eFeature Extraction Library (eFEL) is now open source and available on GitHub

#1

The library that has historically been in use in the BlueBrain Project for feature extraction (spike amplitude, spike width, spike frequency, etc.) from electrophysiological voltage/current traces is now open source.
Everybody can access it from:

The eFEL will provide a great opportunity for the HBP members to standardise on the exact implementation of eFeatures.

#2

Awesome news.

Who’s using that currently?

#3

I heard Allen Brain Institute is using it. Is that true?

#4

Yes, indeed. In our collaboration with the ABI, we use the eFEL to both extract features from the experimental data provided by the ABI, and during the optimisation of electrical models.

#5

Hello,
I wanted to try it on a windows machine (W7, 64bits) and Enthought Canopy Python 2.7.6.
From both a bash shell or a DOS command prompt as administrator
pip install git+git://github.com/BlueBrain/eFEL
results in
“Running setup.py install for efel … error”

I do not have Visual Studio 2008, so installed mingw with
python setup.py build_ext -c mingw64
but it did not solve the problem.
Any suggestion? Thank you.

#6

Hi,
Could you try to run
pip -v install git+git://github.com/BlueBrain/eFEL
and show us the output ?
Could you also try ‘pip install efel’ and see if that gives the same error ?

Thanks, Cheers,

Werner

#7

Hi,

Just to be sure. Did you install the actual mingw64 with:
enpkg mingw
?

I don’t have access to a Windows machine, but here:


I read the suggestion to compile as follows after installing mingw:
pip install --global-option build_ext --global-option --compiler=mingw32 efel

#8

As an alternative. Is there a possibility for you to install Visual Studio ?

#9

Unfortunately, I’m also not a windows user, but I do know that Microsoft is providing a compiler you can use to make extension modules. I also believe that it is how Canopy is expecting to compile things moving forward (if you’re using Canopy 1.5.3 or above):

In that article, they have this caveat:

>     The MinGW stack is another solution that is very often used on Windows. On 32-bit, it tends to work pretty nicely for some trivial cases, but has the very same drawbacks as using a different version of Visual Studio, mentioned above. On 64-bit, MinGW is not entirely stable yet.

So I probably wouldn’t try to us MinGW unless the compiler for Python on Windows (https://www.microsoft.com/en-us/download/details.aspx?id=44266) doesn’t work.

#10

Hi,
Is this request still urgent ? We have been trying to build a Windows python wheel for the eFEL. But we ran in lots of issues.
Cheers,
Werner

#11

It is not urgent right now, but most users (included us) use windows. Since the code is public you will surely begin to receive requests as soon as pepole download and try to install it on their windows machines. Probably is would be better to say in the documentation that it does not run on windows until all problems are fixed.
Cheers
Michele