nwb file surgery - electrodes "bad_channel"

[gshvarts]

Hi! As I mentioned earlier, I'm trying to update some values in the electrodes part of many of our nwbs, specifically the bad_channel values, based on newly-updated yaml files. How would you recommend going about updating those before re-inserting them into spyglass? Thanks!

[samuelbray32]

Here's steps to change values in the electrode table without re-writing the whole file:

1. Load in the file and make an array with the updated values

from pynwb import NWBHDF5IO
file_path = "/stelmo/sam/dummy.nwb"

# load the current electrodes dataframe
with NWBHDF5IO(file_path,"r") as io:
    nwb = io.read()
    electrodes_df = nwb.electrodes.to_dataframe()
    current_bad_channels = electrodes_df.bad_channel.values


# make an array with the needed changes to the dataframe column
new_bad_channels = current_bad_channels.copy()
new_bad_channels[11] = True

2. Make the edits through h5py

import h5py
# change the values in the file to the new values
with h5py.File(file_path, "a") as file:
    print(file["general"]["extracellular_ephys"]["electrodes"]["bad_channel"][:])
    file["general"]["extracellular_ephys"]["electrodes"]["bad_channel"][:] = new_bad_channels

3. confirm the changes

# confirm the change
with NWBHDF5IO(file_path,"r") as io:
    nwb = io.read()
    assert (nwb.electrodes.to_dataframe().bad_channel.values == new_bad_channels).all()

[edeno]

Moved this to a discussion in case it's helpful for future folks.

[gshvarts]

Awesome, thanks @samuelbray32 !