def test_event_marking():
"""Test automarking of events"""
start_nexus()
vicon = nexus.viconnexus()
ev_tol = 4 # tolerance for event marking (frames)
events_dict = dict() # ground truth with forceplate info
events_dict['Right'] = dict()
events_dict['Right']['Foot Strike'] = [384, 505, 616]
events_dict['Right']['Foot Off'] = [465, 570]
events_dict['Left'] = dict()
events_dict['Left']['Foot Strike'] = [311, 441, 562]
events_dict['Left']['Foot Off'] = [402, 517]
events_dict_nofp = dict() # ground truth without forceplate info
events_dict_nofp['Right'] = dict()
events_dict_nofp['Right']['Foot Strike'] = [379, 501, 613]
events_dict_nofp['Right']['Foot Off'] = [468, 572]
events_dict_nofp['Left'] = dict()
events_dict_nofp['Left']['Foot Strike'] = [310, 440, 561]
events_dict_nofp['Left']['Foot Off'] = [401, 516]
def _events_check(events_dict):
"""Helper to check whether Nexus events are close to ground truth"""
for context, contextdict in events_dict.items():
for event_type, events in contextdict.items():
nexus_events = vicon.GetEvents(vicon.GetSubjectNames()[0],
context, event_type)[0]
assert_equal(len(events), len(nexus_events))
for j, ev in enumerate(nexus_events):
assert abs(ev - events[j]) <= ev_tol
subj = 'girl6v'
trialname = '2015_10_22_girl6v_IN02.c3d'
trialpath = _trial_path(subj, trialname)
nexus._open_trial(trialpath)
# automatic thresholding (do not respect fp events)
vicon.ClearAllEvents()
evs = utils.automark_events(vicon, events_range=[-1500, 1500])
nexus._create_events(vicon, evs)
_events_check(events_dict_nofp)
# using forceplate-based velocity thresholds
vicon.ClearAllEvents()
fpe = utils.detect_forceplate_events(vicon)
mkrdata = read_data.get_marker_data(
vicon,
cfg.autoproc.left_foot_markers + cfg.autoproc.right_foot_markers)
vel = utils._get_foot_contact_vel(mkrdata, fpe)
evs = utils.automark_events(
vicon,
vel_thresholds=vel,
events_range=[-1500, 1500],
)
nexus._create_events(vicon, evs)
_events_check(events_dict)
def test_event_marking():
"""Test automarking of events"""
ev_tol = 4 # tolerance for event marking (frames)
events_dict = dict() # ground truth with forceplate info
events_dict['Right'] = dict()
events_dict['Right']['Foot Strike'] = [384, 505, 616]
events_dict['Right']['Foot Off'] = [465, 570]
events_dict['Left'] = dict()
events_dict['Left']['Foot Strike'] = [311, 441, 562]
events_dict['Left']['Foot Off'] = [402, 517]
events_dict_nofp = dict() # ground truth without forceplate info
events_dict_nofp['Right'] = dict()
events_dict_nofp['Right']['Foot Strike'] = [379, 501, 613]
events_dict_nofp['Right']['Foot Off'] = [468, 572]
events_dict_nofp['Left'] = dict()
events_dict_nofp['Left']['Foot Strike'] = [310, 440, 561]
events_dict_nofp['Left']['Foot Off'] = [401, 516]
def _events_check(events_dict):
"""Helper to check whether Nexus events are close to ground truth"""
for side, sidedict in events_dict.items():
for event_type, events in sidedict.items():
nexus_events = vicon.GetEvents(vicon.GetSubjectNames()[0],
side, event_type)[0]
assert_equal(len(events), len(nexus_events))
for j, ev in enumerate(nexus_events):
assert_less_equal(abs(ev - events[j]), ev_tol)
_nexus_open_trial('girl6v', '2015_10_22_girl6v_IN02')
# automatic thresholding (do not respect fp events)
vicon.ClearAllEvents()
nexus.automark_events(vicon, events_range=[-1500, 1500])
_events_check(events_dict_nofp)
# using forceplate thresholds
vicon.ClearAllEvents()
fpe = utils.detect_forceplate_events(vicon)
mkrdata = read_data.get_marker_data(
vicon,
cfg.autoproc.left_foot_markers + cfg.autoproc.right_foot_markers)
vel = utils.get_foot_contact_velocity(mkrdata, fpe)
nexus.automark_events(vicon,
vel_thresholds=vel,
events_range=[-1500, 1500],
fp_events=fpe)
_events_check(events_dict)
vicon.SaveTrial(60) # to prevent 'Save trial?' dialog on subsequent loads
def test_c3d_marker_data():
"""Test marker data reads from c3d"""
# lowerbody PiG marker set
c3dfile = _c3d_path('double_contact.c3d')
mkrset = list(utils._pig_markerset().keys())
mkrdata = read_data.get_marker_data(c3dfile, mkrset)
assert utils.is_plugingait_set(mkrdata)
assert len(mkrdata) == 5 * len(mkrset) # vars = P*2, V, A & gaps
# check array dimensions for all markers (gap data has different dims)
for mkr in mkrdata:
if '_gaps' not in mkr:
assert mkrdata[mkr].shape == (442, 3)
# LHEE gaps from 360 to 388
assert_equal(mkrdata['LHEE_gaps'], np.arange(360, 389))
lhee_file = _file_path('lhee_data.npy')
lhee_data = np.load(lhee_file)
# allow some deviation from saved reference data (was read using btk)
assert_allclose(mkrdata['LHEE'], lhee_data, rtol=1e-4)
def test_c3d_extended_chars():
"""See if we can read filenames with extended chars"""
c3dfile = _c3d_path('2020_11_10_postOp5v_säärituet_SSD06.c3d')
read_data.get_analysis(c3dfile, 'c3dtest')
mkrset = ['RASI', 'LASI']
read_data.get_marker_data(c3dfile, mkrset)