Currently bad channels can be detected if selected as part of the pipeline but it might be nice to always detect these and give a warning they exist. This could prompt people to exclude these. something like
def handle_bad_channels(data: Data):
"""
Placeholder function to begin handling bad channel detection. Even if not
requested, it will always be useful to highlight the bad channels.
However, it is not clear whether to print these / log these / provide simple
API argument to remove bad channels.
TODO
----
Need to determine when best to run this detection. Definately after
filtering, need to ask on Slack
see https://spikeinterface.readthedocs.io/en/latest/api.html
https://github.com/int-brain-lab/ibl-neuropixel/blob/d913ede52117bc79d \
e77f8dc9cdb407807ab8a8c/src/neurodsp/voltage.py#L445
"""
bad_channels = spre.detect_bad_channels(data["0-raw"])
utils.message_user(
f"\nThe following channels were detected as dead / noise: {bad_channels[0]}\n"
f"TODO: DO SOMETHING BETTER WITH THIS INFORMATION. SAVE IT SOMEHWERE\n"
f"You may like to automatically remove bad channels "
f"by setting [TO IMPLEMENT]] as a preprocessing option\n"
f"TODO: check how this is handled in SI\n"
)
JoeZiminski
commented
1 year ago
Currently bad channels can be detected if selected as part of the pipeline but it might be nice to always detect these and give a warning they exist. This could prompt people to exclude these. something like