def test_sync_3A(self):
if not self.folder3a.exists():
return
# the assertion is already in the files
# test both residual smoothed and linear
for ses_path in self.folder3a.rglob('raw_ephys_data'):
self.assertTrue(sync_probes.version3A(ses_path.parent))
self.assertTrue(sync_probes.version3A(ses_path.parent, linear=True, tol=2))
def test_sync_3A_single(self):
ses_path = self.folder3a_single.joinpath('sub', '2019-08-09', '004')
self.assertTrue(sync_probes.version3A(ses_path, display=False))
self.assertTrue(
np.all(
np.load(list(ses_path.rglob('*.sync.npy'))[0]) == np.array(
[[0, 0], [1, 1]])))
def test_sync_3A(self):
if not self.folder3a.exists():
return
# the assertion is already in the files
# test both residual smoothed and linear
for ses_path in self.folder3a.rglob('raw_ephys_data'):
# we switched to sync using frame2ttl on November 2019
channel = 12 if '2019-11-05' in str(ses_path) else 2
self.assertTrue(
sync_probes.version3A(ses_path.parent,
type='linear',
tol=2,
display=False))
self.assertTrue(
sync_probes.version3A(ses_path.parent, display=True))
dt = _check_session_sync(ses_path, channel=channel)
self.assertTrue(np.all(np.abs(dt * 30000) < 2))
def validate_ttl_test(ses_path, display=False):
"""
For a mock session on the Ephys Choice world task, check the sync channels for all
device properly connected and perform a synchronization if dual probes to check that
all channels are recorded properly
:param ses_path: session path
:param display: show the probe synchronization plot if several probes
:return: True if tests pass, errors otherwise
"""
def _single_test(assertion, str_ok, str_ko):
if assertion:
_logger.info(str_ok)
return True
else:
_logger.error(str_ko)
return False
EXPECTED_RATES_HZ = {'left_camera': 60, 'right_camera': 150, 'body_camera': 30}
SYNC_RATE_HZ = 1
MIN_TRIALS_NB = 6
ok = True
ses_path = Path(ses_path)
if not ses_path.exists():
return False
rawsync, sync_map = fpga._get_main_probe_sync(ses_path)
last_time = rawsync['times'][-1]
# get upgoing fronts for each
sync = Bunch({})
for k in sync_map:
fronts = fpga._get_sync_fronts(rawsync, sync_map[k])
sync[k] = fronts['times'][fronts['polarities'] == 1]
wheel = fpga.extract_wheel_sync(rawsync, chmap=sync_map, save=False)
frame_rates = {'right_camera': np.round(1 / np.median(np.diff(sync.right_camera))),
'left_camera': np.round(1 / np.median(np.diff(sync.left_camera))),
'body_camera': np.round(1 / np.median(np.diff(sync.body_camera)))}
# check the camera frame rates
for lab in frame_rates:
expect = EXPECTED_RATES_HZ[lab]
ok &= _single_test(assertion=abs((1 - frame_rates[lab] / expect)) < 0.1,
str_ok=f'PASS: {lab} frame rate: {frame_rates[lab]} = {expect} Hz',
str_ko=f'FAILED: {lab} frame rate: {frame_rates[lab]} != {expect} Hz')
# check that the wheel has a minimum rate of activity on both channels
re_test = abs(1 - sync.rotary_encoder_1.size / sync.rotary_encoder_0.size) < 0.1
re_test &= len(wheel['re_pos']) / last_time > 5
ok &= _single_test(assertion=re_test,
str_ok="PASS: Rotary encoder", str_ko="FAILED: Rotary encoder")
# check that the frame 2 ttls has a minimum rate of activity
ok &= _single_test(assertion=len(sync.frame2ttl) / last_time > 0.2,
str_ok="PASS: Frame2TTL", str_ko="FAILED: Frame2TTL")
# the audio has to have at least one event per trial
ok &= _single_test(assertion=len(sync.bpod) > len(sync.audio) > MIN_TRIALS_NB,
str_ok="PASS: audio", str_ko="FAILED: audio")
# the bpod has to have at least twice the amount of min trial pulses
ok &= _single_test(assertion=len(sync.bpod) > MIN_TRIALS_NB * 2,
str_ok="PASS: Bpod", str_ko="FAILED: Bpod")
try:
# note: tried to depend as little as possible on the extraction code but for the valve...
behaviour = fpga.extract_behaviour_sync(rawsync, save=False, chmap=sync_map)
res = behaviour.valve_open.size > 1
except AssertionError:
res = False
# check that the reward valve is actionned at least once
ok &= _single_test(assertion=res,
str_ok="PASS: Valve open", str_ko="FAILED: Valve open not detected")
_logger.info('ALL CHECKS PASSED !')
# the imec sync is for 3B Probes only
if sync.get('imec_sync') is not None:
ok &= _single_test(assertion=np.all(1 - SYNC_RATE_HZ * np.diff(sync.imec_sync) < 0.1),
str_ok="PASS: imec sync", str_ko="FAILED: imec sync")
# second step is to test that we can make the sync. Assertions are whithin the synch code
if sync.get('imec_sync') is not None:
sync_result = sync_probes.version3B(ses_path, display=display)
else:
sync_result = sync_probes.version3A(ses_path, display=display)
ok &= _single_test(assertion=sync_result, str_ok="PASS: synchronisation",
str_ko="FAILED: probe synchronizations threshold exceeded")
if not ok:
raise ValueError('FAILED TTL test')
return ok
