def test_trial_data_read():
"""Test data read from normalized/unnormalized cycles"""
c3dfile = _trial_path('girl6v', '2015_10_22_girl6v_IN02.c3d')
tr = Trial(c3dfile)
with pytest.raises(ValueError): # nonexistent cycle
tr.set_norm_cycle(10)
# read marker data
pig = _pig_markerset(fullbody=True, sacr=True)
for var in pig:
tr.set_norm_cycle(None) # unnormalized
t, data = tr.get_marker_data(var)
assert t.shape == (794, )
assert data.shape == (794, 3)
tr.set_norm_cycle(0) # unnormalized
t, data = tr.get_marker_data(var)
assert t.shape == (101, )
assert data.shape == (101, 3)
# some known values for this cycle
if var == 'SACR':
data_truth = np.array([
[225.61265564, -1224.5526123, 693.34594727],
[223.94009735, -1216.89548584, 692.26601624],
[222.29524506, -1209.13790283, 691.30033325],
])
assert_allclose(data[:3, :], data_truth)
# read model data
for var in list(models.pig_lowerbody.varnames) + list(
models.pig_upperbody.varnames):
tr.set_norm_cycle(None) # unnormalized
t, data = tr.get_model_data(var)
assert t.shape == (794, )
assert data.shape == (794, )
tr.set_norm_cycle(0) # unnormalized
t, data = tr.get_model_data(var)
assert t.shape == (101, )
assert data.shape == (101, )
# some known values for this cycle
if var == 'RHipAnglesX':
data_truth = np.array([
5.12708759,
4.58470859,
4.0733108,
3.60522768,
3.1999483,
2.87095979,
2.62458159,
2.47358855,
2.44552759,
2.53485509,
2.75183632,
3.12467247,
3.65770569,
4.35132931,
5.21909947,
])
assert_allclose(data[:15], data_truth)
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)