info] 	pair 1 (LHMH2, LHMH5): model = 0.0833136, experimental = 0.0956044
[info] 	pair 2 (LUS, LHMH5): model = 0.0757493, experimental = 0.0963641
[info] 	pair 3 (LRS, LHMH2): model = 0.0948001, experimental = 0.107458
[info] 	overall scale factor = 1.1659
[info] Measurement 'finger_r'
[info] 	pair 0 (RHMH2, RFT3): model = 0.0855351, experimental = 0.110241
[info] 	pair 1 (RHMH5, RFT3): model = 0.0959083, experimental = 0.118706
[info] 	overall scale factor = 1.26327
[info] Measurement 'finger_l'
[info] 	pair 0 (LHMH2, LFT3): model = 0.0855351, experimental = 0.100809
[info] 	pair 1 (LHMH5, LFT3): model = 0.0959083, experimental = 0.115544
[info] 	overall scale factor = 1.19165
[info] Wrote model file '../../examples/results/AOT_01/models/wholebody_AOT_01.osim' from model.
[info] Step 3: Placing markers on model
[info] Loaded marker file ../models/OpenSim_models/../../data/AOT_01/AOT_01_ManipStim_static.trc (49 markers, 531 frames)
[info] Averaged frames from time 0.0 to 5.3 in ../models/OpenSim_models/../../data/AOT_01/AOT_01_ManipStim_static.trc (frames 1 to 531)
[info] Deleted 0 unused markers from model AOT_scaled.
[info] Frame at (t = 0.0):	 total squared error = 0.0552466, marker error: RMS = 0.033578, max = 0.0639436 (LGT)
[info] Moved markers in model AOT_scaled to match locations in marker file '../models/OpenSim_models/../../data/AOT_01/AOT_01_ManipStim_static.trc'.
Traceback (most recent call last):
  File "/home/charbie/Documents/Programmation/GaitAnalyzer/examples/example_optimal_estimation.py", line 40, in <module>
    AnalysisPerformer(
  File "/home/charbie/Documents/Programmation/GaitAnalyzer/gait_analyzer/analysis_performer.py", line 59, in __init__
    self.run_analysis()
  File "/home/charbie/Documents/Programmation/GaitAnalyzer/gait_analyzer/analysis_performer.py", line 197, in run_analysis
    results = self.analysis_to_perform(subject_name, subject_mass, static_trial_full_file_path, c3d_file_name, result_folder)
  File "/home/charbie/Documents/Programmation/GaitAnalyzer/examples/example_optimal_estimation.py", line 17, in analysis_to_perform
    results.create_model(osim_model_type=OsimModels.WholeBody(), skip_if_existing=False)
  File "/home/charbie/Documents/Programmation/GaitAnalyzer/gait_analyzer/result_manager.py", line 65, in create_model
    self.model_creator = ModelCreator(subject_name=self.subject_name,
  File "/home/charbie/Documents/Programmation/GaitAnalyzer/gait_analyzer/model_creator.py", line 173, in __init__
    self.scale_opensim_model()
  File "/home/charbie/Documents/Programmation/GaitAnalyzer/gait_analyzer/model_creator.py", line 256, in scale_opensim_model
    tool.run()
  File "/home/charbie/miniconda3/envs/dev_gait/lib/python3.10/site-packages/opensim/tools.py", line 2129, in run
    return _tools.ScaleTool_run(self)
RuntimeError: std::exception in 'bool OpenSim::ScaleTool::run() const': SimTK Exception thrown at Xml.cpp:113:
  Error detected by Simbody method Xml::writeToFile(): Failed to write to the Xml file '../models/OpenSim_models/../../examples/results/AOT_01/models/wholebody_AOT_01.osim' with error ' (line=1, col=1)'.
  (Required condition 'saveOK' was not met.)

Ubuntu 22.04
Python 3.10.16
OpenSim 4.5.1

[EveCharbie]

No I am pretty sure it is a path problem since when I put all files (original_model.osim, static.trc, output_scaled_model.osim, output_scaled.xml) in the current directory it works without any problem :)

Moreover, I had to hack my way into accessing the right paths in the xml in the first place:

# Modify the original xml with the participants information
tree = ET.parse(self.osim_model_type.xml_setup_file)
root = tree.getroot()
for elem in root.iter():
    if elem.tag == "model_file":
        elem.text = os.path.abspath(self.osim_model_type.original_osim_model_full_path)
    elif elem.tag == "output_model_file":
        # Due to OpenSim, this path must be relative to xml
        rel_path = os.path.relpath(self.osim_model_full_path, os.path.dirname(self.new_xml_path))
        elem.text = rel_path
    elif elem.tag == "mass":
        elem.text = f"{self.subject_mass}"
    elif elem.tag == "marker_file":
        # Due to OpenSim, this path must be relative to original_osim_model_full_path
        trc_file_relative_path = os.path.relpath(self.trc_file_path,
                                                 os.path.abspath(
                                                     self.osim_model_type.original_osim_model_full_path))[
                                 3:]
        elem.text = trc_file_relative_path
tree.write(self.new_xml_path)

tool = osim.ScaleTool(self.new_xml_path)
tool.run()