issue kwik-gui channel-group

[Marcos Coletti]

Hi!!

We are using klusta for spike sorting (tetrodes), and phy kwik-gui to see the Kwik files (phy2) and manual clustering. 

We have an issue when we try to switch shanks (phy kwik-gui --channel-group N path), it always shows the same shank. Even if you enter N = 23234 (which makes nonense) you get no error and the same shank is display.

Phy kwik-describe shows the correct number of shanks. Also, klusta makes the spike sorting in all the electrode groups.

With the previous version we have no problem.

Marcos Coletti
Grupo Neurociencia de Sistemas,

IFIBIO-Houssay

Dpto de Fisiología, 

Facultad de Medicina,

Universidad de Buenos Aires
Buenos Aires, Argentina

[Jose Guzman]

If I understood correctly, phy2 does not work with klusta anymore (at least in my hands). When I tested with the parameters and raw files provided in https://klusta.readthedocs.io/en/latest/, I found:

(sorting) segundo.martinez@pcl-imba-3:klusta$ ls

hybrid_10sec.dat  hybrid_10sec.kwik  hybrid_10sec.kwx  hybrid_10sec.prm

(sorting) segundo.martinez@pcl-imba-3:klusta$ phy kwik-gui hybrid_10sec.kwik 

Traceback (most recent call last):

  File "/home/segundo.martinez/miniconda3/envs/sorting/bin/phy", line 11, in <module>

    load_entry_point('phy', 'console_scripts', 'phy')()

  File "/home/segundo.martinez/miniconda3/envs/sorting/lib/python3.6/site-packages/click/core.py", line 764, in __call__

    return self.main(*args, **kwargs)

  File "/home/segundo.martinez/miniconda3/envs/sorting/lib/python3.6/site-packages/click/core.py", line 717, in main

    rv = self.invoke(ctx)

  File "/home/segundo.martinez/miniconda3/envs/sorting/lib/python3.6/site-packages/click/core.py", line 1137, in invoke

    return _process_result(sub_ctx.command.invoke(sub_ctx))

  File "/home/segundo.martinez/miniconda3/envs/sorting/lib/python3.6/site-packages/click/core.py", line 956, in invoke

    return ctx.invoke(self.callback, **ctx.params)

  File "/home/segundo.martinez/miniconda3/envs/sorting/lib/python3.6/site-packages/click/core.py", line 555, in invoke

    return callback(*args, **kwargs)

  File "/home/segundo.martinez/miniconda3/envs/sorting/lib/python3.6/site-packages/click/decorators.py", line 17, in new_func

    return f(get_current_context(), *args, **kwargs)

  File "/home/segundo.martinez/git/phy/phy/apps/__init__.py", line 161, in cli_kwik_gui

    from .kwik.gui import kwik_gui

  File "/home/segundo.martinez/git/phy/phy/apps/kwik/__init__.py", line 11, in <module>

    from .gui import KwikController, kwik_describe, kwik_gui  # noqa

  File "/home/segundo.martinez/git/phy/phy/apps/kwik/gui.py", line 47, in <module>

    class KwikModelGUI(KwikModel):

NameError: name 'KwikModel' is not defined

[Cyrille Rossant]

Hi

Do you have the same problem if you do "pip install klusta" in the "sorting" conda environment before launching phy? Phy 2 is supposed to work with klusta as before.

Cyrille

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[Jose Guzman]

Hi Cyrille!!!

I did install klusta and everything works greatly! Thanks so much for your help!

Jose