python-neo icon indicating copy to clipboard operation
python-neo copied to clipboard

Published 20 hours ago • verified publisher icon NeuralEnsemble

BiocamIO: support sparse event based recordings

Open mahlzahn opened this issue 10 months ago • 9 comments

This PR includes some code extracted from the 3Brain documentation and added with kind permission by 3Brain.

I wrote:

I am contributing to the inclusion of reading recordings from 3brain with python-neo, probeinterface and spikeinterface. May I ask you the permission to

  1. include the example code in python-neo under the BSD 3-Clause License https://github.com/NeuralEnsemble/python-neo
  2. upload the latest file documentation to https://gin.g-node.org/NeuralEnsemble/ephy_testing_data/src/master/biocam

and got the answer:

Regarding your request for permission, yes, please, you can upload your files.

mahlzahn avatar Mar 27 '24 14:03 mahlzahn

@mahlzahn, just wanted to ping you to see if you have the bandwidth to work on our comments?

zm711 avatar May 29 '24 09:05 zm711

Since I can't directly contribute to the PR, I forked it and make some updates here. Opening a separate PR might be a bit messy ?

The main improvement is exposing a use_synthetic_noise argument, as well as true_zeroes. The latter, when False, makes sure that zeroes are actually read as zeroes once the recording is converted from unsigned to signed.

Regarding some of the other comments, I'm still not sure what if stdDev is None: (here) is meant for.

Also, if we indexed the data as [j - startFrame, chIdx] instead of [chIdx][j - startFrame] and intialized the array as np.zeros((numFrames, nch)), I don't think we would need to transpose when returning the filled array ? Not sure how much overhead it actually adds, the bit-by-bit parsing is slow enough as is.

b-grimaud avatar Jun 10 '24 17:06 b-grimaud

I'm honestly neutral on keeping with this PR or opening a new one. If @mahlzahn doesn't have the bandwidth then a new PR that will be worked on is an okay number. Do you want to comment on if you'll have time to work on this soon @mahlzahn or whether @b-grimaud should take over?

zm711 avatar Jul 02 '24 18:07 zm711

Hi all, sorry for my silence. I indeed didn’t have much time recently. I now added @b-grimaud as collaborator to my python-neo repository. Maybe you want to push your work to that branch?

mahlzahn avatar Jul 02 '24 19:07 mahlzahn

Thanks all, whatever works the best for you two! Life gets busy we totally understand! We will leave this on the top of the review pile for now and if you both get too busy then we can retag for future review.

zm711 avatar Jul 03 '24 12:07 zm711

Thanks for the update ! It looks like my initial commit was retroactively included in the thread already.

b-grimaud avatar Jul 05 '24 15:07 b-grimaud