Complete AlphaOmegaIO

[apdavison]

It is a proof of concept for the moment.

---

Imported from Trac ticket:40

Opened: 2011-11-02 17:46:11
Last modified: 2012-02-02 16:01:10
Component: io
Priority: major
Owner: somebody
Reporter: sgarcia

[fstj]

At the INT we are currently working on improving AlphaOmegaIO in Neo.

We already made some progress and are now able to read most of the different Neo relevant types of data available in the AlphaOmega files, for the version of the format that we use in our Institute.

We will soon push this improved version of the IO here: https://github.com/leaandre/python-neo

The steps that we still need to perform in order to complete the IO are:

• Store the relevant metadata in the Neo annotations.
• Make the IO work with Python 3.
• Clarify what versions of the Alpha Omega file format exists, and support a many versions as possible.
• Test thoroughly the IO.

[samuelgarcia]

This is a good news.
The main difficulty is that alpha omega have 2 files formats old (map) and new (mpx).
And the neo neo is moving toward 0.4.
Good idea to work in 0.3.x branch.

Good luck for everything.

[fstj]

As I said in my previous comment, we have been working at the INT on improving AlphaOmegaIO in Neo, thanks to an internship last year.

This led to good results, but there wasn't enough time to fully finish it and to complete the associated tests. I was hoping to find at some point the time to complete it and contribute back our improved version of the reader to the Neo project. But I never got that time, and I am now leaving my neuroscience lab to join a lab in a completely different field (fundamental computer science).
So I won't be able to finish the development of AlphaOmegaIO.

But as it would be a pity to loose the work that we have done, I have put our current version here:
https://github.com/fstj/python-neo/tree/0.3.x

This fork also contains an improved (but unfinished) version of NeoMatlabIO supporting all kinds of Neo objects and their annotations.
Both improved versions of AlphaOmegaIO and NeoMatlabIO are only available in the 0.3.x branch.

I was hoping that somebody in the Neo project might be interested in finishing these IO modules.
If it is the case, please contact me. As I said, I won't be contributing code, but I can share what we have learned about the AlphaOmega format and provide some test files, and give all the precisions about what we have done that might be needed.

[samuelgarcia]

Partially done in #1049.
Closing now