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Add DataFrame outputs to bodykin_from_mot_osim_func #217

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Add DataFrame outputs to bodykin_from_mot_osim_func #217

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10 changes: 9 additions & 1 deletion Pose2Sim/Utilities/bodykin_from_mot_osim.py
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Original file line number Diff line number Diff line change
Expand Up @@ -29,6 +29,7 @@
## INIT
import os
import numpy as np
import pandas as pd
import opensim as osim
import argparse
from scipy import signal
Expand Down Expand Up @@ -218,6 +219,9 @@ def bodykin_from_mot_osim_func(*args):
if '_rot' in col:
loc_rot_frame_all_np[:,n] = np.unwrap(loc_rot_frame_all_np[:,n],period=2*np.pi)

# Create DataFrame
loc_rot_frame_all_df = pd.DataFrame(loc_rot_frame_all_np, columns=bodyHeader.split(', '))

# calculate CoM velocity using the position and time data
if calculate_com_vel:

Expand All @@ -229,6 +233,8 @@ def bodykin_from_mot_osim_func(*args):
# calculate the velocity of the CoM using the numpy gradient function
CoM_vel_array = np.gradient(CoM_pos_array, np.array(times), axis=0)

CoM_df = pd.DataFrame(np.hstack((np.array(times).reshape(-1, 1), CoM_pos_array, CoM_vel_array)), columns=['time', 'com_x', 'com_y', 'com_z', 'com_x_vel', 'com_y_vel', 'com_z_vel'])

if save_com_file:
# save the CoM position, velocity, and time to a file
com_data = np.hstack((np.array(times).reshape(-1, 1), CoM_pos_array, CoM_vel_array))
Expand All @@ -240,7 +246,9 @@ def bodykin_from_mot_osim_func(*args):
print(f'CSV file generated at {os.path.splitext(output_csv_file)[0]+".csv"}.\n')

if calculate_com_vel:
return CoM_pos_array, CoM_vel_array
return CoM_pos_array, CoM_vel_array, loc_rot_frame_all_df, CoM_df
else:
return loc_rot_frame_all_df

if __name__ == '__main__':
main()
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