def test_fieldtrip_client():
"""Test fieldtrip_client"""
neuromag2ft_fname = op.realpath(
op.join(os.environ['NEUROMAG2FT_ROOT'], 'neuromag2ft'))
kill_signal = queue.Queue()
thread = threading.Thread(target=_run_buffer,
args=(kill_signal, neuromag2ft_fname))
thread.daemon = True
thread.start()
time.sleep(0.25)
try:
# Start the FieldTrip buffer
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always')
with FieldTripClient(host='localhost',
port=1972,
tmax=5,
wait_max=1) as rt_client:
tmin_samp1 = rt_client.tmin_samp
time.sleep(1) # Pause measurement
assert_true(len(w) >= 1)
# Start the FieldTrip buffer again
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always')
with FieldTripClient(host='localhost',
port=1972,
tmax=5,
wait_max=1) as rt_client:
raw_info = rt_client.get_measurement_info()
tmin_samp2 = rt_client.tmin_samp
picks = mne.pick_types(raw_info,
meg='grad',
eeg=False,
stim=False,
eog=False)
epoch = rt_client.get_data_as_epoch(n_samples=5, picks=picks)
n_channels, n_samples = epoch.get_data().shape[1:]
epoch2 = rt_client.get_data_as_epoch(n_samples=5, picks=picks)
n_channels2, n_samples2 = epoch2.get_data().shape[1:]
# case of picks=None
epoch = rt_client.get_data_as_epoch(n_samples=5)
assert_true(tmin_samp2 > tmin_samp1)
assert_true(len(w) >= 1)
assert_equal(n_samples, 5)
assert_equal(n_samples2, 5)
assert_equal(n_channels, len(picks))
assert_equal(n_channels2, len(picks))
kill_signal.put(False) # stop the buffer
except Exception:
kill_signal.put(False) # stop the buffer even if tests fail
raise
def test_fieldtrip_client():
"""Test fieldtrip_client"""
neuromag2ft_fname = op.realpath(
op.join(os.environ['NEUROMAG2FT_ROOT'], 'neuromag2ft'))
kill_signal = queue.Queue()
thread = threading.Thread(target=_run_buffer,
args=(kill_signal, neuromag2ft_fname))
thread.daemon = True
thread.start()
# Start the FieldTrip buffer
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always')
with FieldTripClient(host='localhost', port=1972, tmax=5,
wait_max=1) as rt_client:
tmin_samp1 = rt_client.tmin_samp
time.sleep(1) # Pause measurement
assert_true(len(w) == 1)
# Start the FieldTrip buffer again
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always')
with FieldTripClient(host='localhost', port=1972, tmax=5,
wait_max=1) as rt_client:
print(rt_client.tmin_samp)
tmin_samp2 = rt_client.tmin_samp
kill_signal.put(False) # stop the buffer
assert_true(tmin_samp2 > tmin_samp1)
assert_true(len(w) == 1)
def test_fieldtrip_client(free_tcp_port):
"""Test fieldtrip_client"""
kill_signal = _start_buffer_thread(free_tcp_port)
time.sleep(0.5)
try:
# Start the FieldTrip buffer
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always')
with FieldTripClient(host='localhost',
port=free_tcp_port,
tmax=5,
wait_max=2) as rt_client:
tmin_samp1 = rt_client.tmin_samp
time.sleep(1) # Pause measurement
assert len(w) >= 1
# Start the FieldTrip buffer again
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always')
with FieldTripClient(host='localhost',
port=free_tcp_port,
tmax=5,
wait_max=2) as rt_client:
raw_info = rt_client.get_measurement_info()
tmin_samp2 = rt_client.tmin_samp
picks = pick_types(raw_info,
meg='grad',
eeg=False,
stim=False,
eog=False)
epoch = rt_client.get_data_as_epoch(n_samples=5, picks=picks)
n_channels, n_samples = epoch.get_data().shape[1:]
epoch2 = rt_client.get_data_as_epoch(n_samples=5, picks=picks)
n_channels2, n_samples2 = epoch2.get_data().shape[1:]
# case of picks=None
epoch = rt_client.get_data_as_epoch(n_samples=5)
assert tmin_samp2 > tmin_samp1
assert len(w) >= 1
assert n_samples == 5
assert n_samples2 == 5
assert n_channels == len(picks)
assert n_channels2 == len(picks)
finally:
kill_signal.put(False) # stop the buffer
def test_fieldtrip_rtepochs(free_tcp_port, tmpdir):
"""Test FieldTrip RtEpochs."""
raw_tmax = 7
raw = read_raw_fif(raw_fname, preload=True)
raw.crop(tmin=0, tmax=raw_tmax)
events_offline = find_events(raw, stim_channel='STI 014')
event_id = list(np.unique(events_offline[:, 2]))
tmin, tmax = -0.2, 0.5
epochs_offline = Epochs(raw, events_offline, event_id=event_id,
tmin=tmin, tmax=tmax)
epochs_offline.drop_bad()
isi_max = (np.max(np.diff(epochs_offline.events[:, 0])) /
raw.info['sfreq']) + 1.0
neuromag2ft_fname = op.realpath(op.join(os.environ['NEUROMAG2FT_ROOT'],
'neuromag2ft'))
# Works with neuromag2ft-3.0.2
cmd = (neuromag2ft_fname, '--file', raw_fname, '--speed', '8.0',
'--bufport', str(free_tcp_port))
with running_subprocess(cmd, after='terminate', verbose=False):
data_rt = None
events_ids_rt = None
with pytest.warns(RuntimeWarning, match='Trying to guess it'):
with FieldTripClient(host='localhost', port=free_tcp_port,
tmax=raw_tmax, wait_max=2) as rt_client:
# get measurement info guessed by MNE-Python
raw_info = rt_client.get_measurement_info()
assert ([ch['ch_name'] for ch in raw_info['chs']] ==
[ch['ch_name'] for ch in raw.info['chs']])
# create the real-time epochs object
epochs_rt = RtEpochs(rt_client, event_id, tmin, tmax,
stim_channel='STI 014', isi_max=isi_max)
epochs_rt.start()
time.sleep(0.5)
for ev_num, ev in enumerate(epochs_rt.iter_evoked()):
if ev_num == 0:
data_rt = ev.data[None, :, :]
events_ids_rt = int(
ev.comment) # comment attribute contains event_id
else:
data_rt = np.concatenate(
(data_rt, ev.data[None, :, :]), axis=0)
events_ids_rt = np.append(events_ids_rt,
int(ev.comment))
_call_base_epochs_public_api(epochs_rt, tmpdir)
epochs_rt.stop(stop_receive_thread=True)
assert_array_equal(events_ids_rt, epochs_rt.events[:, 2])
assert_array_equal(data_rt, epochs_rt.get_data())
assert len(epochs_rt) == len(epochs_offline)
assert_array_equal(events_ids_rt, epochs_offline.events[:, 2])
assert_allclose(epochs_rt.get_data(), epochs_offline.get_data(),
rtol=1.e-5, atol=1.e-8) # defaults of np.isclose
def test_fieldtrip_rtepochs(free_tcp_port, tmpdir):
"""Test FieldTrip RtEpochs."""
raw_tmax = 7
raw = read_raw_fif(raw_fname, preload=True)
raw.crop(tmin=0, tmax=raw_tmax)
events_offline = find_events(raw, stim_channel='STI 014')
event_id = list(np.unique(events_offline[:, 2]))
tmin, tmax = -0.2, 0.5
epochs_offline = Epochs(raw, events_offline, event_id=event_id,
tmin=tmin, tmax=tmax)
epochs_offline.drop_bad()
isi_max = (np.max(np.diff(epochs_offline.events[:, 0])) /
raw.info['sfreq']) + 1.0
kill_signal = _start_buffer_thread(free_tcp_port)
try:
data_rt = None
events_ids_rt = None
with pytest.warns(RuntimeWarning, match='Trying to guess it'):
with FieldTripClient(host='localhost', port=free_tcp_port,
tmax=raw_tmax, wait_max=2) as rt_client:
# get measurement info guessed by MNE-Python
raw_info = rt_client.get_measurement_info()
assert ([ch['ch_name'] for ch in raw_info['chs']] ==
[ch['ch_name'] for ch in raw.info['chs']])
# create the real-time epochs object
epochs_rt = RtEpochs(rt_client, event_id, tmin, tmax,
stim_channel='STI 014', isi_max=isi_max)
epochs_rt.start()
time.sleep(0.5)
for ev_num, ev in enumerate(epochs_rt.iter_evoked()):
if ev_num == 0:
data_rt = ev.data[None, :, :]
events_ids_rt = int(
ev.comment) # comment attribute contains event_id
else:
data_rt = np.concatenate(
(data_rt, ev.data[None, :, :]), axis=0)
events_ids_rt = np.append(events_ids_rt,
int(ev.comment))
_call_base_epochs_public_api(epochs_rt, tmpdir)
epochs_rt.stop(stop_receive_thread=True)
assert_array_equal(events_ids_rt, epochs_rt.events[:, 2])
assert_array_equal(data_rt, epochs_rt.get_data())
assert len(epochs_rt) == len(epochs_offline)
assert_array_equal(events_ids_rt, epochs_offline.events[:, 2])
assert_allclose(epochs_rt.get_data(), epochs_offline.get_data(),
rtol=1.e-5, atol=1.e-8) # defaults of np.isclose
finally:
kill_signal.put(False) # stop the buffer
def test_fieldtrip_client(free_tcp_port):
"""Test fieldtrip_client."""
neuromag2ft_fname = op.realpath(op.join(os.environ['NEUROMAG2FT_ROOT'],
'neuromag2ft'))
# Works with neuromag2ft-3.0.2
cmd = (neuromag2ft_fname, '--file', raw_fname, '--speed', '8.0',
'--bufport', str(free_tcp_port))
time.sleep(0.5)
with running_subprocess(cmd, after='terminate', verbose=False):
# Start the FieldTrip buffer
with pytest.warns(RuntimeWarning):
with FieldTripClient(host='localhost', port=free_tcp_port,
tmax=5, wait_max=2) as rt_client:
tmin_samp1 = rt_client.tmin_samp
time.sleep(1) # Pause measurement
# Start the FieldTrip buffer again
with pytest.warns(RuntimeWarning):
with FieldTripClient(host='localhost', port=free_tcp_port,
tmax=5, wait_max=2) as rt_client:
raw_info = rt_client.get_measurement_info()
tmin_samp2 = rt_client.tmin_samp
picks = pick_types(raw_info, meg='grad', eeg=False,
stim=False, eog=False)
epoch = rt_client.get_data_as_epoch(n_samples=5, picks=picks)
n_channels, n_samples = epoch.get_data().shape[1:]
epoch2 = rt_client.get_data_as_epoch(n_samples=5, picks=picks)
n_channels2, n_samples2 = epoch2.get_data().shape[1:]
# case of picks=None
epoch = rt_client.get_data_as_epoch(n_samples=5)
assert tmin_samp2 > tmin_samp1
assert n_samples == 5
assert n_samples2 == 5
assert n_channels == len(picks)
assert n_channels2 == len(picks)
from mne.viz import plot_events
from mne.realtime import FieldTripClient, RtEpochs
print(__doc__)
# select the left-auditory condition
event_id, tmin, tmax = 1, -0.2, 0.5
# user must provide list of bad channels because
# FieldTrip header object does not provide that
bads = ['MEG 2443', 'EEG 053']
plt.ion() # make plot interactive
_, ax = plt.subplots(2, 1, figsize=(8, 8)) # create subplots
with FieldTripClient(host='localhost', port=1972, tmax=150,
wait_max=10) as rt_client:
# get measurement info guessed by MNE-Python
raw_info = rt_client.get_measurement_info()
# select gradiometers
picks = mne.pick_types(raw_info,
meg='grad',
eeg=False,
eog=True,
stim=True,
exclude=bads)
# create the real-time epochs object
rt_epochs = RtEpochs(rt_client,
event_id,
_, ax = plt.subplots(2, 1, figsize=(8, 8)) # create subplots
speedup = 10
command = [
"neuromag2ft", "--file",
"{}/MEG/sample/sample_audvis_raw.fif".format(data_path), "--speed",
str(speedup)
]
with running_subprocess(command,
after='kill',
stdout=subprocess.PIPE,
stderr=subprocess.PIPE):
with FieldTripClient(host='localhost',
port=1972,
tmax=30,
wait_max=5,
info=info) as rt_client:
# get measurement info guessed by MNE-Python
raw_info = rt_client.get_measurement_info()
# select gradiometers
picks = mne.pick_types(raw_info,
meg='grad',
eeg=False,
eog=True,
stim=True,
exclude=bads)
# create the real-time epochs object and start acquisition
current_event_type) in enumerate(recent_event_list):
recent_data[ind] = np.array(
ftc.getData([
np.int(current_event_ind - self.n_sample_per_trial_neg),
current_event_ind + self.n_sample_per_trial_pos
])).T
recent_epochs = mne.EpochsArray(recent_data,
self.raw_info,
tmin=self.trial_tmin,
baseline=None,
proj=False)
return recent_epochs, recent_event_list
if __name__ == "__main__":
# test
rt_client = FieldTripClient(info=None,
host="localhost",
port=1972,
tmax=150,
wait_max=10)
with FieldTripClient(host='localhost', port=1972, tmax=150,
wait_max=10) as rt_client:
recent_epochs_obj = biosemi_fieldtrip_recent_epochs(rt_client)
recent_epochs, recent_event_list = recent_epochs_obj.get_recent_epochs(
)
recent_epochs.resample(512.0)
recent_epochs.apply_baseline((None, 0))
ftc_mne.connect('localhost', 1972) # might throw IOError
print ftc_mne.getHeader().nSamples
ftc_mne.getHeader().labels
ftc_mne.disconnect()
# the FieldTripClient class in MNE initializes and connects only in the
#__enter__ function
with FieldTripClient(host='localhost', port=1972,
tmax=150, wait_max=10) as rt_client:
a = rt_client.get_data_as_epoch()
# debugging, simulate the with clause
rt_client = FieldTripClient(info = None, host = "localhost", port = 1972,
tmax = 150, wait_max = 10)
rt_client.__enter__()
print rt_client.ft_client.getHeader().labels
n_sample = rt_client.ft_client.getHeader().nSamples
tmp_data = rt_client.ft_client.getData([n_sample-50000, n_sample])
# debugging: last 280 were all of it
tmp_data1 = tmp_data[:,-280::]
plt.figure()
plt.plot(tmp_data1.mean(axis = 0),'*-')
plt.figure()
plt.plot(tmp_data1.std(axis = 0),'*-')
plt.figure()
plt.plot(tmp_data1[:,277])
plt.figure()
plt.plot(tmp_data1[:,278::])