def test_trial_metadata():
"""Test metadata reading from c3d"""
# 1-forceplate system
c3dfile = _trial_path('girl6v', '2015_10_22_girl6v_IN02.c3d')
tr = Trial(c3dfile)
# default tolerance of assert_allclose is 1e-7
# could also use pytest.approx()
assert_allclose(tr.analograte, 1000.0)
assert_equal(tr.framerate, 100.0)
assert_allclose(tr.subj_params['Bodymass'], 24.0)
assert_equal(tr.name, 'Iiris')
assert_equal(tr.n_forceplates, 1)
assert_equal(tr.length, 794)
assert_equal(tr.samplesperframe, 10.0)
# 3-fp system
c3dfile = _trial_path('adult_3fp', 'astrid_080515_02.c3d')
tr = Trial(c3dfile)
assert_equal(tr.analograte, 1000.0)
assert_equal(tr.framerate, 200.0)
assert_allclose(tr.subj_params['Bodymass'], 65.59999, rtol=1e-4)
assert_equal(tr.name, 'Astrid')
assert_equal(tr.n_forceplates, 3)
assert_equal(tr.length, 639)
assert_equal(tr.samplesperframe, 5)
# 5-fp system
c3dfile = _trial_path('runner', 'JL brooks 2,8 51.c3d')
tr = Trial(c3dfile)
assert_equal(tr.analograte, 1500.0)
assert_equal(tr.framerate, 300.0)
assert_allclose(tr.subj_params['Bodymass'], 74.0, rtol=1e-4)
assert_equal(tr.name, 'JL')
assert_equal(tr.n_forceplates, 5)
assert_equal(tr.length, 391)
assert_equal(tr.samplesperframe, 5)
def test_get_cycles():
"""Test cycle getter"""
c3dfile = _trial_path('girl6v', '2015_10_22_girl6v_IN02.c3d')
tr = Trial(c3dfile)
cycs = tr.get_cycles('forceplate')
assert len(cycs) == 1
assert cycs[0].on_forceplate
cycs = tr.get_cycles('all')
assert len(cycs) == 4
cycs = tr.get_cycles('all', max_cycles_per_context=1)
assert len(cycs) == 2
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_trial_data_read():
"""Test data read from normalized/unnormalized cycles"""
c3dfile = _trial_path('girl6v', '2015_10_22_girl6v_IN02.c3d')
tr = Trial(c3dfile)
# read marker data
pig = _pig_markerset(fullbody=True, sacr=True)
for var in pig:
t, data = tr.get_marker_data(var) # unnormalized
assert t.shape == (794,)
assert data.shape == (794, 3)
t, data = tr.get_marker_data(var, 0) # 1st cycle
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
):
t, data = tr.get_model_data(var) # unnormalized
assert t.shape == (794,)
assert data.shape == (794,)
t, data = tr.get_model_data(var, 0)
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_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_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)