def _read_events(p, subj, ridx, raw, picker=None):
ridx = np.array(ridx)
assert ridx.ndim == 1
if picker == 'restrict': # limit to events that will be processed
ids = p.in_numbers
picker = None
print(' Events restricted to those in params.in_numbers')
else:
ids = None
events = list()
for fname in get_event_fnames(p, subj, ridx):
# gracefully handle empty events (e.g., resting state)
with open(fname, 'r') as fid:
content = fid.read().strip()
if not content:
these_events = np.empty((0, 3), int)
else:
these_events = read_events(fname, include=ids)
events.append(these_events)
if len(events) == 1 and len(raw._first_samps) > 1: # for split raw
first_samps = raw._first_samps[:1]
last_samps = raw._last_samps[-1:]
else:
first_samps = raw._first_samps
last_samps = raw._last_samps
events = concatenate_events(events, first_samps, last_samps)
if picker:
events = _pick_events(events, picker)
if len(np.unique(events[:, 0])) != len(events):
raise RuntimeError('Non-unique event samples found after '
'concatenation')
# do time adjustment
t_adj = int(np.round(-p.t_adjust * raw.info['sfreq']))
events[:, 0] += t_adj
return events
def _read_events(p, subj, ridx, raw):
ridx = np.array(ridx)
assert ridx.ndim == 1
events = list()
for fname in get_event_fnames(p, subj, ridx):
these_events = read_events(fname)
if len(np.unique(these_events[:, 0])) != len(these_events):
raise RuntimeError('Non-unique event samples found in %s' %
(fname, ))
events.append(these_events)
if len(events) == 1 and len(raw._first_samps) > 1: # for split raw
first_samps = raw._first_samps[:1]
last_samps = raw._last_samps[-1:]
else:
first_samps = raw._first_samps
last_samps = raw._last_samps
events = concatenate_events(events, first_samps, last_samps)
if len(np.unique(events[:, 0])) != len(events):
raise RuntimeError('Non-unique event samples found after '
'concatenation')
# do time adjustment
t_adj = int(np.round(-p.t_adjust * raw.info['sfreq']))
events[:, 0] += t_adj
return events
elif events[cnt, 2] == 5:
filtered_events.append(np.array([events[cnt, 0], 0, 5]))
event_order.append('STB')
cnt += 1
filtered_events = np.array(filtered_events)
# we need to keep all events at this point because we'll need them
# in the correct order in order to match with behavior
# filtering raw to remove breathing artifacts and stuff we won't need
# for evoked analysis. Do it here because mne_process_raw wipes out
# events channel
raw.filter(1, 100)
if f > 0:
all_events = mne.concatenate_events([all_events, filtered_events], [all_raw.first_samp, raw.first_samp], [all_raw.last_samp, raw.last_samp])
all_raw = mne.concatenate_raws([all_raw, raw])
else:
all_raw = raw
all_events = filtered_events
event_id = {'STG': 1, 'STI': 3, 'STB': 5}
picks = mne.pick_types(raw.info, meg=True, ref_meg=True)
epochs = mne.Epochs(all_raw, all_events, event_id, tmin, tmax,
baseline=(None, 0), proj=False, preload=True, picks=picks)
print subj
print epochs
# checking that we have at least 8 blocks of data
if np.sum(epochs.events[:, 2] == 1) < 352:
def test_multiple_files():
"""Test loading multiple files simultaneously
"""
# split file
tempdir = _TempDir()
raw = Raw(fif_fname).crop(0, 10)
raw.load_data()
raw.load_data() # test no operation
split_size = 3. # in seconds
sfreq = raw.info['sfreq']
nsamp = (raw.last_samp - raw.first_samp)
tmins = np.round(np.arange(0., nsamp, split_size * sfreq))
tmaxs = np.concatenate((tmins[1:] - 1, [nsamp]))
tmaxs /= sfreq
tmins /= sfreq
assert_equal(raw.n_times, len(raw.times))
# going in reverse order so the last fname is the first file (need later)
raws = [None] * len(tmins)
for ri in range(len(tmins) - 1, -1, -1):
fname = op.join(tempdir, 'test_raw_split-%d_raw.fif' % ri)
raw.save(fname, tmin=tmins[ri], tmax=tmaxs[ri])
raws[ri] = Raw(fname)
events = [find_events(r, stim_channel='STI 014') for r in raws]
last_samps = [r.last_samp for r in raws]
first_samps = [r.first_samp for r in raws]
# test concatenation of split file
assert_raises(ValueError, concatenate_raws, raws, True, events[1:])
all_raw_1, events1 = concatenate_raws(raws,
preload=False,
events_list=events)
assert_equal(raw.first_samp, all_raw_1.first_samp)
assert_equal(raw.last_samp, all_raw_1.last_samp)
assert_allclose(raw[:, :][0], all_raw_1[:, :][0])
raws[0] = Raw(fname)
all_raw_2 = concatenate_raws(raws, preload=True)
assert_allclose(raw[:, :][0], all_raw_2[:, :][0])
# test proper event treatment for split files
events2 = concatenate_events(events, first_samps, last_samps)
events3 = find_events(all_raw_2, stim_channel='STI 014')
assert_array_equal(events1, events2)
assert_array_equal(events1, events3)
# test various methods of combining files
raw = Raw(fif_fname, preload=True)
n_times = raw.n_times
# make sure that all our data match
times = list(range(0, 2 * n_times, 999))
# add potentially problematic points
times.extend([n_times - 1, n_times, 2 * n_times - 1])
raw_combo0 = Raw([fif_fname, fif_fname], preload=True)
_compare_combo(raw, raw_combo0, times, n_times)
raw_combo = Raw([fif_fname, fif_fname], preload=False)
_compare_combo(raw, raw_combo, times, n_times)
raw_combo = Raw([fif_fname, fif_fname], preload='memmap8.dat')
_compare_combo(raw, raw_combo, times, n_times)
assert_raises(ValueError, Raw, [fif_fname, ctf_fname])
assert_raises(ValueError, Raw, [fif_fname, fif_bad_marked_fname])
assert_equal(raw[:, :][0].shape[1] * 2, raw_combo0[:, :][0].shape[1])
assert_equal(raw_combo0[:, :][0].shape[1], raw_combo0.n_times)
# with all data preloaded, result should be preloaded
raw_combo = Raw(fif_fname, preload=True)
raw_combo.append(Raw(fif_fname, preload=True))
assert_true(raw_combo.preload is True)
assert_equal(raw_combo.n_times, raw_combo._data.shape[1])
_compare_combo(raw, raw_combo, times, n_times)
# with any data not preloaded, don't set result as preloaded
raw_combo = concatenate_raws(
[Raw(fif_fname, preload=True),
Raw(fif_fname, preload=False)])
assert_true(raw_combo.preload is False)
assert_array_equal(find_events(raw_combo, stim_channel='STI 014'),
find_events(raw_combo0, stim_channel='STI 014'))
_compare_combo(raw, raw_combo, times, n_times)
# user should be able to force data to be preloaded upon concat
raw_combo = concatenate_raws(
[Raw(fif_fname, preload=False),
Raw(fif_fname, preload=True)],
preload=True)
assert_true(raw_combo.preload is True)
_compare_combo(raw, raw_combo, times, n_times)
raw_combo = concatenate_raws(
[Raw(fif_fname, preload=False),
Raw(fif_fname, preload=True)],
preload='memmap3.dat')
_compare_combo(raw, raw_combo, times, n_times)
raw_combo = concatenate_raws(
[Raw(fif_fname, preload=True),
Raw(fif_fname, preload=True)],
preload='memmap4.dat')
_compare_combo(raw, raw_combo, times, n_times)
raw_combo = concatenate_raws(
[Raw(fif_fname, preload=False),
Raw(fif_fname, preload=False)],
preload='memmap5.dat')
_compare_combo(raw, raw_combo, times, n_times)
# verify that combining raws with different projectors throws an exception
raw.add_proj([], remove_existing=True)
assert_raises(ValueError, raw.append, Raw(fif_fname, preload=True))
# now test event treatment for concatenated raw files
events = [
find_events(raw, stim_channel='STI 014'),
find_events(raw, stim_channel='STI 014')
]
last_samps = [raw.last_samp, raw.last_samp]
first_samps = [raw.first_samp, raw.first_samp]
events = concatenate_events(events, first_samps, last_samps)
events2 = find_events(raw_combo0, stim_channel='STI 014')
assert_array_equal(events, events2)
# check out the len method
assert_equal(len(raw), raw.n_times)
assert_equal(len(raw), raw.last_samp - raw.first_samp + 1)
def test_multiple_files():
"""Test loading multiple files simultaneously
"""
# split file
raw = Raw(fif_fname, preload=True)
split_size = 10. # in seconds
sfreq = raw.info['sfreq']
nsamp = (raw.last_samp - raw.first_samp)
tmins = np.round(np.arange(0., nsamp, split_size * sfreq))
tmaxs = np.concatenate((tmins[1:] - 1, [nsamp]))
tmaxs /= sfreq
tmins /= sfreq
# going in reverse order so the last fname is the first file (need later)
raws = [None] * len(tmins)
for ri in range(len(tmins) - 1, -1, -1):
fname = op.join(tempdir, 'test_raw_split-%d_raw.fif' % ri)
raw.save(fname, tmin=tmins[ri], tmax=tmaxs[ri])
raws[ri] = Raw(fname)
events = [find_events(r) for r in raws]
last_samps = [r.last_samp for r in raws]
first_samps = [r.first_samp for r in raws]
# test concatenation of split file
all_raw_1 = concatenate_raws(raws, preload=False)
assert_true(raw.first_samp == all_raw_1.first_samp)
assert_true(raw.last_samp == all_raw_1.last_samp)
assert_array_almost_equal(raw[:, :][0], all_raw_1[:, :][0])
raws[0] = Raw(fname)
all_raw_2 = concatenate_raws(raws, preload=True)
assert_array_almost_equal(raw[:, :][0], all_raw_2[:, :][0])
# test proper event treatment for split files
events = concatenate_events(events, first_samps, last_samps)
events2 = find_events(all_raw_2)
assert_array_equal(events, events2)
# test various methods of combining files
n_combos = 9
raw_combos = [None] * n_combos
raw = Raw(fif_fname, preload=True)
raw_combos[0] = Raw([fif_fname, fif_fname], preload=True)
raw_combos[1] = Raw([fif_fname, fif_fname], preload=False)
raw_combos[2] = Raw([fif_fname, fif_fname], preload='memmap8.dat')
assert_raises(ValueError, Raw, [fif_fname, ctf_fname])
assert_raises(ValueError, Raw, [fif_fname, fif_bad_marked_fname])
n_times = len(raw._times)
assert_true(raw[:, :][0].shape[1] * 2 == raw_combos[0][:, :][0].shape[1])
assert_true(raw_combos[0][:, :][0].shape[1] == len(raw_combos[0]._times))
# with all data preloaded, result should be preloaded
raw_combos[3] = Raw(fif_fname, preload=True)
raw_combos[3].append(Raw(fif_fname, preload=True))
assert_true(raw_combos[0]._preloaded == True)
# with any data not preloaded, don't set result as preloaded
raw_combos[4] = concatenate_raws([Raw(fif_fname, preload=True),
Raw(fif_fname, preload=False)])
assert_true(raw_combos[1]._preloaded == False)
assert_array_equal(find_events(raw_combos[4]), find_events(raw_combos[0]))
# user should be able to force data to be preloaded upon concat
raw_combos[5] = concatenate_raws([Raw(fif_fname, preload=False),
Raw(fif_fname, preload=True)],
preload=True)
assert_true(raw_combos[2]._preloaded == True)
raw_combos[6] = concatenate_raws([Raw(fif_fname, preload=False),
Raw(fif_fname, preload=True)],
preload='memmap3.dat')
raw_combos[7] = concatenate_raws([Raw(fif_fname, preload=True),
Raw(fif_fname, preload=True)],
preload='memmap4.dat')
raw_combos[8] = concatenate_raws([Raw(fif_fname, preload=False),
Raw(fif_fname, preload=False)],
preload='memmap5.dat')
# make sure that all our data match
times = range(0, 2 * n_times, 999)
# add potentially problematic points
times.extend([n_times - 1, n_times, 2 * n_times - 1])
for ti in times: # let's do a subset of points for speed
orig = raw[:, ti % n_times][0]
for raw_combo in raw_combos:
# these are almost_equals because of possible dtype differences
assert_array_almost_equal(orig, raw_combo[:, ti][0])
# verify that combining raws with different projectors throws an exception
raw.add_proj([], remove_existing=True)
assert_raises(ValueError, raw.append, Raw(fif_fname, preload=True))
# now test event treatment for concatenated raw files
events = [find_events(raw), find_events(raw)]
last_samps = [raw.last_samp, raw.last_samp]
first_samps = [raw.first_samp, raw.first_samp]
events = concatenate_events(events, first_samps, last_samps)
events2 = find_events(raw_combos[0])
assert_array_equal(events, events2)
# check out the len method
assert_true(len(raw) == raw.n_times)
assert_true(len(raw) == raw.last_samp - raw.first_samp + 1)
def test_multiple_files():
"""Test loading multiple files simultaneously
"""
# split file
raw = Raw(fif_fname, preload=True).crop(0, 10)
split_size = 3. # in seconds
sfreq = raw.info['sfreq']
nsamp = (raw.last_samp - raw.first_samp)
tmins = np.round(np.arange(0., nsamp, split_size * sfreq))
tmaxs = np.concatenate((tmins[1:] - 1, [nsamp]))
tmaxs /= sfreq
tmins /= sfreq
assert_equal(raw.n_times, len(raw._times))
# going in reverse order so the last fname is the first file (need later)
raws = [None] * len(tmins)
for ri in range(len(tmins) - 1, -1, -1):
fname = op.join(tempdir, 'test_raw_split-%d_raw.fif' % ri)
raw.save(fname, tmin=tmins[ri], tmax=tmaxs[ri])
raws[ri] = Raw(fname)
events = [find_events(r, stim_channel='STI 014') for r in raws]
last_samps = [r.last_samp for r in raws]
first_samps = [r.first_samp for r in raws]
# test concatenation of split file
all_raw_1 = concatenate_raws(raws, preload=False)
assert_true(raw.first_samp == all_raw_1.first_samp)
assert_true(raw.last_samp == all_raw_1.last_samp)
assert_allclose(raw[:, :][0], all_raw_1[:, :][0])
raws[0] = Raw(fname)
all_raw_2 = concatenate_raws(raws, preload=True)
assert_allclose(raw[:, :][0], all_raw_2[:, :][0])
# test proper event treatment for split files
events = concatenate_events(events, first_samps, last_samps)
events2 = find_events(all_raw_2, stim_channel='STI 014')
assert_array_equal(events, events2)
# test various methods of combining files
raw = Raw(fif_fname, preload=True)
n_times = len(raw._times)
# make sure that all our data match
times = list(range(0, 2 * n_times, 999))
# add potentially problematic points
times.extend([n_times - 1, n_times, 2 * n_times - 1])
raw_combo0 = Raw([fif_fname, fif_fname], preload=True)
_compare_combo(raw, raw_combo0, times, n_times)
raw_combo = Raw([fif_fname, fif_fname], preload=False)
_compare_combo(raw, raw_combo, times, n_times)
raw_combo = Raw([fif_fname, fif_fname], preload='memmap8.dat')
_compare_combo(raw, raw_combo, times, n_times)
assert_raises(ValueError, Raw, [fif_fname, ctf_fname])
assert_raises(ValueError, Raw, [fif_fname, fif_bad_marked_fname])
assert_true(raw[:, :][0].shape[1] * 2 == raw_combo0[:, :][0].shape[1])
assert_true(raw_combo0[:, :][0].shape[1] == len(raw_combo0._times))
# with all data preloaded, result should be preloaded
raw_combo = Raw(fif_fname, preload=True)
raw_combo.append(Raw(fif_fname, preload=True))
assert_true(raw_combo._preloaded is True)
assert_true(len(raw_combo._times) == raw_combo._data.shape[1])
_compare_combo(raw, raw_combo, times, n_times)
# with any data not preloaded, don't set result as preloaded
raw_combo = concatenate_raws([Raw(fif_fname, preload=True),
Raw(fif_fname, preload=False)])
assert_true(raw_combo._preloaded is False)
assert_array_equal(find_events(raw_combo, stim_channel='STI 014'),
find_events(raw_combo0, stim_channel='STI 014'))
_compare_combo(raw, raw_combo, times, n_times)
# user should be able to force data to be preloaded upon concat
raw_combo = concatenate_raws([Raw(fif_fname, preload=False),
Raw(fif_fname, preload=True)],
preload=True)
assert_true(raw_combo._preloaded is True)
_compare_combo(raw, raw_combo, times, n_times)
raw_combo = concatenate_raws([Raw(fif_fname, preload=False),
Raw(fif_fname, preload=True)],
preload='memmap3.dat')
_compare_combo(raw, raw_combo, times, n_times)
raw_combo = concatenate_raws([Raw(fif_fname, preload=True),
Raw(fif_fname, preload=True)],
preload='memmap4.dat')
_compare_combo(raw, raw_combo, times, n_times)
raw_combo = concatenate_raws([Raw(fif_fname, preload=False),
Raw(fif_fname, preload=False)],
preload='memmap5.dat')
_compare_combo(raw, raw_combo, times, n_times)
# verify that combining raws with different projectors throws an exception
raw.add_proj([], remove_existing=True)
assert_raises(ValueError, raw.append, Raw(fif_fname, preload=True))
# now test event treatment for concatenated raw files
events = [find_events(raw, stim_channel='STI 014'),
find_events(raw, stim_channel='STI 014')]
last_samps = [raw.last_samp, raw.last_samp]
first_samps = [raw.first_samp, raw.first_samp]
events = concatenate_events(events, first_samps, last_samps)
events2 = find_events(raw_combo0, stim_channel='STI 014')
assert_array_equal(events, events2)
# check out the len method
assert_true(len(raw) == raw.n_times)
assert_true(len(raw) == raw.last_samp - raw.first_samp + 1)
def test_multiple_files():
"""Test loading multiple files simultaneously
"""
# split file
raw = Raw(fif_fname, preload=True)
split_size = 10. # in seconds
sfreq = raw.info['sfreq']
nsamp = (raw.last_samp - raw.first_samp)
tmins = np.round(np.arange(0., nsamp, split_size * sfreq))
tmaxs = np.concatenate((tmins[1:] - 1, [nsamp]))
tmaxs /= sfreq
tmins /= sfreq
# going in reverse order so the last fname is the first file (need later)
raws = [None] * len(tmins)
for ri in range(len(tmins) - 1, -1, -1):
fname = op.join(tempdir, 'test_raw_split-%d_raw.fif' % ri)
raw.save(fname, tmin=tmins[ri], tmax=tmaxs[ri])
raws[ri] = Raw(fname)
events = [find_events(r, stim_channel='STI 014') for r in raws]
last_samps = [r.last_samp for r in raws]
first_samps = [r.first_samp for r in raws]
# test concatenation of split file
all_raw_1 = concatenate_raws(raws, preload=False)
assert_true(raw.first_samp == all_raw_1.first_samp)
assert_true(raw.last_samp == all_raw_1.last_samp)
assert_allclose(raw[:, :][0], all_raw_1[:, :][0])
raws[0] = Raw(fname)
all_raw_2 = concatenate_raws(raws, preload=True)
assert_allclose(raw[:, :][0], all_raw_2[:, :][0])
# test proper event treatment for split files
events = concatenate_events(events, first_samps, last_samps)
events2 = find_events(all_raw_2, stim_channel='STI 014')
assert_array_equal(events, events2)
# test various methods of combining files
n_combos = 9
raw_combos = [None] * n_combos
raw = Raw(fif_fname, preload=True)
raw_combos[0] = Raw([fif_fname, fif_fname], preload=True)
raw_combos[1] = Raw([fif_fname, fif_fname], preload=False)
raw_combos[2] = Raw([fif_fname, fif_fname], preload='memmap8.dat')
assert_raises(ValueError, Raw, [fif_fname, ctf_fname])
assert_raises(ValueError, Raw, [fif_fname, fif_bad_marked_fname])
n_times = len(raw._times)
assert_true(raw[:, :][0].shape[1] * 2 == raw_combos[0][:, :][0].shape[1])
assert_true(raw_combos[0][:, :][0].shape[1] == len(raw_combos[0]._times))
# with all data preloaded, result should be preloaded
raw_combos[3] = Raw(fif_fname, preload=True)
raw_combos[3].append(Raw(fif_fname, preload=True))
assert_true(raw_combos[0]._preloaded == True)
assert_true(len(raw_combos[3]._times) == raw_combos[3]._data.shape[1])
# with any data not preloaded, don't set result as preloaded
raw_combos[4] = concatenate_raws(
[Raw(fif_fname, preload=True),
Raw(fif_fname, preload=False)])
assert_true(raw_combos[1]._preloaded == False)
assert_array_equal(find_events(raw_combos[4], stim_channel='STI 014'),
find_events(raw_combos[0], stim_channel='STI 014'))
# user should be able to force data to be preloaded upon concat
raw_combos[5] = concatenate_raws(
[Raw(fif_fname, preload=False),
Raw(fif_fname, preload=True)],
preload=True)
assert_true(raw_combos[2]._preloaded == True)
raw_combos[6] = concatenate_raws(
[Raw(fif_fname, preload=False),
Raw(fif_fname, preload=True)],
preload='memmap3.dat')
raw_combos[7] = concatenate_raws(
[Raw(fif_fname, preload=True),
Raw(fif_fname, preload=True)],
preload='memmap4.dat')
raw_combos[8] = concatenate_raws(
[Raw(fif_fname, preload=False),
Raw(fif_fname, preload=False)],
preload='memmap5.dat')
# make sure that all our data match
times = range(0, 2 * n_times, 999)
# add potentially problematic points
times.extend([n_times - 1, n_times, 2 * n_times - 1])
for ti in times: # let's do a subset of points for speed
orig = raw[:, ti % n_times][0]
for raw_combo in raw_combos:
# these are almost_equals because of possible dtype differences
assert_allclose(orig, raw_combo[:, ti][0])
# verify that combining raws with different projectors throws an exception
raw.add_proj([], remove_existing=True)
assert_raises(ValueError, raw.append, Raw(fif_fname, preload=True))
# now test event treatment for concatenated raw files
events = [
find_events(raw, stim_channel='STI 014'),
find_events(raw, stim_channel='STI 014')
]
last_samps = [raw.last_samp, raw.last_samp]
first_samps = [raw.first_samp, raw.first_samp]
events = concatenate_events(events, first_samps, last_samps)
events2 = find_events(raw_combos[0], stim_channel='STI 014')
assert_array_equal(events, events2)
# check out the len method
assert_true(len(raw) == raw.n_times)
assert_true(len(raw) == raw.last_samp - raw.first_samp + 1)
### QUICK HACK ###
raw_list[-1].apply_proj()
#raw_list[-1].proj = False
#raw_list[-1]._projector = None
############
raw_list[-1].info['projs'] = projOverwrite
#concatenate raw
raw = mne.concatenate_raws(raw_list)
#raw = mne.io.RawFIFF(raw_fileNames, add_eeg_ref=True)
# Read in list of events
events = mne.concatenate_events([mne.read_events(l_dir)
for l_dir in list_fileNames],
raw._first_samps, raw._last_samps)
###################################
# generate epochs object from events list and raw file
#tempEpo = generateEpochs(raw_dir, list_dir))
eventDict = {'pitch_maintain': 1, 'space_maintain': 2,
'pitch_switch': 3, 'space_switch': 4}
tmin = -0.2
tmax = 4.75
tempEpo = mne.Epochs(raw, events, event_id=eventDict, tmin=tmin,
tmax=tmax, preload=True, proj=True, verbose=False)
#tempEpo.drop_bad_epochs() #Done if preload=True above
assert all(len(x) == 0 or 'IGNORED' in x for x in tempEpo.drop_log)