def test_nexus_set_forceplate_data():
"""Test forceplate data setter"""
start_nexus()
vicon = nexus.viconnexus()
subj = 'D0063_RR'
trialname = '2018_12_17_preOp_RR06.c3d'
session = 'autoproc_session'
trialpath = _trial_path(subj, trialname, session=session)
nexus._open_trial(trialpath)
meta = nexus._get_metadata(vicon)
data_len = int(meta['length'] * meta['samplesperframe'])
# set data to ones
data = np.ones((data_len, 3))
# invalid plate index
with pytest.raises(RuntimeError):
nexus.set_forceplate_data(vicon, 4, data)
# invalid arg
with pytest.raises(ValueError):
nexus.set_forceplate_data(vicon, 0, data, kind='foo')
# the setter writes data in device local coords
nexus.set_forceplate_data(vicon, 0, data)
# try reading the data back
# get device id corresponding to plate index
devid = nexus._get_forceplate_ids(vicon)[0]
fpdata = nexus._get_1_forceplate_data(vicon, devid)
F_read = fpdata['F']
data_global = np.dot(fpdata['wR'], data.T).T
def test_autoproc():
"""Test autoprocessing.
This requires preprocessing and model pipelines to be set up correctly in
Nexus.
"""
# SDK does not have open_session(), so we need to open a trial
start_nexus()
subj = 'D0063_RR'
trialname = '2018_12_17_preOp_RR04.c3d'
session = 'autoproc_session'
trialpath = _trial_path(subj, trialname, session=session)
nexus._open_trial(trialpath)
# check that we ended up in correct session
# (otherwise autoproc could take forever, or cause damage)
assert 'autoproc' in str(nexus.get_sessionpath())
# run the autoprocessing
autoprocess.autoproc_session()
# check the resulting c3d files
for c3dn in [1, 4, 5, 6]:
c3dname = '2018_12_17_preOp_RR0%d.c3d' % c3dn
c3dpath = trialpath.parent / c3dname
assert c3dpath.is_file()
# check that dynamic files were modified in the last 10 minutes,
# and static is older (unmodified by processing)
mtime = datetime.fromtimestamp(c3dpath.lstat().st_mtime)
if c3dn == 4:
assert (datetime.now() - mtime).total_seconds() > 3600
else:
assert (datetime.now() - mtime).total_seconds() < 600
def test_nexus_reader():
"""Test basic data reading and Trial instance creation"""
start_nexus()
vicon = nexus.viconnexus()
# from old Helsinki lab
trialname = '2015_10_22_girl6v_IN13'
subject = 'girl6v'
trialpath = _trial_path(subject, trialname)
nexus._open_trial(trialpath)
tr = Trial(vicon)
# XXX: probably with pytest, there is no benefit in using assert_equal
assert_equal(tr.analograte, 1000.0)
assert_equal(tr.framerate, 100.0)
# assert_equal(tr.bodymass, 24.0)
assert_equal(tr.subject_name, 'Iiris')
assert_equal(tr.n_forceplates, 1)
assert_equal(tr.samplesperframe, 10.0)
assert_equal(tr.length, 488)
assert_equal(tr.trialname, trialname)
assert_equal(tr.ncycles, 5)
assert_equal(tr.offset, 1)
cycs = tr.get_cycles({'R': 'all'})
cyc = cycs[1]
assert_equal(cyc.start, 230)
assert_equal(cyc.end, 321)
assert_equal(cyc.context, 'R')
assert_equal(cyc.on_forceplate, True)
assert_equal(cyc.toeoff, 282)
cyc = cycs[0]
assert_equal(cyc.start, 145)
assert_equal(cyc.context, 'R')
assert_equal(cyc.on_forceplate, False)
# from Trondheim
trialname = 'astrid_080515_02'
subject = 'adult_3fp'
trialpath = _trial_path(subject, trialname)
nexus._open_trial(trialpath)
tr = Trial(vicon)
assert_equal(tr.analograte, 1000.0)
assert_equal(tr.framerate, 200.0)
# assert_equal(tr.bodymass, 70.0)
assert_equal(tr.subject_name, 'Astrid')
assert_equal(tr.n_forceplates, 3)
assert_equal(tr.samplesperframe, 5.0)
assert_equal(tr.length, 1986)
assert_equal(tr.trialname, trialname)
assert_equal(tr.ncycles, 4)
assert_equal(tr.offset, 1)
cycs = tr.get_cycles({'L': 'all'})
cyc = cycs[1]
assert_equal(cyc.start, 1161)
assert_equal(cyc.end, 1387)
assert_equal(cyc.context, 'L')
assert_equal(cyc.on_forceplate, True)
assert_equal(cyc.toeoff, 1303)
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_nexus_plot():
"""Test basic plot from Nexus"""
start_nexus()
vicon = nexus.viconnexus()
trialname = '2015_10_22_girl6v_IN13'
subject = 'girl6v'
trialpath = _trial_path(subject, trialname)
nexus._open_trial(trialpath)
tr = Trial(vicon)
pl = plots.plot_trials([tr], backend='matplotlib')
assert isinstance(pl, Figure)
def test_nexus_get_forceplate_ids():
"""Test forceplate id getter"""
start_nexus()
vicon = nexus.viconnexus()
subj = 'D0063_RR'
trialname = '2018_12_17_preOp_RR06.c3d'
session = 'autoproc_session'
trialpath = _trial_path(subj, trialname, session=session)
nexus._open_trial(trialpath)
fpids = nexus._get_forceplate_ids(vicon)
assert fpids == [1, 2, 3, 5]
def test_nexus_get_forceplate_data():
"""Test forceplate data getter"""
start_nexus()
vicon = nexus.viconnexus()
subj = 'D0063_RR'
trialname = '2018_12_17_preOp_RR06.c3d'
session = 'autoproc_session'
trialpath = _trial_path(subj, trialname, session=session)
nexus._open_trial(trialpath)
meta = nexus._get_metadata(vicon)
# make a slice of relevant analog frames
analog_roi = slice(*(int(x * meta['samplesperframe'])
for x in vicon.GetTrialRegionOfInterest()))
fpdata_local = nexus._get_1_forceplate_data(vicon, 1, coords='local')
fpdata_global = nexus._get_1_forceplate_data(vicon, 1, coords='global')
# rotation and translation local -> global
R = fpdata_global['wR']
trans = fpdata_global['wT']
# check rotation matrix
assert_array_almost_equal(fpdata_local['wR'],
np.array([[0, 1, 0], [-1, 0, 0], [0, 0, 1]]))
assert_array_almost_equal(fpdata_global['wR'],
np.array([[0, 1, 0], [-1, 0, 0], [0, 0, 1]]))
# check global data against rotated local data
assert_allclose(fpdata_global['F'],
np.dot(R, fpdata_local['F'].T).T,
atol=0,
rtol=1e-5)
assert_allclose(fpdata_global['M'],
np.dot(R, fpdata_local['M'].T).T,
atol=0,
rtol=1e-5)
# CoP is more finicky than F and M
assert_allclose(
fpdata_global['CoP'][analog_roi, :],
np.dot(R, fpdata_local['CoP'][analog_roi, :].T).T + trans,
rtol=1e-5,
atol=0.001,
)
# check some values
# XXX: these seem to be unstable, should investigate
# assert_almost_equal(fpdata_local['F'][:, 0].max(), 103.394)
# assert_almost_equal(fpdata_local['F'][:, 1].max(), 32.8074)
# assert_almost_equal(fpdata_local['F'][:, 2].min(), -597.624)
corners = np.array([
[-232.0, -254.0, 0.0],
[-232.0, 254.0, 0.0],
[232.0, 254.0, 0.0],
[232.0, -254.0, 0.0],
])
assert_almost_equal(fpdata_local['plate_corners'], corners)
def test_compare_to_c3d():
"""Compare data reads from Nexus and corresponding Nexus written .c3d"""
start_nexus()
vicon = nexus.viconnexus()
# set the correct EMG device name for the old data
cfg.emg.devname = 'Myon'
# can only get 3 decimals of agreement between Nexus/c3d model vars (??)
NDEC = 3
# vars to test
modelvars = models.pig_lowerbody.varlabels.keys()
emg_chs = [
'LGas',
'LGlut',
'LHam',
'LPer',
'LRec',
'LSol',
'LTibA',
'LVas',
'RGas',
'RGlut',
'RHam',
'RPer',
'RRec',
'RSol',
'RTibA',
'RVas',
]
subj = 'girl6v'
trialname = '2015_10_22_girl6v_IN03.c3d'
trialpath = _trial_path(subj, trialname)
nexus._open_trial(trialpath)
tr_nexus = Trial(vicon)
tr_c3d = Trial(trialpath)
# metadata
attrs = [
'analograte',
'framerate',
'subject_name',
'n_forceplates',
'samplesperframe',
'length',
'trialname',
'ncycles',
]
for attr in attrs:
assert_equal(getattr(tr_nexus, attr), getattr(tr_c3d, attr))
# model data
for var in modelvars:
# read unnormalized model and compare
xn, dn = tr_nexus.get_model_data(var)
assert_array_equal(xn, range(tr_nexus.length))
xc, dc = tr_c3d.get_model_data(var)
assert_array_equal(xc, range(tr_nexus.length))
assert_array_almost_equal(dn, dc, decimal=NDEC)
# read normalized model and compare
for j in range(4):
for var in modelvars:
xn, dn = tr_nexus.get_model_data(var, j)
xc, dc = tr_c3d.get_model_data(var, j)
assert_array_equal(xn, np.arange(101))
assert_array_equal(xc, np.arange(101))
assert_array_almost_equal(dn, dc, decimal=NDEC)
# read unnormalized EMG and compare
for ch in emg_chs:
xn, dn = tr_nexus.get_emg_data(ch)
xc, dc = tr_c3d.get_emg_data(ch)
assert_array_equal(
xn, np.arange(tr_nexus.length * tr_nexus.samplesperframe))
assert_array_equal(xn, xc)
assert_array_almost_equal(dn, dc, decimal=NDEC)
# read normalized EMG and compare
for j in range(4):
for ch in emg_chs:
xn, dn = tr_nexus.get_emg_data(ch, j)
xc, dc = tr_c3d.get_emg_data(ch, j)
assert_array_equal(xn, xc)
assert_array_almost_equal(dn, dc, decimal=NDEC)