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MainOSim.py
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MainOSim.py
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# -*- coding: utf-8 -*-
"""
BFUNC Main OpenSim Processing
Outputs:
Scaled Model
IK - all trials
ID - dynamic trials
@author: Emily Eichenlaub, November 2023
"""
import os
import numpy as np
import pandas as pd
from scipy.spatial.transform import Rotation as R
from scipy.linalg import svd
from scipy.signal import butter, filtfilt
import sys
import opensim as osim
import json
import pyomeca
import matplotlib.pyplot as plt
import OSimProcFunctions
sys.path.append('C:\\Users\\emily\\OneDrive\\Desktop\\Misc\\UNC Research\\OpenSim_Python')
if __name__ == "__main__":
# Setup Directories
CurrPath = os.getcwd()
path = 'C:\\Users\\emily\\OneDrive\\Desktop\\Misc\\UNC Research\\BFUNC\\MGH'
# Modular Settings
settings = {
'Site': 'MGH',
'Scale': 'Yes',
'IK': 'Yes',
'ID': 'Yes'
}
# Set up OpenSim tools
geopath = 'C:/OpenSim 4.4/Geometry'
# Set up tool directories
GenericFilePath = 'C:/Users/emily/OneDrive/Desktop/Misc/UNC Research/OpenSim_Python/OpenSimProcessingFiles'
model = osim.Model(os.path.join(GenericFilePath,'gait2392_frontHingesKnee_BFUNC.osim'))
osim.ModelVisualizer.addDirToGeometrySearchPaths(geopath)
sys.path.append(GenericFilePath)
GenericDir = os.listdir(GenericFilePath)
settings["GenericPath"] = GenericFilePath
settings["GenericDir"] = GenericDir
sys.path.append('C:/Users/emily/OneDrive/Desktop/Misc/UNC Research/OpenSim_Python/Functions')
# Set location of directories
if os.path.exists(path):
subjectPath = path
else:
subjectPath = input('Select Folder Containing Subject Data: ')
json_file_path = os.path.join(subjectPath,'Subjects.json')
if os.path.exists(json_file_path):
with open(json_file_path, 'r') as json_file:
Subjects = json.load(json_file)
# Set up paths
os.chdir('C:/Users/emily/OneDrive/Desktop/Misc/UNC Research/OpenSim_Python')
if settings["Scale"] == 'Yes':
for S in range(0, len(Subjects)):
for t in range(0,len(Subjects[S]['Trials'])):
if 'Static' in Subjects[S]['Trials'][t]['name'] or 'static' in Subjects[S]['Trials'][t]['name'] or 'STATIC' in Subjects[S]['Trials'][t]['name']:
trial_name = Subjects[S]['Trials'][t]['name']
subj_trial_folder = os.path.join(Subjects[S]['Trials'][0]['folder'], trial_name+ '.c3d')
osim_folder = Subjects[S]['Folders.OpenSimFolder']
print('Scaling Subject: ', Subjects[S],' Trial:', trial_name)
OSimProcFunctions.Scale(Subjects,settings, subj_trial_folder, osim_folder, S)
if settings["IK"] == 'Yes':
for S in range(0, len(Subjects)):
for T in range(0,len(Subjects[S]['Trials'])):
subj_trial_folder = Subjects[S]['Folders.OpenSimFolder']
osim_folder = Subjects[S]['Folders.OpenSimFolder']
print('Running IK on Subject: ', S,' Trial:', T)
OSimProcFunctions.IK(settings, subj_trial_folder, osim_folder, Subjects[S]['name'], Subjects[S]['Trials'][T]['name'])
if settings['ID'] == 'Yes':
for S in range(0, len(Subjects)):
for T in range(0,len(Subjects[S]['Trials'])):
if 'Static' in Subjects[S]['Trials'][T]['name'] or 'STATIC' in Subjects[S]['Trials'][T]['name'] or 'static' in Subjects[S]['Trials'][T]['name']:
continue
else:
subj_trial_folder = Subjects[S]['Folders.OpenSimFolder']
osim_folder = Subjects[S]['Folders.OpenSimFolder']
print('Running ID on Subject: ', Subjects[S]['name'],' Trial:', Subjects[S]['Trials'][T]['name'])
OSimProcFunctions.ID(settings, subj_trial_folder, osim_folder, Subjects[S]['name'], Subjects[S]['Trials'][T]['name'],T,Subjects)