CSD: session.get_current_source_density() hanging

Technical
, , ,
4

@eabhorrocks

Thanks for your patience!

I tried session.get_current_source_density() with session 719161530 and for probe id 729445648 using AllenSDK 1.6.0 and Python 3.7.7 and was able to get CSD data from the NWB file from my home computer. What follows is a guess as to what may have gone wrong as well as some additional troubleshooting tips:

  1. The CSD data is stored on a NWB file (which are typically multiple gigabytes) that is separate from the session NWB data. So the ‘hanging’ you experience, may be the AllenSDK trying to download a separate probe NWB file.

  2. If your download speed is not great, you may also want to set a longer duration for the NWB download timeout (which defaults to 10 minutes before giving up on a download). You can find an example code snippet for setting a custom download timeout here: Failed to get session data

  3. You can add the following snippet at the start of a script or notebook to get more information about what the AllenSDK is doing in the background. As mentioned in 1. I suspect when you call get_current_source_density() the logging will show the AllenSDK taking a while to download the separate probe NWB file that I mentioned.

import logging
logging.getLogger().setLevel(logging.DEBUG)

Let me know though if you are still encountering issues!