SpikeSortingLoader has no raw_electrophysiology attribute error

1

I can’t use the streaming of lfp tutorial. I have updates both ibllib and brainbox. I am trying to stream the lfp around a certain event but I get an error stating that SpikeSortingLoader has no raw_electrophysiology attribute.

ibllib is version 2.35.2, brainbox is version 0.0.7 in my environment. I just upgraded them and it did not fix the error.

Code:

from one.api import ONE

from brainbox.io.one import SpikeSortingLoader

import matplotlib.pyplot as plt

import scipy.signal

from brainbox.ephys_plots import plot_brain_regions

from ibllib.plots import Density
ssl = SpikeSortingLoader(pid=probe_id, one=one)

# The channels information is contained in a dict table / dataframe

channels = ssl.load_channels()

# Get AP and LFP spikeglx.Reader objects

sr_lf = ssl.raw_electrophysiology(band="lf", stream=True)

Error:
--------------------------------------------------------------------------- AttributeError Traceback (most recent call last) Cell In[48], [line 6](vscode-notebook-cell:?execution_count=48&line=6) [3](vscode-notebook-cell:?execution_count=48&line=3) channels = ssl.load_channels() [5](vscode-notebook-cell:?execution_count=48&line=5) # Get AP and LFP spikeglx.Reader objects ----> [6](vscode-notebook-cell:?execution_count=48&line=6) sr_lf = ssl.raw_electrophysiology(band="lf", stream=True) AttributeError: 'SpikeSortingLoader' object has no attribute 'raw_electrophysiology'

Note I am planning on plotting using this code later, I do not need the ap.

Plotting to do:

sos_lf = scipy.signal.butter(3,   2 / sr_lf.fs /2, btype='highpass', output='sos')  #   2 Hz high pass LF band
filtered_lf = scipy.signal.sosfiltfilt(sos_lf, raw_lf)

# displays the AP band and LFP band around this stim_on event
fig, ax = plt.subplots(figsize=(9, 6))
Density(- filtered_lf, fs=sr_lf.fs, taxis=1, ax=ax)
plot_brain_regions(channels["atlas_id"], channel_depths=channels["axial_um"], ax=ax, display=True)
2

Hello,

To investigate further, could you please run the following in a Python shell with your environment ?

from pathlib import Path
import ibllib
print(ibllib.__version__)
print(ibllib.__file__)

import brainbox
print(brainbox.__file__)


assert Path(*Path(brainbox.__file__).parts[:-2]) == Path(*Path(ibllib.__file__).parts[:-2]),\
    'oops it seems brainbox and ibllib are not in the same package'

And the following in a terminal:
pip list | grep brainbox
pip list | grep ibllib

I wonder if there could be this brainbox package that is still free floating in your environment.

If you are not using it then just unistall it pip uninstall brainbox.

3

Gave me the following output…

2.35.2
/home/acampbell/miniconda3/envs/ONE_ibl_env/lib/python3.10/site-packages/ibllib/__init__.py
/home/acampbell/miniconda3/envs/ONE_ibl_env/lib/python3.10/site-packages/brainbox/__init__.py

Yes that could be the issue if that old brainbox is still in there, or if some paths are still going to it.