def test_drop_epochs():
epochs = Epochs(raw,
events,
event_id,
tmin,
tmax,
picks=picks,
baseline=(None, 0))
events1 = events[events[:, 2] == event_id]
# Bound checks
assert_raises(IndexError, epochs.drop_epochs, [len(epochs.events)])
assert_raises(IndexError, epochs.drop_epochs, [-1])
assert_raises(ValueError, epochs.drop_epochs, [[1, 2], [3, 4]])
# Test selection attribute
assert_array_equal(epochs.selection, np.where(events[:, 2] == event_id)[0])
assert_equal(len(epochs.drop_log), len(events))
assert_true(
all(epochs.drop_log[k] == ['IGNORED']
for k in set(range(len(events))) - set(epochs.selection)))
selection = epochs.selection.copy()
epochs.drop_epochs([2, 4], reason='d')
assert_equal(len(epochs.drop_log), len(events))
assert_equal([epochs.drop_log[k] for k in selection[[2, 4]]],
[['d'], ['d']])
assert_array_equal(events[epochs.selection], events1[[0, 1, 3, 5, 6]])
assert_array_equal(events[epochs[3:].selection], events1[[5, 6]])
assert_array_equal(events[epochs['1'].selection], events1[[0, 1, 3, 5, 6]])
def test_drop_epochs():
"""Test dropping of epochs.
"""
raw, events, picks = _get_data()
epochs = Epochs(raw, events, event_id, tmin, tmax, picks=picks,
baseline=(None, 0))
events1 = events[events[:, 2] == event_id]
# Bound checks
assert_raises(IndexError, epochs.drop_epochs, [len(epochs.events)])
assert_raises(IndexError, epochs.drop_epochs, [-1])
assert_raises(ValueError, epochs.drop_epochs, [[1, 2], [3, 4]])
# Test selection attribute
assert_array_equal(epochs.selection,
np.where(events[:, 2] == event_id)[0])
assert_equal(len(epochs.drop_log), len(events))
assert_true(all(epochs.drop_log[k] == ['IGNORED']
for k in set(range(len(events))) - set(epochs.selection)))
selection = epochs.selection.copy()
n_events = len(epochs.events)
epochs.drop_epochs([2, 4], reason='d')
assert_equal(epochs.drop_log_stats(), 2. / n_events * 100)
assert_equal(len(epochs.drop_log), len(events))
assert_equal([epochs.drop_log[k]
for k in selection[[2, 4]]], [['d'], ['d']])
assert_array_equal(events[epochs.selection], events1[[0, 1, 3, 5, 6]])
assert_array_equal(events[epochs[3:].selection], events1[[5, 6]])
assert_array_equal(events[epochs['1'].selection], events1[[0, 1, 3, 5, 6]])
def test_drop_epochs():
epochs = Epochs(raw, events, event_id, tmin, tmax, picks=picks, baseline=(None, 0))
events1 = events[events[:, 2] == event_id]
# Bound checks
assert_raises(IndexError, epochs.drop_epochs, [len(epochs.events)])
assert_raises(IndexError, epochs.drop_epochs, [-1])
assert_raises(ValueError, epochs.drop_epochs, [[1, 2], [3, 4]])
# Test selection attribute
assert_array_equal(epochs.selection, np.where(events[:, 2] == event_id)[0])
assert_equal(len(epochs.drop_log), len(events))
assert_true(all(epochs.drop_log[k] == ["IGNORED"] for k in set(range(len(events))) - set(epochs.selection)))
selection = epochs.selection.copy()
epochs.drop_epochs([2, 4], reason="d")
assert_equal(len(epochs.drop_log), len(events))
assert_equal([epochs.drop_log[k] for k in selection[[2, 4]]], [["d"], ["d"]])
assert_array_equal(events[epochs.selection], events1[[0, 1, 3, 5, 6]])
assert_array_equal(events[epochs[3:].selection], events1[[5, 6]])
assert_array_equal(events[epochs["1"].selection], events1[[0, 1, 3, 5, 6]])
def test_read_write_epochs():
"""Test epochs from raw files with IO as fif file
"""
epochs = Epochs(raw, events, event_id, tmin, tmax, picks=picks, baseline=(None, 0))
evoked = epochs.average()
data = epochs.get_data()
epochs_no_id = Epochs(raw, pick_events(events, include=event_id), None, tmin, tmax, picks=picks, baseline=(None, 0))
assert_array_equal(data, epochs_no_id.get_data())
eog_picks = pick_types(raw.info, meg=False, eeg=False, stim=False, eog=True, exclude="bads")
eog_ch_names = [raw.ch_names[k] for k in eog_picks]
epochs.drop_channels(eog_ch_names)
assert_true(len(epochs.info["chs"]) == len(epochs.ch_names) == epochs.get_data().shape[1])
data_no_eog = epochs.get_data()
assert_true(data.shape[1] == (data_no_eog.shape[1] + len(eog_picks)))
# test decim kwarg
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always")
epochs_dec = Epochs(raw, events, event_id, tmin, tmax, picks=picks, baseline=(None, 0), decim=4)
assert_equal(len(w), 1)
data_dec = epochs_dec.get_data()
assert_array_equal(data[:, :, epochs_dec._decim_idx], data_dec)
evoked_dec = epochs_dec.average()
assert_array_equal(evoked.data[:, epochs_dec._decim_idx], evoked_dec.data)
n = evoked.data.shape[1]
n_dec = evoked_dec.data.shape[1]
n_dec_min = n // 4
assert_true(n_dec_min <= n_dec <= n_dec_min + 1)
assert_true(evoked_dec.info["sfreq"] == evoked.info["sfreq"] / 4)
# test IO
epochs.save(op.join(tempdir, "test-epo.fif"))
epochs_read = read_epochs(op.join(tempdir, "test-epo.fif"))
assert_array_almost_equal(epochs_read.get_data(), epochs.get_data())
assert_array_equal(epochs_read.times, epochs.times)
assert_array_almost_equal(epochs_read.average().data, evoked.data)
assert_equal(epochs_read.proj, epochs.proj)
bmin, bmax = epochs.baseline
if bmin is None:
bmin = epochs.times[0]
if bmax is None:
bmax = epochs.times[-1]
baseline = (bmin, bmax)
assert_array_almost_equal(epochs_read.baseline, baseline)
assert_array_almost_equal(epochs_read.tmin, epochs.tmin, 2)
assert_array_almost_equal(epochs_read.tmax, epochs.tmax, 2)
assert_equal(epochs_read.event_id, epochs.event_id)
epochs.event_id.pop("1")
epochs.event_id.update({"a:a": 1}) # test allow for ':' in key
epochs.save(op.join(tempdir, "foo-epo.fif"))
epochs_read2 = read_epochs(op.join(tempdir, "foo-epo.fif"))
assert_equal(epochs_read2.event_id, epochs.event_id)
# add reject here so some of the epochs get dropped
epochs = Epochs(raw, events, event_id, tmin, tmax, picks=picks, baseline=(None, 0), reject=reject)
epochs.save(op.join(tempdir, "test-epo.fif"))
# ensure bad events are not saved
epochs_read3 = read_epochs(op.join(tempdir, "test-epo.fif"))
assert_array_equal(epochs_read3.events, epochs.events)
data = epochs.get_data()
assert_true(epochs_read3.events.shape[0] == data.shape[0])
# test copying loaded one (raw property)
epochs_read4 = epochs_read3.copy()
assert_array_almost_equal(epochs_read4.get_data(), data)
# test equalizing loaded one (drop_log property)
epochs_read4.equalize_event_counts(epochs.event_id)
epochs.drop_epochs([1, 2], reason="can we recover orig ID?")
epochs.save("test-epo.fif")
epochs_read5 = read_epochs("test-epo.fif")
assert_array_equal(epochs_read5.selection, epochs.selection)
assert_array_equal(epochs_read5.drop_log, epochs.drop_log)
# Test that one can drop channels on read file
epochs_read5.drop_channels(epochs_read5.ch_names[:1])
# test warnings on bad filenames
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always")
epochs_badname = op.join(tempdir, "test-bad-name.fif.gz")
epochs.save(epochs_badname)
read_epochs(epochs_badname)
assert_true(len(w) == 2)
def test_read_write_epochs():
"""Test epochs from raw files with IO as fif file
"""
epochs = Epochs(raw,
events,
event_id,
tmin,
tmax,
picks=picks,
baseline=(None, 0))
evoked = epochs.average()
data = epochs.get_data()
epochs_no_id = Epochs(raw,
pick_events(events, include=event_id),
None,
tmin,
tmax,
picks=picks,
baseline=(None, 0))
assert_array_equal(data, epochs_no_id.get_data())
eog_picks = fiff.pick_types(raw.info,
meg=False,
eeg=False,
stim=False,
eog=True,
exclude='bads')
eog_ch_names = [raw.ch_names[k] for k in eog_picks]
epochs.drop_channels(eog_ch_names)
assert_true(
len(epochs.info['chs']) == len(epochs.ch_names) ==
epochs.get_data().shape[1])
data_no_eog = epochs.get_data()
assert_true(data.shape[1] == (data_no_eog.shape[1] + len(eog_picks)))
# test decim kwarg
with warnings.catch_warnings(record=True) as w:
epochs_dec = Epochs(raw,
events,
event_id,
tmin,
tmax,
picks=picks,
baseline=(None, 0),
decim=4)
assert_equal(len(w), 1)
data_dec = epochs_dec.get_data()
assert_array_equal(data[:, :, epochs_dec._decim_idx], data_dec)
evoked_dec = epochs_dec.average()
assert_array_equal(evoked.data[:, epochs_dec._decim_idx], evoked_dec.data)
n = evoked.data.shape[1]
n_dec = evoked_dec.data.shape[1]
n_dec_min = n // 4
assert_true(n_dec_min <= n_dec <= n_dec_min + 1)
assert_true(evoked_dec.info['sfreq'] == evoked.info['sfreq'] / 4)
# test IO
epochs.save(op.join(tempdir, 'test-epo.fif'))
epochs_read = read_epochs(op.join(tempdir, 'test-epo.fif'))
assert_array_almost_equal(epochs_read.get_data(), epochs.get_data())
assert_array_equal(epochs_read.times, epochs.times)
assert_array_almost_equal(epochs_read.average().data, evoked.data)
assert_equal(epochs_read.proj, epochs.proj)
bmin, bmax = epochs.baseline
if bmin is None:
bmin = epochs.times[0]
if bmax is None:
bmax = epochs.times[-1]
baseline = (bmin, bmax)
assert_array_almost_equal(epochs_read.baseline, baseline)
assert_array_almost_equal(epochs_read.tmin, epochs.tmin, 2)
assert_array_almost_equal(epochs_read.tmax, epochs.tmax, 2)
assert_equal(epochs_read.event_id, epochs.event_id)
epochs.event_id.pop('1')
epochs.event_id.update({'a:a': 1}) # test allow for ':' in key
epochs.save(op.join(tempdir, 'foo-epo.fif'))
epochs_read2 = read_epochs(op.join(tempdir, 'foo-epo.fif'))
assert_equal(epochs_read2.event_id, epochs.event_id)
# add reject here so some of the epochs get dropped
epochs = Epochs(raw,
events,
event_id,
tmin,
tmax,
picks=picks,
baseline=(None, 0),
reject=reject)
epochs.save(op.join(tempdir, 'test-epo.fif'))
# ensure bad events are not saved
epochs_read3 = read_epochs(op.join(tempdir, 'test-epo.fif'))
assert_array_equal(epochs_read3.events, epochs.events)
data = epochs.get_data()
assert_true(epochs_read3.events.shape[0] == data.shape[0])
# test copying loaded one (raw property)
epochs_read4 = epochs_read3.copy()
assert_array_almost_equal(epochs_read4.get_data(), data)
# test equalizing loaded one (drop_log property)
epochs_read4.equalize_event_counts(epochs.event_id)
epochs.drop_epochs([1, 2], reason='can we recover orig ID?')
epochs.save('test-epo.fif')
epochs_read5 = read_epochs('test-epo.fif')
assert_array_equal(epochs_read5.selection, epochs.selection)
assert_array_equal(epochs_read5.drop_log, epochs.drop_log)
# Test that one can drop channels on read file
epochs_read5.drop_channels(epochs_read5.ch_names[:1])
def test_read_write_epochs():
"""Test epochs from raw files with IO as fif file
"""
epochs = Epochs(raw, events, event_id, tmin, tmax, picks=picks,
baseline=(None, 0))
evoked = epochs.average()
data = epochs.get_data()
epochs_no_id = Epochs(raw, pick_events(events, include=event_id),
None, tmin, tmax, picks=picks,
baseline=(None, 0))
assert_array_equal(data, epochs_no_id.get_data())
eog_picks = fiff.pick_types(raw.info, meg=False, eeg=False, stim=False,
eog=True, exclude='bads')
epochs.drop_picks(eog_picks)
assert_true(len(epochs.info['chs']) == len(epochs.ch_names)
== epochs.get_data().shape[1])
data_no_eog = epochs.get_data()
assert_true(data.shape[1] == (data_no_eog.shape[1] + len(eog_picks)))
# test decim kwarg
with warnings.catch_warnings(record=True) as w:
epochs_dec = Epochs(raw, events, event_id, tmin, tmax, picks=picks,
baseline=(None, 0), decim=4)
assert_equal(len(w), 1)
data_dec = epochs_dec.get_data()
assert_array_equal(data[:, :, epochs_dec._decim_idx], data_dec)
evoked_dec = epochs_dec.average()
assert_array_equal(evoked.data[:, epochs_dec._decim_idx], evoked_dec.data)
n = evoked.data.shape[1]
n_dec = evoked_dec.data.shape[1]
n_dec_min = n // 4
assert_true(n_dec_min <= n_dec <= n_dec_min + 1)
assert_true(evoked_dec.info['sfreq'] == evoked.info['sfreq'] / 4)
# test IO
epochs.save(op.join(tempdir, 'test-epo.fif'))
epochs_read = read_epochs(op.join(tempdir, 'test-epo.fif'))
assert_array_almost_equal(epochs_read.get_data(), epochs.get_data())
assert_array_equal(epochs_read.times, epochs.times)
assert_array_almost_equal(epochs_read.average().data, evoked.data)
assert_equal(epochs_read.proj, epochs.proj)
bmin, bmax = epochs.baseline
if bmin is None:
bmin = epochs.times[0]
if bmax is None:
bmax = epochs.times[-1]
baseline = (bmin, bmax)
assert_array_almost_equal(epochs_read.baseline, baseline)
assert_array_almost_equal(epochs_read.tmin, epochs.tmin, 2)
assert_array_almost_equal(epochs_read.tmax, epochs.tmax, 2)
assert_equal(epochs_read.event_id, epochs.event_id)
epochs.event_id.pop('1')
epochs.event_id.update({'a': 1})
epochs.save(op.join(tempdir, 'foo-epo.fif'))
epochs_read2 = read_epochs(op.join(tempdir, 'foo-epo.fif'))
assert_equal(epochs_read2.event_id, epochs.event_id)
# add reject here so some of the epochs get dropped
epochs = Epochs(raw, events, event_id, tmin, tmax, picks=picks,
baseline=(None, 0), reject=reject)
epochs.save(op.join(tempdir, 'test-epo.fif'))
# ensure bad events are not saved
epochs_read3 = read_epochs(op.join(tempdir, 'test-epo.fif'))
assert_array_equal(epochs_read3.events, epochs.events)
data = epochs.get_data()
assert_true(epochs_read3.events.shape[0] == data.shape[0])
# test copying loaded one (raw property)
epochs_read4 = epochs_read3.copy()
assert_array_almost_equal(epochs_read4.get_data(), data)
# test equalizing loaded one (drop_log property)
epochs_read4.equalize_event_counts(epochs.event_id)
epochs.drop_epochs([1, 2], reason='can we recover orig ID?')
epochs.save('test-epo.fif')
epochs_read5 = read_epochs('test-epo.fif')
assert_array_equal(epochs_read5.selection, epochs.selection)
assert_array_equal(epochs_read5.drop_log, epochs.drop_log)