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marker augmentation works when no neck nor midhip data

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davidpagnon 2024-06-08 17:42:42 +02:00
parent f64a8b3591
commit 34781a855a
1 changed files with 26 additions and 8 deletions
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34
Pose2Sim/markerAugmentation.py
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@ -34,7 +34,7 @@ from Pose2Sim.common import convert_to_c3d
## AUTHORSHIP INFORMATION
__author__ = "Antoine Falisse, adapted by HunMin Kim"
__author__ = "Antoine Falisse, adapted by HunMin Kim and David Pagnon"
__copyright__ = "Copyright 2022, OpenCap"
__credits__ = ["Antoine Falisse", "HunMin Kim"]
__license__ = "Apache-2.0 License"
@ -46,7 +46,7 @@ __status__ = "Development"
## FUNCTIONS
# subject_height must be in meters
def get_midhip_data(trc_file):
def check_midhip_data(trc_file):
try:
# Find MidHip data
midhip_data = trc_file.marker("CHip")
@ -57,8 +57,25 @@ def get_midhip_data(trc_file):
rhip_data = trc_file.marker("RHip")
lhip_data = trc_file.marker("LHip")
midhip_data = (rhip_data + lhip_data) / 2
trc_file.add_marker('CHip', *midhip_data.T)
return midhip_data
return trc_file
def check_neck_data(trc_file):
try:
# Find Neck data
neck_data = trc_file.marker("Neck")
if neck_data is None or len(neck_data) == 0:
raise ValueError("Neck data is empty")
except (KeyError, ValueError):
# If Neck data is not found, calculate it from RShoulder and LShoulder
rshoulder_data = trc_file.marker("RShoulder")
lshoulder_data = trc_file.marker("LShoulder")
neck_data = (rshoulder_data + lshoulder_data) / 2
trc_file.add_marker('Neck', *neck_data.T)
return trc_file
def augmentTRC(config_dict):
@ -123,6 +140,11 @@ def augmentTRC(config_dict):
except:
raise ValueError('Cannot read TRC file. You may need to enable interpolation in Config.toml while triangulating.')
# add neck and midhip data if not in file
trc_file = check_midhip_data(trc_file)
trc_file = check_neck_data(trc_file)
trc_file.write(pathInputTRCFile)
# Verify that all feature markers are present in the TRC file.
feature_markers_joined = set(feature_markers_all[0]+feature_markers_all[1])
trc_markers = set(trc_file.marker_names)
@ -145,14 +167,10 @@ def augmentTRC(config_dict):
# %% Pre-process inputs.
# Step 1: import .trc file with OpenPose marker trajectories.
trc_data = TRC2numpy(pathInputTRCFile, feature_markers)
# Calculate the midHip marker as the average of RHip and LHip
midhip_data = get_midhip_data(trc_file)
trc_data_data = trc_data[:,1:]
# Step 2: Normalize with reference marker position.
referenceMarker_data = midhip_data # instead of trc_file.marker(referenceMarker) # change by HunMin
referenceMarker_data = trc_file.marker("CHip") # instead of trc_file.marker(referenceMarker) # change by HunMin
norm_trc_data_data = np.zeros((trc_data_data.shape[0],
trc_data_data.shape[1]))
for i in range(0,trc_data_data.shape[1],3):