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optional argument for specifying marker list to export

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David PAGNON 2024-07-22 22:44:31 +02:00 committed by GitHub
parent ac037e05ce
commit 1a8253aa24
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1 changed files with 29 additions and 33 deletions
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62
Pose2Sim/Utilities/trc_from_mot_osim.py
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@ -7,18 +7,14 @@
## Build trc from mot and osim files ##
##################################################
Build a trc file which stores all real and virtual markers
Build a trc file which stores real and virtual markers
calculated from a .mot motion file and a .osim model file.
Beware, it can be quite slow depending on the ccomplexity
of the model and on the number of frames.
Also, make sure that OpenSim is installed (e.g. via conda)
If no marker list is specified, all markers are included.
Usage:
from Pose2Sim.Utilities import trc_from_mot_osim; trc_from_mot_osim.trc_from_mot_osim_func(r'<input_mot_file>', r'<output_osim_file>', r'<output_trc_file>')
from Pose2Sim.Utilities import trc_from_mot_osim; trc_from_mot_osim.trc_from_mot_osim_func(input_mot_file=r'<input_mot_file>', input_osim_file=r'<output_osim_file>', trc_output_file=r'<trc_output_file>', marker_list=['_rknee', 'r_hip'])
python -m trc_from_mot_osim -m input_mot_file -o input_osim_file
python -m trc_from_mot_osim -m input_mot_file -o input_osim_file -t output_trc_file
python -m trc_from_mot_osim -m input_mot_file -o input_osim_file -t trc_output_file -l r_knee r_hip
'''
@ -42,13 +38,15 @@ __status__ = "Development"
## FUNCTIONS
def get_marker_positions(motion_data, model, in_degrees=True):
def get_marker_positions(motion_data, model, in_degrees=True, marker_list=[]):
'''
Get dataframe of marker positions
INPUTS:
- motion_data: .mot file opened with osim.TimeSeriesTable
- model: .osim file opened with osim.Model
- in_degrees: True if the motion data is in degrees, False if in radians
- marker_list: list of marker names to include in the trc file. All if not specified
OUTPUT:
- marker_positions_pd: DataFrame of marker positions
@ -57,6 +55,11 @@ def get_marker_positions(motion_data, model, in_degrees=True):
# Markerset
marker_set = model.getMarkerSet()
marker_set_names = [mk.getName() for mk in list(marker_set)]
if len(marker_list)>0:
marker_set_names = [marker for marker in marker_list if marker in marker_set_names]
absent_markers = [marker for marker in marker_list if marker not in marker_set_names]
if len(absent_markers)>0:
print(f'The following markers were not found in the model: {absent_markers}')
marker_set_names_xyz = np.array([[m+'_x', m+'_y', m+'_z'] for m in marker_set_names]).flatten()
# Data
@ -85,34 +88,29 @@ def get_marker_positions(motion_data, model, in_degrees=True):
marker_positions_pd.insert(0, 'time', times)
marker_positions_pd.insert(0, 'frame', np.arange(len(times)))
return marker_positions_pd
return marker_positions_pd, marker_set_names
def trc_from_mot_osim_func(*args):
def trc_from_mot_osim_func(**args):
'''
Build a trc file which stores all real and virtual markers
Build a trc file which stores real and virtual markers
calculated from a .mot motion file and a .osim model file.
If no marker list is specified, all markers are included.
Usage:
from Pose2Sim.Utilities import trc_from_mot_osim; trc_from_mot_osim.trc_from_mot_osim_func(r'<input_mot_file>', r'<output_osim_file>', r'<trc_output_file>')
from Pose2Sim.Utilities import trc_from_mot_osim; trc_from_mot_osim.trc_from_mot_osim_func(input_mot_file=r'<input_mot_file>', input_osim_file=r'<output_osim_file>', trc_output_file=r'<trc_output_file>', marker_list=['_rknee', 'r_hip'])
python -m trc_from_mot_osim -m input_mot_file -o input_osim_file
python -m trc_from_mot_osim -m input_mot_file -o input_osim_file -t trc_output_file
python -m trc_from_mot_osim -m input_mot_file -o input_osim_file -t trc_output_file -l r_knee r_hip
'''
try:
motion_path = args[0]['input_mot_file'] # invoked with argparse
osim_path = args[0]['input_osim_file']
if args[0]['trc_output_file'] == None:
trc_path = motion_path.replace('.mot', '.trc')
else:
trc_path = args[0]['trc_output_file']
except:
motion_path = args[0] # invoked as a function
osim_path = args[1]
try:
trc_path = args[2]
except:
trc_path = motion_path.replace('.mot', '.trc')
motion_path = args.get('input_mot_file') # invoked with argparse
osim_path = args.get('input_osim_file')
trc_path = args.get('trc_output_file')
if trc_path == None:
trc_path = motion_path.replace('.mot', '.trc')
marker_list = args.get('marker_list')
if marker_list == None:
marker_list = []
# Create dataframe with marker positions
model = osim.Model(osim_path)
@ -129,13 +127,10 @@ def trc_from_mot_osim_func(*args):
else:
in_degrees = False
marker_positions_pd = get_marker_positions(motion_data, model, in_degrees=in_degrees)
marker_positions_pd, marker_set_names = get_marker_positions(motion_data, model, in_degrees=in_degrees, marker_list=marker_list)
# Trc header
times = motion_data.getIndependentColumn()
marker_set = model.getMarkerSet()
marker_set_names = [mk.getName() for mk in list(marker_set)]
fps = str( int(1/ ((times[-1]-times[0]) / (len(times)-1))))
nb_frames = str(len(times))
nb_markers = str(len(marker_set_names))
@ -170,6 +165,7 @@ if __name__ == '__main__':
parser.add_argument('-m', '--input_mot_file', required = True, help='input mot file')
parser.add_argument('-o', '--input_osim_file', required = True, help='input osim file')
parser.add_argument('-t', '--trc_output_file', required=False, help='trc output file')
parser.add_argument('-l', '--marker_list', required=False, nargs='+', default=[], help='list of markers to include in the trc file. All if not specified')
args = vars(parser.parse_args())
trc_from_mot_osim_func(args)
trc_from_mot_osim_func(**args)