"""Inspect and annotate BIDS raw data."""
# Authors: The MNE-BIDS developers
# SPDX-License-Identifier: BSD-3-Clause
from pathlib import Path
import mne
import numpy as np
from mne.preprocessing import annotate_amplitude
from mne.utils import logger, verbose
from mne.viz import use_browser_backend
from mne_bids import mark_channels, read_raw_bids
from mne_bids.config import ALLOWED_DATATYPE_EXTENSIONS
from mne_bids.read import _from_tsv, _read_events
from mne_bids.write import _events_tsv
[docs]
@verbose
def inspect_dataset(
bids_path,
find_flat=True,
l_freq=None,
h_freq=None,
show_annotations=True,
verbose=None,
):
"""Inspect and annotate BIDS raw data.
This function allows you to browse MEG, EEG, and iEEG raw data stored in a
BIDS dataset. You can toggle the status of a channel (bad or good) by
clicking on the traces, and when closing the browse window, you will be
asked whether you want to save the changes to the existing BIDS dataset or
discard them.
.. warning:: This functionality is still experimental and will be extended
in the future. Its API will likely change. Planned features
include automated bad channel detection and visualization of
MRI images.
.. note:: Currently, only MEG, EEG, and iEEG data can be inspected.
To add or modify annotations, press ``A`` to toggle annotation mode.
Parameters
----------
bids_path : BIDSPath
A :class:`mne_bids.BIDSPath` containing at least a ``root``. All
matching files will be inspected. To select only a subset of the data,
set more :class:`mne_bids.BIDSPath` attributes. If ``datatype`` is not
set and multiple datatypes are found, they will be inspected in the
following order: MEG, EEG, iEEG.
To read a specific file, set all the :class:`mne_bids.BIDSPath`
attributes required to uniquely identify the file: If this ``BIDSPath``
is accepted by :func:`mne_bids.read_raw_bids`, it will work here.
find_flat : bool
Whether to auto-detect channels producing "flat" signals, i.e., with
unusually low variability. Flat **segments** will be added to
``*_events.tsv``, while channels with more than 5 percent of flat data
will be marked as ``bad`` in ``*_channels.tsv``.
.. note::
This function calls ``mne.preprocessing.annotate_amplitude``
(MNE-Python 1.0 or newer) or ``mne.preprocessing.annotate_flat``
(older versions of MNE-Python)
and will only consider segments of at least **50 ms consecutive
flatness** as "flat" (deviating from MNE-Python's default of 5 ms).
If more than 5 percent of a channel's data has been marked as flat,
the entire channel will be added to the list of bad channels. Only
flat time segments applying to channels **not** marked as bad will
be added to ``*_events.tsv``.
l_freq : float | None
The high-pass filter cutoff frequency to apply when displaying the
data. This can be useful when inspecting data with slow drifts. If
``None``, no high-pass filter will be applied.
h_freq : float | None
The low-pass filter cutoff frequency to apply when displaying the
data. This can be useful when inspecting data with high-frequency
artifacts. If ``None``, no low-pass filter will be applied.
show_annotations : bool
Whether to show annotations (events, bad segments, …) or not. If
``False``, toggling annotations mode by pressing ``A`` will be disabled
as well.
%(verbose)s
Examples
--------
Disable flat channel & segment detection, and apply a filter with a
passband of 1–30 Hz.
>>> from mne_bids import BIDSPath
>>> root = Path('./mne_bids/tests/data/tiny_bids').absolute()
>>> bids_path = BIDSPath(subject='01', task='rest', session='eeg',
... suffix='eeg', extension='.vhdr', root=root)
>>> inspect_dataset(bids_path=bids_path, find_flat=False, # doctest: +SKIP
... l_freq=1, h_freq=30)
"""
allowed_extensions = set(
ALLOWED_DATATYPE_EXTENSIONS["meg"]
+ ALLOWED_DATATYPE_EXTENSIONS["eeg"]
+ ALLOWED_DATATYPE_EXTENSIONS["ieeg"]
)
bids_paths = [
p
for p in bids_path.match(check=True)
if (p.extension is None or p.extension in allowed_extensions)
and p.acquisition != "crosstalk"
]
for bids_path_ in bids_paths:
_inspect_raw(
bids_path=bids_path_,
l_freq=l_freq,
h_freq=h_freq,
find_flat=find_flat,
show_annotations=show_annotations,
)
# XXX This this should probably be refactored into a class attribute someday.
_global_vars = dict(raw_fig=None, dialog_fig=None, mne_close_key=None)
# do you think we should expose the verbose of this functions?
@verbose
def _inspect_raw(
*, bids_path, l_freq, h_freq, find_flat, show_annotations, verbose=None
):
"""Raw data inspection."""
# Delay the import
import matplotlib
import matplotlib.pyplot as plt
extra_params = dict()
if bids_path.extension == ".fif":
extra_params["allow_maxshield"] = "yes"
raw = read_raw_bids(bids_path, extra_params=extra_params, verbose="error")
old_bads = raw.info["bads"].copy()
old_annotations = raw.annotations.copy()
if find_flat:
raw.load_data() # Speeds up processing dramatically
flat_annot, flat_chans = annotate_amplitude(
raw=raw, flat=0, min_duration=0.05, bad_percent=5
)
new_annot = raw.annotations + flat_annot
raw.set_annotations(new_annot)
raw.info["bads"] = list(set(raw.info["bads"] + flat_chans))
del new_annot, flat_annot
else:
flat_chans = []
show_options = bids_path.datatype == "meg"
with use_browser_backend("matplotlib"):
fig = raw.plot(
title=f"{bids_path.root.name}: {bids_path.basename}",
highpass=l_freq,
lowpass=h_freq,
show_options=show_options,
block=False,
show=False,
verbose="warning",
)
# Add our own event handlers so that when the MNE Raw Browser is being
# closed, our dialog box will pop up, asking whether to save changes.
def _handle_close(event):
mne_raw_fig = event.canvas.figure
# Bads alterations are only transferred to `inst` once the figure is
# closed; Annotation changes are immediately reflected in `inst`
new_bads = mne_raw_fig.mne.info["bads"].copy()
new_annotations = mne_raw_fig.mne.inst.annotations.copy()
if not new_annotations:
# Ensure it's not an empty list, but an empty set of Annotations.
new_annotations = mne.Annotations(
onset=[],
duration=[],
description=[],
orig_time=mne_raw_fig.mne.info["meas_date"],
)
_save_raw_if_changed(
old_bads=old_bads,
new_bads=new_bads,
flat_chans=flat_chans,
old_annotations=old_annotations,
new_annotations=new_annotations,
bids_path=bids_path,
)
_global_vars["raw_fig"] = None
def _keypress_callback(event):
if event.key == _global_vars["mne_close_key"]:
_handle_close(event)
fig.canvas.mpl_connect("close_event", _handle_close)
fig.canvas.mpl_connect("key_press_event", _keypress_callback)
if not show_annotations:
# Remove annotations and kill `_toggle_annotation_fig` method, since
# we cannot directly and easily remove the associated `a` keyboard
# event callback.
fig._clear_annotations()
fig._toggle_annotation_fig = lambda: None
# Ensure it's not an empty list, but an empty set of Annotations.
old_annotations = mne.Annotations(
onset=[], duration=[], description=[], orig_time=raw.info["meas_date"]
)
if matplotlib.get_backend().lower() != "agg":
plt.show(block=True)
_global_vars["raw_fig"] = fig
_global_vars["mne_close_key"] = fig.mne.close_key
def _annotations_almost_equal(old_annotations, new_annotations):
"""Allow for a tiny bit of floating point precision loss."""
if (
np.array_equal(old_annotations.description, new_annotations.description)
and np.array_equal(old_annotations.orig_time, new_annotations.orig_time)
and np.allclose(old_annotations.onset, new_annotations.onset)
and np.allclose(old_annotations.duration, new_annotations.duration)
):
return True
else:
return False
def _save_annotations(*, annotations, bids_path):
# Attach the new Annotations to our raw data so we can easily convert them
# to events, which will be stored in the *_events.tsv sidecar.
extra_params = dict()
if bids_path.extension == ".fif":
extra_params["allow_maxshield"] = "yes"
raw = read_raw_bids(
bids_path=bids_path, extra_params=extra_params, verbose="warning"
)
raw.set_annotations(annotations)
events, durs, descrs = _read_events(
events=None, event_id=None, bids_path=bids_path, raw=raw
)
# Write sidecar – or remove it if no events are left.
events_tsv_fname = bids_path.copy().update(suffix="events", extension=".tsv").fpath
if len(events) > 0:
_events_tsv(
events=events,
durations=durs,
raw=raw,
fname=events_tsv_fname,
trial_type=descrs,
overwrite=True,
)
elif events_tsv_fname.exists():
logger.info(
f"No events remaining after interactive inspection, "
f"removing {events_tsv_fname.name}"
)
events_tsv_fname.unlink()
def _save_raw_if_changed(
*, old_bads, new_bads, flat_chans, old_annotations, new_annotations, bids_path
):
"""Save bad channel selection if it has been changed.
Parameters
----------
old_bads : list
The original bad channels.
new_bads : list
The updated set of bad channels (i.e. **all** of them, not only the
changed ones).
flat_chans : list
The auto-detected flat channels. This is either an empty list or a
subset of ``new_bads``.
old_annotations : mne.Annotations
The original Annotations.
new_annotations : mne.Annotations
The new Annotations.
"""
assert set(flat_chans).issubset(set(new_bads))
if set(old_bads) == set(new_bads):
bads = None
bad_descriptions = []
else:
bads = new_bads
bad_descriptions = []
# Generate entries for the `status_description` column.
channels_tsv_fname = (
bids_path.copy().update(suffix="channels", extension=".tsv").fpath
)
channels_tsv_data = _from_tsv(channels_tsv_fname)
for ch_name in bads:
idx = channels_tsv_data["name"].index(ch_name)
if channels_tsv_data["status"][idx] == "bad":
# Channel was already marked as bad in the data, so retain
# existing description.
description = channels_tsv_data["status_description"][idx]
elif ch_name in flat_chans:
description = "Flat channel, auto-detected via MNE-BIDS"
else:
# Channel has been manually marked as bad during inspection
description = "Interactive inspection via MNE-BIDS"
bad_descriptions.append(description)
del ch_name, description
del (
channels_tsv_data,
channels_tsv_fname,
)
if _annotations_almost_equal(old_annotations, new_annotations):
annotations = None
else:
annotations = new_annotations
if bads is None and annotations is None:
# Nothing has changed, so we can just exit.
return None
return _save_raw_dialog_box(
bads=bads,
bad_descriptions=bad_descriptions,
annotations=annotations,
bids_path=bids_path,
)
def _save_raw_dialog_box(*, bads, bad_descriptions, annotations, bids_path):
"""Display a dialog box asking whether to save the changes."""
# Delay the imports
import matplotlib
import matplotlib.pyplot as plt
from matplotlib.widgets import Button
from mne.viz.utils import figure_nobar
title = "Save changes?"
message = "You have modified "
if bads is not None and annotations is None:
message += "the bad channel selection "
figsize = (7.5, 2.5)
elif bads is None and annotations is not None:
message += "the bad segments selection "
figsize = (7.5, 2.5)
else:
message += "the bad channel and\nannotations selection "
figsize = (8.5, 3)
message += (
f"of\n"
f"{bids_path.basename}.\n\n"
f"Would you like to save these changes to the\n"
f"BIDS dataset?"
)
icon_fname = str(Path(__file__).parent / "assets" / "help-128px.png")
icon = plt.imread(icon_fname)
fig = figure_nobar(figsize=figsize)
fig.canvas.manager.set_window_title("MNE-BIDS Inspector")
fig.suptitle(title, y=0.95, fontsize="xx-large", fontweight="bold")
gs = fig.add_gridspec(1, 2, width_ratios=(1.5, 5))
# The dialog box tet.
ax_msg = fig.add_subplot(gs[0, 1])
ax_msg.text(
x=0,
y=0.8,
s=message,
fontsize="large",
verticalalignment="top",
horizontalalignment="left",
multialignment="left",
)
ax_msg.axis("off")
# The help icon.
ax_icon = fig.add_subplot(gs[0, 0])
ax_icon.imshow(icon)
ax_icon.axis("off")
# Buttons.
ax_save = fig.add_axes([0.6, 0.05, 0.3, 0.1])
ax_dont_save = fig.add_axes([0.1, 0.05, 0.3, 0.1])
save_button = Button(ax=ax_save, label="Save")
save_button.label.set_fontsize("medium")
save_button.label.set_fontweight("bold")
dont_save_button = Button(ax=ax_dont_save, label="Don't save")
dont_save_button.label.set_fontsize("medium")
dont_save_button.label.set_fontweight("bold")
# Store references to keep buttons alive.
fig.save_button = save_button
fig.dont_save_button = dont_save_button
# Define callback functions.
def _save_callback(event):
plt.close(event.canvas.figure) # Close dialog
_global_vars["dialog_fig"] = None
if bads is not None:
_save_bads(bads=bads, descriptions=bad_descriptions, bids_path=bids_path)
if annotations is not None:
_save_annotations(annotations=annotations, bids_path=bids_path)
def _dont_save_callback(event):
plt.close(event.canvas.figure) # Close dialog
_global_vars["dialog_fig"] = None
def _keypress_callback(event):
if event.key in ["enter", "return"]:
_save_callback(event)
elif event.key == _global_vars["mne_close_key"]:
_dont_save_callback(event)
# Connect events to callback functions.
save_button.on_clicked(_save_callback)
dont_save_button.on_clicked(_dont_save_callback)
fig.canvas.mpl_connect("close_event", _dont_save_callback)
fig.canvas.mpl_connect("key_press_event", _keypress_callback)
if matplotlib.get_backend().lower() != "agg":
fig.show()
_global_vars["dialog_fig"] = fig
def _save_bads(*, bads, descriptions, bids_path):
"""Update the set of channels marked as bad.
Parameters
----------
bads : list
The complete list of bad channels.
descriptions : list
The values to be written to the `status_description` column.
"""
# We first make all channels not passed as bad here to be marked as good.
mark_channels(bids_path=bids_path, ch_names="all", status="good")
mark_channels(
bids_path=bids_path, ch_names=bads, status="bad", descriptions=descriptions
)