se.read_openephys ValueError: invalid literal for int() spikeinterface 0.98.1

[gmaggi]

Hi,

I was testing the extractor for a spikeinterface user. I got this error

In [6]: se.read_openephys(Path("/mnt/takeokalab/takeokalabwip2023/JJ/20230706/"))
---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
Cell In[6], line 1
----> 1 se.read_openephys(Path("/mnt/takeokalab/takeokalabwip2023/JJ/20230706/"))

And at the end:

File /opt/anaconda/anaconda3/envs/spikeinterfacefull_0.98.1/lib/python3.10/site-packages/neo/rawio/openephysbinaryrawio.py:481, in explore_folder(dirname, experiment_names)
    479 experiment_folder = root.parents[0]
    480 experiment_name = experiment_folder.stem
--> 481 experiment_id = int(experiment_name.replace('experiment', ''))
    482 if experiment_name not in possible_experiment_names:
    483     possible_experiment_names.append(experiment_name)

ValueError: invalid literal for int() with base 10: 'JJ'

The content of the dir is:

ls /mnt/takeokalab/takeokalabwip2023/JJ/20230706
continuous.dat  continuous.nrs  continuous.xml  sample_numbers.npy  structure.oebin

Any idea what could be? Thanks in advance!

[alejoe91]

Yes. The open ephys outputs a folder structure as follows:

record node -> experiment{experimentID} -> recording{recordingID} -> continuous

The structure.oebin is in the recording{recordingID}, the .dat and .npy files in the continuous. The folder that you have is a mix and has been probably manually modified so it's not a valid Open Ephys folder, unfortunately.

[gmaggi]

Thank you!. I am waiting for the user feedback. Feel free to close this ticket.

[alejoe91]

Closing then :)