def test_inspect_bads_and_annotations(tmp_path):
"""Test adding bads and Annotations in one go."""
from mne.utils._testing import _click_ch_name
import matplotlib
import matplotlib.pyplot as plt
matplotlib.use('Agg')
plt.close('all')
bids_root = setup_bids_test_dir(tmp_path)
bids_path = _bids_path.copy().update(root=bids_root)
raw = read_raw_bids(bids_path=bids_path, verbose='error')
orig_bads = raw.info['bads'].copy()
inspect_dataset(bids_path, find_flat=False)
raw_fig = mne_bids.inspect._global_vars['raw_fig']
# Mark some channels as bad by clicking on their name.
_click_ch_name(raw_fig, ch_index=0, button=1)
# Add custom Annotation.
_add_annotation(raw_fig)
# Close window and save changes.
raw_fig.canvas.key_press_event(raw_fig.mne.close_key)
fig_dialog = mne_bids.inspect._global_vars['dialog_fig']
fig_dialog.canvas.key_press_event('return')
# Check that the changes were saved.
raw = read_raw_bids(bids_path=bids_path, verbose='error')
new_bads = raw.info['bads']
expected_bads = orig_bads + ['MEG 0113']
assert set(new_bads) == set(expected_bads)
assert 'BAD_test' in raw.annotations.description
def test_inspect_single_file(return_bids_test_dir, save_changes):
from mne.utils._testing import _click_ch_name
import matplotlib
matplotlib.use('Agg')
bids_path = _bids_path.copy().update(root=return_bids_test_dir)
raw = read_raw_bids(bids_path=bids_path, verbose='error')
old_bads = raw.info['bads'].copy()
inspect_dataset(bids_path)
raw_fig = mne_bids.inspect._global_vars['raw_fig']
# Mark some channels as bad by clicking on their name.
_click_ch_name(raw_fig, ch_index=0, button=1)
_click_ch_name(raw_fig, ch_index=1, button=1)
_click_ch_name(raw_fig, ch_index=4, button=1)
# Closing the window should open a dialog box.
raw_fig.canvas.key_press_event(raw_fig.mne.close_key)
fig_dialog = mne_bids.inspect._global_vars['dialog_fig']
if save_changes:
key = 'return'
else:
key = 'escape'
fig_dialog.canvas.key_press_event(key)
raw = read_raw_bids(bids_path=bids_path, verbose='error')
new_bads = raw.info['bads'].copy()
if save_changes:
assert len(new_bads) > len(old_bads)
else:
assert old_bads == new_bads
def test_inspect_dont_show_annotations(tmp_path):
"""Test if show_annotations=False works."""
import matplotlib
import matplotlib.pyplot as plt
matplotlib.use('Agg')
plt.close('all')
bids_root = setup_bids_test_dir(tmp_path)
bids_path = _bids_path.copy().update(root=bids_root)
inspect_dataset(bids_path, find_flat=False, show_annotations=False)
raw_fig = mne_bids.inspect._global_vars['raw_fig']
assert not raw_fig.mne.annotations
def test_inspect_annotations_remove_all(tmp_path):
"""Test behavior if all Annotations are removed by the user."""
import matplotlib
import matplotlib.pyplot as plt
matplotlib.use('Agg')
plt.close('all')
bids_root = setup_bids_test_dir(tmp_path)
bids_path = _bids_path.copy().update(root=bids_root)
events_tsv_fpath = (bids_path.copy().update(suffix='events',
extension='.tsv').fpath)
# Remove all Annotations.
raw = read_raw_bids(bids_path=bids_path, verbose='error')
raw.set_annotations(None)
raw.load_data()
raw.save(raw.filenames[0], overwrite=True)
# Delete events.tsv sidecar.
(bids_path.copy().update(suffix='events', extension='.tsv').fpath.unlink())
# Add custom Annotation.
inspect_dataset(bids_path, find_flat=False)
raw_fig = mne_bids.inspect._global_vars['raw_fig']
_add_annotation(raw_fig)
# Close window and save changes.
raw_fig.canvas.key_press_event(raw_fig.mne.close_key)
fig_dialog = mne_bids.inspect._global_vars['dialog_fig']
fig_dialog.canvas.key_press_event('return')
# events.tsv sidecar should have been created.
assert events_tsv_fpath.exists()
# Remove the Annotation.
inspect_dataset(bids_path, find_flat=False)
raw_fig = mne_bids.inspect._global_vars['raw_fig']
data_ax = raw_fig.mne.ax_main
raw_fig.canvas.key_press_event('a') # Toggle Annotation mode
_fake_click(raw_fig,
data_ax, [1., 1.],
xform='data',
button=3,
kind='press')
# Close window and save changes.
raw_fig.canvas.key_press_event(raw_fig.mne.close_key)
fig_dialog = mne_bids.inspect._global_vars['dialog_fig']
fig_dialog.canvas.key_press_event('return')
# events.tsv sidecar should not exist anymore.
assert not events_tsv_fpath.exists()
def test_inspect_auto_flats(tmp_path, save_changes):
"""Test flat channel & segment detection."""
import matplotlib
import matplotlib.pyplot as plt
matplotlib.use('Agg')
plt.close('all')
bids_root = setup_bids_test_dir(tmp_path)
bids_path = _bids_path.copy().update(root=bids_root)
channels_tsv_fname = bids_path.copy().update(suffix='channels',
extension='.tsv')
raw = read_raw_bids(bids_path=bids_path, verbose='error')
# Inject an entirely flat channel.
raw.load_data()
raw._data[10] = np.zeros_like(raw._data[10], dtype=raw._data.dtype)
# Add a a flat time segment (approx. 100 ms) to another channel
raw._data[20, 500:500 + int(np.ceil(0.1 * raw.info['sfreq']))] = 0
raw.save(raw.filenames[0], overwrite=True)
old_bads = raw.info['bads'].copy()
inspect_dataset(bids_path)
raw_fig = mne_bids.inspect._global_vars['raw_fig']
# Closing the window should open a dialog box.
raw_fig.canvas.key_press_event(raw_fig.mne.close_key)
fig_dialog = mne_bids.inspect._global_vars['dialog_fig']
if save_changes:
key = 'return'
else:
key = 'escape'
fig_dialog.canvas.key_press_event(key)
raw = read_raw_bids(bids_path=bids_path, verbose='error')
if save_changes:
assert old_bads != raw.info['bads']
assert raw.ch_names[10] in raw.info['bads']
channels_tsv_data = _from_tsv(channels_tsv_fname)
assert (channels_tsv_data['status_description'][10] ==
'Flat channel, auto-detected via MNE-BIDS')
# This channel should not have been added to `bads`, but produced a
# flat annotation.
assert raw.ch_names[20] not in raw.info['bads']
assert 'BAD_flat' in raw.annotations.description
else:
assert old_bads == raw.info['bads']
assert 'BAD_flat' not in raw.annotations.description
def test_inspect_multiple_files(return_bids_test_dir):
import matplotlib
matplotlib.use('Agg')
bids_path = _bids_path.copy().update(root=return_bids_test_dir)
# Create a second subject
raw = read_raw_bids(bids_path=bids_path, verbose='error')
write_raw_bids(raw, bids_path.copy().update(subject='02'))
del raw
# Inspection should end with the second subject.
inspect_dataset(bids_path.copy().update(subject=None))
raw_fig = mne_bids.inspect._global_vars['raw_fig']
assert raw_fig.mne.info['subject_info']['participant_id'] == 'sub-02'
raw_fig.canvas.key_press_event(raw_fig.mne.close_key)
def test_inspect_annotations(tmp_path):
"""Test inspection of Annotations."""
import matplotlib
import matplotlib.pyplot as plt
matplotlib.use('Agg')
plt.close('all')
bids_root = setup_bids_test_dir(tmp_path)
bids_path = _bids_path.copy().update(root=bids_root)
raw = read_raw_bids(bids_path=bids_path, verbose='error')
orig_annotations = raw.annotations.copy()
inspect_dataset(bids_path, find_flat=False)
raw_fig = mne_bids.inspect._global_vars['raw_fig']
_add_annotation(raw_fig)
# Close window and save changes.
raw_fig.canvas.key_press_event(raw_fig.mne.close_key)
fig_dialog = mne_bids.inspect._global_vars['dialog_fig']
fig_dialog.canvas.key_press_event('return')
# Ensure changes were saved.
raw = read_raw_bids(bids_path=bids_path, verbose='error')
assert 'BAD_test' in raw.annotations.description
annot_idx = raw.annotations.description == 'BAD_test'
assert raw.annotations.duration[annot_idx].squeeze() == 4
# Remove the Annotation.
inspect_dataset(bids_path, find_flat=False)
raw_fig = mne_bids.inspect._global_vars['raw_fig']
data_ax = raw_fig.mne.ax_main
raw_fig.canvas.key_press_event('a') # Toggle Annotation mode
_fake_click(raw_fig,
data_ax, [1., 1.],
xform='data',
button=3,
kind='press')
# Close window and save changes.
raw_fig.canvas.key_press_event(raw_fig.mne.close_key)
fig_dialog = mne_bids.inspect._global_vars['dialog_fig']
fig_dialog.canvas.key_press_event('return')
# Ensure changes were saved.
raw = read_raw_bids(bids_path=bids_path, verbose='error')
assert 'BAD_test' not in raw.annotations.description
assert raw.annotations == orig_annotations
def test_inspect_set_and_unset_bads(tmp_path):
"""Test marking channels as bad and later marking them as good again."""
from mne.utils._testing import _click_ch_name
import matplotlib
import matplotlib.pyplot as plt
matplotlib.use('Agg')
plt.close('all')
bids_root = setup_bids_test_dir(tmp_path)
bids_path = _bids_path.copy().update(root=bids_root)
raw = read_raw_bids(bids_path=bids_path, verbose='error')
orig_bads = raw.info['bads'].copy()
# Mark some channels as bad by clicking on their name.
inspect_dataset(bids_path, find_flat=False)
raw_fig = mne_bids.inspect._global_vars['raw_fig']
_click_ch_name(raw_fig, ch_index=0, button=1)
_click_ch_name(raw_fig, ch_index=1, button=1)
_click_ch_name(raw_fig, ch_index=4, button=1)
# Close window and save changes.
raw_fig.canvas.key_press_event(raw_fig.mne.close_key)
fig_dialog = mne_bids.inspect._global_vars['dialog_fig']
fig_dialog.canvas.key_press_event('return')
# Inspect the data again, click on two of the bad channels to mark them as
# good.
inspect_dataset(bids_path, find_flat=False)
raw_fig = mne_bids.inspect._global_vars['raw_fig']
_click_ch_name(raw_fig, ch_index=1, button=1)
_click_ch_name(raw_fig, ch_index=4, button=1)
# Close window and save changes.
raw_fig.canvas.key_press_event(raw_fig.mne.close_key)
fig_dialog = mne_bids.inspect._global_vars['dialog_fig']
fig_dialog.canvas.key_press_event('return')
# Check marking the channels as good has actually worked.
expected_bads = orig_bads + ['MEG 0113']
raw = read_raw_bids(bids_path=bids_path, verbose='error')
new_bads = raw.info['bads']
assert set(new_bads) == set(expected_bads)
def test_inspect_multiple_files(tmp_path):
"""Test inspecting a dataset consisting of more than one file."""
import matplotlib
import matplotlib.pyplot as plt
matplotlib.use('Agg')
plt.close('all')
bids_root = setup_bids_test_dir(tmp_path)
bids_path = _bids_path.copy().update(root=bids_root)
# Create a second subject
raw = read_raw_bids(bids_path=bids_path, verbose='error')
write_raw_bids(raw, bids_path.copy().update(subject='02'))
del raw
# Inspection should end with the second subject.
inspect_dataset(bids_path.copy().update(subject=None))
raw_fig = mne_bids.inspect._global_vars['raw_fig']
assert raw_fig.mne.info['subject_info']['participant_id'] == 'sub-02'
raw_fig.canvas.key_press_event(raw_fig.mne.close_key)
def run():
"""Run the mark_channels command."""
from mne.commands.utils import get_optparser
parser = get_optparser(__file__, usage="usage: %prog options args",
prog_prefix='mne_bids',
version=mne_bids.__version__)
parser.add_option('--bids_root', dest='bids_root',
help='The path of the folder containing the BIDS '
'dataset')
parser.add_option('--subject_id', dest='subject',
help=('Subject name'))
parser.add_option('--session_id', dest='session',
help='Session name')
parser.add_option('--task', dest='task',
help='Task name')
parser.add_option('--acq', dest='acquisition',
help='Acquisition parameter')
parser.add_option('--run', dest='run',
help='Run number')
parser.add_option('--proc', dest='processing',
help='Processing label.')
parser.add_option('--rec', dest='recording',
help='Recording name')
parser.add_option('--type', dest='datatype',
help='Recording data type, e.g. meg, ieeg or eeg')
parser.add_option('--suffix', dest='suffix',
help='The filename suffix, i.e. the last part before '
'the extension')
parser.add_option('--ext', dest='extension',
help='The filename extension, including the leading '
'period, e.g. .fif')
parser.add_option('--find_flat', dest='find_flat',
help='Whether to auto-detect flat channels and time '
'segments')
parser.add_option('--l_freq', dest='l_freq',
help='The high-pass filter cutoff frequency')
parser.add_option('--h_freq', dest='h_freq',
help='The low-pass filter cutoff frequency')
parser.add_option('--verbose', dest='verbose', action='store_true',
help='Whether do generate additional diagnostic output')
opt, args = parser.parse_args()
if args:
parser.print_help()
parser.error(f'Please do not specify arguments without flags. '
f'Got: {args}.\n')
if opt.bids_root is None:
parser.print_help()
parser.error('You must specify bids_root')
bids_path = BIDSPath(subject=opt.subject, session=opt.session,
task=opt.task, acquisition=opt.acquisition,
run=opt.run, processing=opt.processing,
recording=opt.recording, datatype=opt.datatype,
suffix=opt.suffix, extension=opt.extension,
root=opt.bids_root)
find_flat = True if opt.find_flat is None else bool(opt.find_flat)
l_freq = None if opt.l_freq is None else float(opt.l_freq)
h_freq = None if opt.h_freq is None else float(opt.h_freq)
logger.info(f'Inspecting {bids_path.basename} …')
inspect_dataset(bids_path=bids_path, find_flat=find_flat,
l_freq=l_freq, h_freq=h_freq,
verbose=opt.verbose)
raw.info['line_freq'] = 60 # Specify power line frequency as required by BIDS. write_raw_bids(raw, bids_path=bids_path, overwrite=True, verbose=False) ############################################################################### # Interactive use # --------------- # # Using :func:`mne_bids.inspect_dataset`, we can interactively explore the raw # data and toggle the channel status – ``bad`` or ``good`` – by clicking on the # respective traces or channel names. If there are any SSP projectors stored # with the data, a small popup window will allow you to toggle the projectors # on and off. If you changed the selection of bad channels, you will be # prompted whether you would like to save the changes when closing the main # window. inspect_dataset(bids_path) ############################################################################### # You can even apply frequency filters when viewing the data: A high-pass # filter can remove slow drifts, while a low-pass filter will get rid of # high-frequency artifacts. This can make visual inspection easier. Let's # apply filters with a 1-Hz high-pass cutoff, and a 30-Hz low-pass cutoff: inspect_dataset(bids_path, l_freq=1., h_freq=30.) ############################################################################### # Non-interactive (programmatic) bad channel selection # ---------------------------------------------------- # # Read the (now BIDS-formatted) data and print a list of channels currently # marked as bad.
def test_inspect_freq_filter(return_bids_test_dir, l_freq, h_freq):
bids_path = _bids_path.copy().update(root=return_bids_test_dir)
inspect_dataset(bids_path, l_freq=l_freq, h_freq=h_freq)
def test_inspect_freq_filter(tmp_path, l_freq, h_freq):
"""Test frequency filter for Raw display."""
bids_root = setup_bids_test_dir(tmp_path)
bids_path = _bids_path.copy().update(root=bids_root)
inspect_dataset(bids_path, l_freq=l_freq, h_freq=h_freq, find_flat=False)
