FED3 Python package / FED3Viz archival

[Tom Earnest]

Hi all!

Posting to share a couple updates on FED3 Python Stuff...

New Python package: fed3

I have been developing a Python package for working with FED3 data (called "fed3", hopefully not too confusing...).   Here a some links:

• The project GitHub: https://github.com/earnestt1234/fed3
• The code base documentation: https://earnestt1234.github.io/fed3/fed3/index.html.  This is a work in progress, but I am slowly filling it in
• Some examples showing the plotting interface: https://earnestt1234.github.io/fed3/fed3/plot/index.html

This is basically intended to provide an interface for loading and working with FED3 data in Python.  So, it provides functionality for loading files, data wrangling (splitting/joining/cropping data), and creating visualizations.  For those familiar, the project is like half an extension of pandas (for interacting with tabular FED3 data) and half matplotlib functions (for making graphs).

I am hoping this will be useful for those trying to automate FED3 data analyses or those working with FED3 data and trying to learn Python.  If anyone does give it a try and have feedback/questions, please let me know!  This code has really been only run by me, so there are plenty of bugs to find and features to add.

Archival of FED3Viz

I previously developed the FED3Viz graphing program while working as a tech with Lex.  Based on my work on the fed3 Python package, I have decided to "archive" the GitHub repository for FED3Viz.  All this really means is that I don't plan to update it anymore - all the currently existing code will continue to be available.  And I will still be happy to field questions about it via this Google group.  I appreciate everyone that has been able to use it, and hope it can still be a useful tool!

I include a little more context on this decision in the readme for the fed3 package, which I am just pasting below:

Many of the functions and visualizations in fed3 are taken from FED3VIZ, a previously-developed GUI for working with FED3 data. There is currently incomplete overlap between these two softwares; i.e. some stuff from FED3VIZ can't be done with fed3, and some new things in fed3 can't be done with FED3VIZ. An immediate goal of the fed3 package is to address the first point by porting all the remaining FED3VIZ functions to fed3 (see the Development section above).

I would like to also have FED3VIZ be expanded to include new operations being developed in this repository. However, the implementation of FED3VIZ is somewhat of a mess, due to a lot of learn-on-the-job software code . And unfortunately, updating that program requires far more effort than updating this package.

Instead, I hope to reimplement FED3VIZ using the fed3 package (and some better coding practices). Ideally, some of the interface will be automatically generated based on functions available in fed3. This will most likely require a rewrite of FED3Viz, rather than an update. Plus, the fed3 package is still very immature, and needs much more development and testing. Therefore, this reimplementation of FED3VIZ is probably a long way off.

[Lex Kravitz]

Tom thanks so much for your continued work on this!  This is a huge step forward for analyzing FED3 data, especially as so many people are running custom tasks that go beyond what we envisioned when FED3VIZ was made.

For anyone who doesn't know Tom Earnest, he's an incredible scientist with superhero data and computational chops.  Tom was a research technician in my lab from 2020-2021, which was when he wrote the original FED3VIZ. He is now a PhD Student in the Division of Computational and Data Sciences here at Wash U and he's worked on this new FED3 Python package in his spare time.  So give him your thanks (and buy him a beer if you ever run into him in person!) 

-Lex

[James McCutcheon]

Hi Lex and Tom,

This looks fantastic - looking forward to integrating the fed3 package with our code.

Will definitely buy you beer when we cross paths!

Cheers

Jaime

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[Allison Lindquist]

Hi Tom! I was bothering you on github about all the FED3Viz things recently. I appreciate everything you have done to make this usable for so many people, and using this code will definitely be beneficial for our experiments in the future!

Stay well,

Alli

[Tom Earnest]

Alli - not a bother at all!!!

Thanks all for the interest!  Cheers to you all for such a positive and helpful community 🥂

Best,

Tom