def test_get_c3ds():
"""Test c3ds getter"""
# should get all
c3ds = sessionutils.get_c3ds(sessiondir_abs)
assert len(c3ds) == 22
c3ds = sessionutils.get_c3ds(sessiondir_abs, trial_type='dynamic')
assert len(c3ds) == 21
c3ds = sessionutils.get_c3ds(sessiondir_abs, trial_type='static')
assert len(c3ds) == 1
c3ds = sessionutils.get_c3ds(sessiondir_abs, tags=['E1'])
assert len(c3ds) == 1
c3ds = sessionutils.get_c3ds(sessiondir_abs, tags=['foo'])
assert len(c3ds) == 0
def test_average_model_data():
"""Test averaging of model data"""
c3ds = sessionutils.get_c3ds(sessiondir_abs, trial_type='dynamic')
data_all, nc = stats.collect_trial_data(c3ds,
collect_types={
'model': True,
'emg': False
})
data_model = data_all['model']
avgdata, stddata, ncycles_ok = stats.average_model_data(
data_model, reject_outliers=None)
# test whether data was averaged for all vars
# except CGM2 forefoot (which are not in the c3d data)
desired_vars = set.union(
set(models.pig_lowerbody.varnames),
set(models.pig_lowerbody_kinetics.varnames),
set(models.musclelen.varnames),
) - set(
[var for var in models.pig_lowerbody.varnames if 'ForeFoot' in var])
for var in desired_vars:
assert avgdata[var] is not None and avgdata[var].shape == (101, )
assert stddata[var] is not None and stddata[var].shape == (101, )
# test with median stats
avgdata, stddata, ncycles_ok = stats.average_model_data(
data_model, reject_outliers=None, use_medians=True)
for var in desired_vars:
assert avgdata[var] is not None and avgdata[var].shape == (101, )
assert stddata[var] is not None and stddata[var].shape == (101, )
# test outlier rejection
avgdata, stddata, ncycles_ok_reject = stats.average_model_data(
data_model, reject_outliers=1e-3)
for var in desired_vars:
assert avgdata[var] is not None and avgdata[var].shape == (101, )
assert stddata[var] is not None and stddata[var].shape == (101, )
assert any(ncycles_ok_reject[var] < ncycles_ok[var] for var in ncycles_ok)
def test_rm_dead_channels():
"""Test removing dead chs from EMG layout"""
cfg.emg.autodetect_bads = True
c3ds = sessionutils.get_c3ds(sessiondir2_abs, trial_type='dynamic')
emgs = [trial.Trial(fn).emg for fn in c3ds]
emg = emgs[0]
lout = [
['LGlut', 'RGlut'],
['LHam', 'RHam'],
['LRec', 'RRec'],
['LVas', 'RVas'],
['LTibA', 'RTibA'],
['LPer', 'RPer'],
['LGas', 'RGas'],
['LSol', 'RSol'],
]
lout_ = [
['LHam', 'RHam'],
['LRec', 'RRec'],
['LTibA', 'RTibA'],
['LPer', 'RPer'],
['LGas', 'RGas'],
['LSol', 'RSol'],
]
# assert that Glut and Vas get removed for both single and multiple EMG
# instances
assert layouts._rm_dead_channels(emg, lout) == lout_
assert layouts._rm_dead_channels(emgs, lout) == lout_
cfg.emg.autodetect_bads = False
def test_collect_trial_data():
"""Test collection of trial data"""
c3ds = sessionutils.get_c3ds(sessiondir_abs, trial_type='dynamic')
data_all, cycles_all = stats.collect_trial_data(c3ds)
data_model = data_all['model']
collected_vars = set(data_model.keys())
# test whether data was collected for all vars
# except CGM2 forefoot (which are not in the c3d data)
desired_vars = (set.union(
set(models.pig_lowerbody.varnames),
set(models.pig_lowerbody_kinetics.varnames),
set(models.musclelen.varnames),
) - set(
[var for var in models.pig_lowerbody.varnames if 'ForeFoot' in var]))
assert collected_vars == desired_vars
# check that the correct number of cycles was collected
assert len(cycles_all['model']['LHipMomentX']) == 17
assert data_model['LHipMomentX'].shape[0] == 17
assert data_model['RAnkleMomentX'].shape[0] == 19
assert len(cycles_all['model']['RKneeAnglesX']) == 46
assert data_model['RKneeAnglesX'].shape[0] == 46
assert data_model['fubar'] is None
# forceplate cycles only
data_all, cycles_all = stats.collect_trial_data(c3ds, fp_cycles_only=True)
data_model = data_all['model']
assert data_model['RKneeAnglesX'].shape[0] == 19
assert data_model['RAnkleMomentX'].shape[0] == 19
assert data_model['RKneeAnglesX'].shape[1] == 101
assert len(cycles_all['model']['RKneeAnglesX']) == 19
# EMG data collection
data_all, cycles_all = stats.collect_trial_data(c3ds,
collect_types=['emg'],
analog_len=501)
assert 'model' not in data_all
data_emg = data_all['emg']
emg_chs = [
'LGas',
'LGlut',
'LHam',
'LPer',
'LRec',
'LSol',
'LTibA',
'LVas',
'RGas',
'RGlut',
'RHam',
'RPer',
'RRec',
'RSol',
'RTibA',
'RVas',
]
assert set(data_emg.keys()) == set(emg_chs)
assert all(data.shape[0] == 46 for ch, data in data_emg.items()
if ch[0] == 'R')
assert all(data.shape[0] == 42 for ch, data in data_emg.items()
if ch[0] == 'L')
assert all(data.shape[1] == 501 for data in data_emg.values())
def test_trials_extract_values():
"""Test curve value extraction from trials"""
c3ds = sessionutils.get_c3ds(sessiondir_abs, trial_type='dynamic')
extr_vals = stats._trials_extract_values(
c3ds, from_models=[models.pig_lowerbody])
# forefoot vars are not present in our test data
forefoot = models._list_with_context(
['ForeFootAnglesX', 'ForeFootAnglesY', 'ForeFootAnglesZ'])
assert set(extr_vals.keys()) == (set(models.pig_lowerbody.varnames) -
set(forefoot))
def test_avgtrial():
"""Test the AvgTrial class"""
# create from trials
c3ds = sessionutils.get_c3ds(sessiondir_abs, trial_type='dynamic')
atrial = stats.AvgTrial.from_trials(
c3ds,
sessionpath=sessiondir_abs,
reject_outliers=1e-3,
)
assert atrial.sessionpath == sessiondir_abs
assert atrial.trialname
assert atrial.t.shape == (101, )
assert len(atrial.cycles) == atrial.ncycles == 2
assert atrial.cycles[0].trial == atrial
with pytest.raises(ValueError):
atrial.set_norm_cycle(None)
adata, t = atrial.get_model_data('RKneeAnglesX')
assert adata.shape == (101, )
cycs = atrial.get_cycles('all')
assert len(cycs) == 2
cycs = atrial.get_cycles('forceplate')
assert len(cycs) == 2
# create from already averaged data
data_all, nc = stats.collect_trial_data(c3ds,
collect_types={
'model': True,
'emg': True
})
data_model = data_all['model']
avgdata_model, stddata_model, ncycles_ok = stats.average_model_data(
data_model, reject_outliers=None)
data_emg = data_all['emg']
avgdata_emg, stddata_emg, ncycles_ok = stats.average_analog_data(
data_emg, reject_outliers=None)
atrial = stats.AvgTrial(
avgdata_model=avgdata_model,
stddata_model=stddata_model,
avgdata_emg=avgdata_emg,
stddata_emg=stddata_emg,
sessionpath=sessiondir_abs,
nfiles=len(c3ds),
)
assert atrial.sessionpath == sessiondir_abs
assert atrial.trialname
assert atrial.t.shape == (101, )
assert len(atrial.cycles) == atrial.ncycles == 2
assert atrial.cycles[0].trial == atrial
with pytest.raises(ValueError):
atrial.set_norm_cycle(None)
adata, t = atrial.get_model_data('RKneeAnglesX')
assert adata.shape == (101, )
cycs = atrial.get_cycles('all')
assert len(cycs) == 2
cycs = atrial.get_cycles('forceplate')
assert len(cycs) == 2
def test_plot_trials():
"""Test individual trial plotter"""
c3ds = sessionutils.get_c3ds(sessiondir_abs)
trials = [trial.Trial(fn) for fn in c3ds]
for backend in ['plotly', 'matplotlib']:
# XXX: we don't test the figs for the time being
fig = plots.plot_trials(trials, backend=backend)
# fig = plots.plot_trials(trials, backend='plotly')
tr = trials[0]
# test different cycle args
fig = plots.plot_trials(tr, cycles='all', backend=backend)
fig = plots.plot_trials(tr, cycles='forceplate', backend=backend)
fig = plots.plot_trials(tr, cycles='unnormalized', backend=backend)
with pytest.raises(ValueError):
fig = plots.plot_trials(tr, cycles='foo', backend=backend)
fig = plots.plot_trials(tr, cycles={'emg': 'all'}, backend=backend)
fig = plots.plot_trials(tr, cycles={'emg': 0}, backend=backend)
def get_static_files(subject, newer_than=None, rootdir=None):
""" Get trial files according to given subject and trial type
(e.g. 'normal') and file extension """
rootdir = rootdir or params['rootdir']
logger.debug('finding static trial files for %s' % subject)
# try to auto find data dirs under subject dir
subjdir = op.join(rootdir, subject)
if not op.isdir(subjdir):
logger.warning('Subject directory not found: %s' % subjdir)
return list()
datadirs = [
file for file in os.listdir(subjdir)
if op.isdir(op.join(subjdir, file))
]
logger.debug('subject data dirs: %s' % datadirs)
for datadir in datadirs:
logger.debug('trying data dir %s/%s' % (subject, datadir))
sessiondir = op.join(subjdir, datadir)
files = sessionutils.get_c3ds(sessiondir,
trial_type='static',
check_if_exists=True)
if not files:
logger.debug('%s is probably not a CP data dir' % datadir)
continue
if newer_than is not None:
sessiondate = sessionutils.get_session_date(sessiondir)
logger.info('session %s timestamp %s' % (datadir, sessiondate))
if sessiondate < newer_than:
logger.info('session %s too old' % datadir)
continue
logger.debug('subject %s, datadir %s, static trials: found %d files' %
(subject, sessiondir, len(files)))
return files
# we did not hit return
logger.info('no acceptable static trials found for %s' % subject)
return list()
def test_collect_trial_data():
"""Test collection of trial data"""
c3ds = sessionutils.get_c3ds(sessiondir_abs, trial_type='dynamic')
data_all, nc = stats.collect_trial_data(c3ds)
data_model = data_all['model']
collected_vars = set(data_model.keys())
# test whether data was collected for all vars
# except CGM2 forefoot (which are not in the c3d data)
desired_vars = set.union(
set(models.pig_lowerbody.varnames),
set(models.pig_lowerbody_kinetics.varnames),
set(models.musclelen.varnames),
) - set(
[var for var in models.pig_lowerbody.varnames if 'ForeFoot' in var])
assert collected_vars == desired_vars
# check that correct number of cycles was collected
assert nc == {'R_fp': 19, 'R': 54, 'L': 53, 'L_fp': 17}
assert data_model['RKneeAnglesX'].shape[0] == nc['R']
assert data_model['RAnkleMomentX'].shape[0] == nc['R_fp']
assert data_model['RKneeAnglesX'].shape[1] == 101
assert data_model['fubar'] is None
# forceplate cycles only
data_all, nc = stats.collect_trial_data(c3ds, fp_cycles_only=True)
data_model = data_all['model']
assert nc == {'R_fp': 19, 'R': 19, 'L': 17, 'L_fp': 17}
assert data_model['RKneeAnglesX'].shape[0] == nc['R']
assert data_model['RAnkleMomentX'].shape[0] == nc['R_fp']
assert data_model['RKneeAnglesX'].shape[1] == 101
# EMG data collection
data_all, nc = stats.collect_trial_data(c3ds,
collect_types={
'model': False,
'emg': True
},
analog_len=501)
assert 'model' not in data_all
data_emg = data_all['emg']
assert set(data_emg.keys()) == set(cfg.emg.channel_labels.keys())
assert all(data.shape[0] == nc['L'] for ch, data in data_emg.items()
if ch[0] == 'L')
assert all(data.shape[0] == nc['R'] for ch, data in data_emg.items()
if ch[0] == 'R')
assert all(data.shape[1] == 501 for data in data_emg.values())
def test_convert_videos():
c3d_file = sessionutils.get_c3ds(
sessiondir_abs, tags=None, trial_type='dynamic', check_if_exists=False
)[0]
original_vids = videos.get_trial_videos(c3d_file, vid_ext='.avi', overlay=False)
assert len(original_vids) == 3
target_vids = videos.get_trial_videos(c3d_file, vid_ext='.ogv', overlay=False)
# remove target videos if they exist
for vidfile in target_vids:
vidfile.unlink()
# check should not find target videos any more
assert not videos.convert_videos(original_vids, check_only=True)
# start conversion process
procs = videos.convert_videos(original_vids)
assert procs
completed = False
# wait in a sleep loop until processes have finished
while not completed:
n_complete = len([p for p in procs if p.poll() is not None])
completed = n_complete == len(procs)
time.sleep(0.1)
# now conversion target videos should exist
assert videos.convert_videos(original_vids, check_only=True)