def test_crop_when_negative_orig_time(windows_like_datetime):
"""Test cropping with orig_time, tmin and tmax previous to 1970."""
# Regression test for gh-6621
orig_time_stamp = -908196945.011331 # 1941-03-22 11:04:14.988669
annot = Annotations(description='foo',
onset=np.arange(0, 0.999, 0.1),
duration=[0],
orig_time=orig_time_stamp)
stamp = _dt_to_stamp(annot.orig_time)
assert_allclose(stamp[0] + stamp[1] * 1e-6, orig_time_stamp)
t = stamp[0] + stamp[1] * 1e-6
assert t == orig_time_stamp
assert len(annot) == 10
# do not raise
annot.crop(verbose='debug')
assert len(annot) == 10
# Crop with negative tmin, tmax
tmin, tmax = [orig_time_stamp + t for t in (0.25, .75)]
assert tmin < 0 and tmax < 0
crop_annot = annot.crop(tmin=tmin, tmax=tmax)
assert_allclose(crop_annot.onset, [0.3, 0.4, 0.5, 0.6, 0.7])
orig_dt = _stamp_to_dt(stamp)
assert crop_annot.orig_time == orig_dt # orig_time does not change
def test_basics():
"""Test annotation class."""
raw = read_raw_fif(fif_fname)
assert raw.annotations is not None # XXX to be fixed in #5416
assert len(raw.annotations.onset) == 0 # XXX to be fixed in #5416
pytest.raises(IOError, read_annotations, fif_fname)
onset = np.array(range(10))
duration = np.ones(10)
description = np.repeat('test', 10)
dt = raw.info['meas_date']
assert isinstance(dt, datetime)
stamp = _dt_to_stamp(dt)
# Test time shifts.
for orig_time in [None, dt, stamp[0], stamp]:
annot = Annotations(onset, duration, description, orig_time)
if orig_time is None:
assert annot.orig_time is None
else:
assert isinstance(annot.orig_time, datetime)
assert annot.orig_time.tzinfo is timezone.utc
pytest.raises(ValueError, Annotations, onset, duration, description[:9])
pytest.raises(ValueError, Annotations, [onset, 1], duration, description)
pytest.raises(ValueError, Annotations, onset, [duration, 1], description)
# Test combining annotations with concatenate_raws
raw2 = raw.copy()
delta = raw.times[-1] + 1. / raw.info['sfreq']
orig_time = (stamp[0] + stamp[1] * 1e-6 + raw2._first_time)
offset = _dt_to_stamp(_handle_meas_date(raw2.info['meas_date']))
offset = offset[0] + offset[1] * 1e-6
offset = orig_time - offset
assert_allclose(offset, raw._first_time)
annot = Annotations(onset, duration, description, orig_time)
assert annot.orig_time is not None
assert ' segments' in repr(annot)
raw2.set_annotations(annot)
assert_allclose(raw2.annotations.onset, onset + offset)
assert raw2.annotations is not annot
assert raw2.annotations.orig_time is not None
concatenate_raws([raw, raw2])
assert_and_remove_boundary_annot(raw)
assert_allclose(onset + offset + delta, raw.annotations.onset, rtol=1e-5)
assert_array_equal(annot.duration, raw.annotations.duration)
assert_array_equal(raw.annotations.description, np.repeat('test', 10))
def test_plot_raw_meas_date(raw, browser_backend):
"""Test effect of mismatched meas_date in raw.plot()."""
raw.set_meas_date(_dt_to_stamp(raw.info['meas_date'])[0])
annot = Annotations([1 + raw.first_samp / raw.info['sfreq']], [5], ['bad'])
with pytest.warns(RuntimeWarning, match='outside data range'):
raw.set_annotations(annot)
with pytest.warns(None): # sometimes projection
raw.plot(group_by='position', order=np.arange(8))
fig = raw.plot()
for key in ['down', 'up', 'escape']:
fig._fake_keypress(key, fig=fig.mne.fig_selection)
def test_raw_array_orig_times():
"""Test combining with RawArray and orig_times."""
data = np.random.randn(2, 1000) * 10e-12
sfreq = 100.
info = create_info(ch_names=['MEG1', 'MEG2'], ch_types=['grad'] * 2,
sfreq=sfreq)
meas_date = _handle_meas_date(np.pi)
info['meas_date'] = meas_date
raws = []
for first_samp in [12300, 100, 12]:
raw = RawArray(data.copy(), info, first_samp=first_samp)
ants = Annotations([1., 2.], [.5, .5], 'x', np.pi + first_samp / sfreq)
raw.set_annotations(ants)
raws.append(raw)
assert_allclose(raws[0].annotations.onset, [124, 125])
raw = RawArray(data.copy(), info)
assert not len(raw.annotations)
raw.set_annotations(Annotations([1.], [.5], 'x', None))
assert_allclose(raw.annotations.onset, [1.])
raws.append(raw)
raw = concatenate_raws(raws, verbose='debug')
assert raw.info['meas_date'] == raw.annotations.orig_time == meas_date
assert_and_remove_boundary_annot(raw, 3)
assert_array_equal(raw.annotations.onset, [124., 125., 134., 135.,
144., 145., 154.])
raw.annotations.delete(2)
assert_array_equal(raw.annotations.onset, [124., 125., 135., 144.,
145., 154.])
raw.annotations.append(5, 1.5, 'y')
assert_array_equal(raw.annotations.onset,
[5., 124., 125., 135., 144., 145., 154.])
assert_array_equal(raw.annotations.duration,
[1.5, .5, .5, .5, .5, .5, .5])
assert_array_equal(raw.annotations.description,
['y', 'x', 'x', 'x', 'x', 'x', 'x'])
# These three things should be equivalent
stamp = _dt_to_stamp(raw.info['meas_date'])
orig_time = _handle_meas_date(stamp)
for empty_annot in (
Annotations([], [], [], stamp),
Annotations([], [], [], orig_time),
Annotations([], [], [], None),
None):
raw.set_annotations(empty_annot)
assert isinstance(raw.annotations, Annotations)
assert len(raw.annotations) == 0
assert raw.annotations.orig_time == orig_time
def test_plot_raw():
"""Test plotting of raw data."""
raw = _get_raw()
raw.info['lowpass'] = 10. # allow heavy decim during plotting
events = _get_events()
plt.close('all') # ensure all are closed
assert len(plt.get_fignums()) == 0
fig = raw.plot(events=events, order=[1, 7, 3], group_by='original')
assert len(plt.get_fignums()) == 1
# make sure fig._mne_params is present
assert isinstance(fig._mne_params, dict)
# test mouse clicks
x = fig.get_axes()[0].lines[1].get_xdata().mean()
y = fig.get_axes()[0].lines[1].get_ydata().mean()
data_ax = fig.axes[0]
_fake_click(fig, data_ax, [x, y], xform='data') # mark a bad channel
_fake_click(fig, data_ax, [x, y], xform='data') # unmark a bad channel
_fake_click(fig, data_ax, [0.5, 0.999]) # click elsewhere in 1st axes
_fake_click(fig, data_ax, [-0.1, 0.9]) # click on y-label
_fake_click(fig, fig.get_axes()[1], [0.5, 0.5]) # change time
_fake_click(fig, fig.get_axes()[2], [0.5, 0.5]) # change channels
assert len(plt.get_fignums()) == 1
# open SSP window
_fake_click(fig, fig.get_axes()[-1], [0.5, 0.5])
_fake_click(fig, fig.get_axes()[-1], [0.5, 0.5], kind='release')
assert len(plt.get_fignums()) == 2
ssp_fig = plt.figure(plt.get_fignums()[-1])
fig.canvas.button_press_event(1, 1, 1) # outside any axes
fig.canvas.scroll_event(0.5, 0.5, -0.5) # scroll down
fig.canvas.scroll_event(0.5, 0.5, 0.5) # scroll up
ax = ssp_fig.get_axes()[0] # only one axis is used
assert _proj_status(ax) == [True] * 3
t = [c for c in ax.get_children() if isinstance(c, matplotlib.text.Text)]
pos = np.array(t[0].get_position()) + 0.01
_fake_click(ssp_fig, ssp_fig.get_axes()[0], pos, xform='data') # off
assert _proj_status(ax) == [False, True, True]
_fake_click(ssp_fig, ssp_fig.get_axes()[0], pos, xform='data') # on
assert _proj_status(ax) == [True] * 3
_fake_click(ssp_fig, ssp_fig.get_axes()[1], [0.5, 0.5]) # all off
_fake_click(ssp_fig, ssp_fig.get_axes()[1], [0.5, 0.5], kind='release')
assert _proj_status(ax) == [False] * 3
assert fig._mne_params['projector'] is None # actually off
_fake_click(ssp_fig, ssp_fig.get_axes()[1], [0.5, 0.5]) # all on
_fake_click(ssp_fig, ssp_fig.get_axes()[1], [0.5, 0.5], kind='release')
assert fig._mne_params['projector'] is not None # on
assert _proj_status(ax) == [True] * 3
# test keypresses
# test for group_by='original'
for key in [
'down', 'up', 'right', 'left', 'o', '-', '+', '=', 'd', 'd',
'pageup', 'pagedown', 'home', 'end', '?', 'f11', 'z', 'escape'
]:
fig.canvas.key_press_event(key)
# test for group_by='selection'
fig = plot_raw(raw, events=events, group_by='selection')
for key in [
'b', 'down', 'up', 'right', 'left', 'o', '-', '+', '=', 'd', 'd',
'pageup', 'pagedown', 'home', 'end', '?', 'f11', 'b', 'z', 'escape'
]:
fig.canvas.key_press_event(key)
# test zen mode
fig = plot_raw(raw, show_scrollbars=False)
# Color setting
pytest.raises(KeyError, raw.plot, event_color={0: 'r'})
pytest.raises(TypeError, raw.plot, event_color={'foo': 'r'})
annot = Annotations([10, 10 + raw.first_samp / raw.info['sfreq']],
[10, 10], ['test', 'test'], raw.info['meas_date'])
with pytest.warns(RuntimeWarning, match='outside data range'):
raw.set_annotations(annot)
fig = plot_raw(raw, events=events, event_color={-1: 'r', 998: 'b'})
plt.close('all')
for group_by, order in zip(
['position', 'selection'],
[np.arange(len(raw.ch_names))[::-3], [1, 2, 4, 6]]):
with pytest.warns(None): # sometimes projection
fig = raw.plot(group_by=group_by, order=order)
x = fig.get_axes()[0].lines[1].get_xdata()[10]
y = fig.get_axes()[0].lines[1].get_ydata()[10]
with pytest.warns(None): # old mpl (at least 2.0) can warn
_fake_click(fig, data_ax, [x, y], xform='data') # mark bad
fig.canvas.key_press_event('down') # change selection
_fake_click(fig, fig.get_axes()[2], [0.5, 0.5]) # change channels
sel_fig = plt.figure(1)
topo_ax = sel_fig.axes[1]
_fake_click(sel_fig, topo_ax, [-0.425, 0.20223853], xform='data')
fig.canvas.key_press_event('down')
fig.canvas.key_press_event('up')
fig.canvas.scroll_event(0.5, 0.5, -1) # scroll down
fig.canvas.scroll_event(0.5, 0.5, 1) # scroll up
_fake_click(sel_fig, topo_ax, [-0.5, 0.], xform='data')
_fake_click(sel_fig, topo_ax, [0.5, 0.], xform='data', kind='motion')
_fake_click(sel_fig, topo_ax, [0.5, 0.5], xform='data', kind='motion')
_fake_click(sel_fig,
topo_ax, [-0.5, 0.5],
xform='data',
kind='release')
plt.close('all')
# test if meas_date is off
raw.set_meas_date(_dt_to_stamp(raw.info['meas_date'])[0])
annot = Annotations([1 + raw.first_samp / raw.info['sfreq']], [5], ['bad'])
with pytest.warns(RuntimeWarning, match='outside data range'):
raw.set_annotations(annot)
with pytest.warns(None): # sometimes projection
raw.plot(group_by='position', order=np.arange(8))
for fig_num in plt.get_fignums():
fig = plt.figure(fig_num)
if hasattr(fig, 'radio'): # Get access to selection fig.
break
for key in ['down', 'up', 'escape']:
fig.canvas.key_press_event(key)
raw._data[:] = np.nan
# this should (at least) not die, the output should pretty clearly show
# that there is a problem so probably okay to just plot something blank
with pytest.warns(None):
raw.plot(scalings='auto')
plt.close('all')
def test_plot_raw_traces(raw):
"""Test plotting of raw data."""
raw.info['lowpass'] = 10. # allow heavy decim during plotting
events = _get_events()
plt.close('all') # ensure all are closed
fig = raw.plot(events=events, order=[1, 7, 5, 2, 3], n_channels=3,
group_by='original')
assert hasattr(fig, 'mne') # make sure fig.mne param object is present
assert len(fig.axes) == 5
# setup
x = fig.mne.traces[0].get_xdata()[5]
y = fig.mne.traces[0].get_ydata()[5]
data_ax = fig.mne.ax_main
hscroll = fig.mne.ax_hscroll
vscroll = fig.mne.ax_vscroll
# test marking bad channels
label = fig.mne.ax_main.get_yticklabels()[0].get_text()
assert label not in fig.mne.info['bads']
_fake_click(fig, data_ax, [x, y], xform='data') # click data to mark bad
assert label in fig.mne.info['bads']
_fake_click(fig, data_ax, [x, y], xform='data') # click data to unmark bad
assert label not in fig.mne.info['bads']
_click_ch_name(fig, ch_index=0, button=1) # click name to mark bad
assert label in fig.mne.info['bads']
# test other kinds of clicks
_fake_click(fig, data_ax, [0.5, 0.999]) # click elsewhere (add vline)
_fake_click(fig, data_ax, [0.5, 0.999], button=3) # remove vline
_fake_click(fig, hscroll, [0.5, 0.5]) # change time
_fake_click(fig, hscroll, [0.5, 0.5]) # shouldn't change time this time
# test scrolling through channels
labels = [label.get_text() for label in data_ax.get_yticklabels()]
assert labels == [raw.ch_names[1], raw.ch_names[7], raw.ch_names[5]]
_fake_click(fig, vscroll, [0.5, 0.01]) # change channels to end
labels = [label.get_text() for label in data_ax.get_yticklabels()]
assert labels == [raw.ch_names[5], raw.ch_names[2], raw.ch_names[3]]
for _ in (0, 0):
# first click changes channels to mid; second time shouldn't change
_fake_click(fig, vscroll, [0.5, 0.5])
labels = [label.get_text() for label in data_ax.get_yticklabels()]
assert labels == [raw.ch_names[7], raw.ch_names[5], raw.ch_names[2]]
assert len(plt.get_fignums()) == 1
# test clicking a channel name in butterfly mode
bads = fig.mne.info['bads'].copy()
fig.canvas.key_press_event('b')
_click_ch_name(fig, ch_index=0, button=1) # should be no-op
assert fig.mne.info['bads'] == bads # unchanged
fig.canvas.key_press_event('b')
# test starting up in zen mode
fig = plot_raw(raw, show_scrollbars=False)
# test order, title, & show_options kwargs
with pytest.raises(ValueError, match='order should be array-like; got'):
raw.plot(order='foo')
with pytest.raises(TypeError, match='title must be None or a string, got'):
raw.plot(title=1)
raw.plot(show_options=True)
plt.close('all')
# Color setting
with pytest.raises(KeyError, match='must be strictly positive, or -1'):
raw.plot(event_color={0: 'r'})
with pytest.raises(TypeError, match='event_color key must be an int, got'):
raw.plot(event_color={'foo': 'r'})
annot = Annotations([10, 10 + raw.first_samp / raw.info['sfreq']],
[10, 10], ['test', 'test'], raw.info['meas_date'])
with pytest.warns(RuntimeWarning, match='outside data range'):
raw.set_annotations(annot)
fig = plot_raw(raw, events=events, event_color={-1: 'r', 998: 'b'})
plt.close('all')
for group_by, order in zip(['position', 'selection'],
[np.arange(len(raw.ch_names))[::-3],
[1, 2, 4, 6]]):
fig = raw.plot(group_by=group_by, order=order)
x = fig.get_axes()[0].lines[1].get_xdata()[10]
y = fig.get_axes()[0].lines[1].get_ydata()[10]
_fake_click(fig, data_ax, [x, y], xform='data') # mark bad
fig.canvas.key_press_event('down') # change selection
_fake_click(fig, fig.get_axes()[2], [0.5, 0.5]) # change channels
sel_fig = plt.figure(1)
topo_ax = sel_fig.axes[1]
_fake_click(sel_fig, topo_ax, [-0.425, 0.20223853],
xform='data')
fig.canvas.key_press_event('down')
fig.canvas.key_press_event('up')
fig.canvas.scroll_event(0.5, 0.5, -1) # scroll down
fig.canvas.scroll_event(0.5, 0.5, 1) # scroll up
_fake_click(sel_fig, topo_ax, [-0.5, 0.], xform='data')
_fake_click(sel_fig, topo_ax, [0.5, 0.], xform='data',
kind='motion')
_fake_click(sel_fig, topo_ax, [0.5, 0.5], xform='data',
kind='motion')
_fake_click(sel_fig, topo_ax, [-0.5, 0.5], xform='data',
kind='release')
plt.close('all')
# test if meas_date is off
raw.set_meas_date(_dt_to_stamp(raw.info['meas_date'])[0])
annot = Annotations([1 + raw.first_samp / raw.info['sfreq']],
[5], ['bad'])
with pytest.warns(RuntimeWarning, match='outside data range'):
raw.set_annotations(annot)
with pytest.warns(None): # sometimes projection
raw.plot(group_by='position', order=np.arange(8))
for fig_num in plt.get_fignums():
fig = plt.figure(fig_num)
if hasattr(fig, 'radio'): # Get access to selection fig.
break
for key in ['down', 'up', 'escape']:
fig.canvas.key_press_event(key)
raw._data[:] = np.nan
# this should (at least) not die, the output should pretty clearly show
# that there is a problem so probably okay to just plot something blank
with pytest.warns(None):
raw.plot(scalings='auto')
plt.close('all')
