Ced sonpy implementation

[samuelgarcia]

Alternative to spike2io based on sonpy (close source package but official) from ced.

[pep8speaks]

Hello @samuelgarcia! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

• In the file neo/rawio/cedrawio.py:

Line 90:100: E501 line too long (108 > 99 characters)

Comment last updated at 2021-06-18 08:54:20 UTC

[samuelgarcia]

As soon as files are merge in gin. This is ready to review.

[samuelgarcia]

@luiztauffer : could you validate this ?

[legouee]

Hello @samuelgarcia.
I would like to read .smrx files. Here is the link :
https://sparc.science/datasets/27?type=dataset  (look under the “Files” tab > primary).

For that, I tested your code. But I have a problem with the installation of sonpy package. I am using python 3.9 as required. It seems to be installed, but when I want to read parse_header(), I get the error message : AssertionError: sonpy must be installed.
Even though I want to import sonpy in an other version of python (3.7.5), I have the error :

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Users/legouee/miniconda3/lib/python3.7/site-packages/sonpy/__init__.py", line 10, in <module>
    import sonpy.darwin.sonpy as lib
ImportError: dlopen(/Users/legouee/miniconda3/lib/python3.7/site-packages/sonpy/darwin/sonpy.so, 2): Symbol not found: __ZdlPvSt11align_val_t
  Referenced from: /Users/legouee/miniconda3/lib/python3.7/site-packages/sonpy/darwin/sonpy.so
  Expected in: /usr/lib/libc++.1.dylib
 in /Users/legouee/miniconda3/lib/python3.7/site-packages/sonpy/darwin/sonpy.so

On your side, is it possible to read these files ? Do you have any idea why I am getting this error ?
I thank you.

[samuelgarcia]

Hi Elodie.
I think you should ask directly to CED for sonpy support.
As I wrote in the code : sonpy is close source and distributed as compiled by CED directly. Too bad!!

For me with python3.8 on ubuntu20.4 import sonpy works without problems.

About your file. I can open "Pig-820_Nodose-002.smrx" without problem but it do not contain any signals.
Maybe it contain other object like event or spiketrain but they are not implemented.

One day, if I have time I will extend the spike2io which is the pure python/numpy implementation to 64bit.
I guess the internal structure is not so diffrents between smr and smrx.

Sam

[legouee]

Ok. I thank you very much @samuelgarcia for your answer.

[samuelgarcia]

Ready to review (and merge maybe)

[samuelgarcia]

@JuliaSprenger : having this merge in the master would be very very helpfull :)