installation of sorters

[WeissShahaf]

after following all installation instructions, only herding spikes is available in spikeinterface when running print available sorters.

tried in windows 7,10, with python 3.7 3.7.4, anaconda3, miniconda.

[WeissShahaf]

any thoughts?

[mhhennig]

Could you describe in a bit more detail what you did? Note that for the matlab sorters you have to set an environment variable, pointing to the relevant directory. However, spykingcircus for example should work if you used pip to install. Can you run it standalone?

[alexmcclanahan]

@mhhennig, super excited to experiment with SpikeInterface; I think it will yield very useful information for the field, so, thanks!

I've experienced similar issues to those outlined by @WeissShahaf. I have successfully installed SpikeInterface. The individual sorters that are python-based do install with pip or conda in terminal. However, they aren't able to be called, as an example (assuming a recording is properly loaded):

import spikesorters as ss (or even import spikeinterface.sorters as ss)
sorting_TDC = ss.run_tridesclous(recording, output_folder='tmp_TDC')

It also appears that the installed_sorters() function returns an empty array, while the available_sorters() returns that list (as it should, when I look in the sorterlist.py file). My intuition is that the sorters are being installed somewhere that the sorter files cannot find when they're called. I will keep tinkering to try to fix this locally on my machine and post if I make headway.

Not sure if this is the same issue as @WeissShahaf, but hopefully this can facilitate a solution.

[samuelgarcia]

Hi @alexmcclanahan
Could you update all sorters python based and all package from spikeinterface:

pip install -- upgrade spikeextractors  spiketoolkit spikeorters spikecomparisons spikewidgets
pip install --upgrade spyking-circus tridesclous herdingspikes

Note that from tridesclous you should install openl (or numba) for high channel counts otherwise it will be slow.

[alexmcclanahan]

@samuelgarcia: thanks -- I've tried that, to no avail. It seems as if the issue on my machine is that the various BaseSorter functions are erroring out as they don't see the sorters they point to during the BaseSorter.init call within the individual sorter. I have tried installing each sorter individually on two systems, after installing SpikeInterface with the same errors both times.

I will continue trying to unravel if this is an issue on my end during off hours.

[samuelgarcia]

Can you do give your pip list ?

[alexmcclanahan]

Sure, here it is:
pip_list.txt

[samuelgarcia]

For tridesclous evrything looks fine.
What happen when you do tridesclous in a console ?

[MingChingChiang]

Hi, I also have problems when executing ss.run_tridesclous,
even I have followed the installation steps from the tridesclous website.
When I type tdc in my terminal, I could launch the tridesclous GUI.
So...I'm not sure what happened to this problem.
I'm using macOS 10.14.6, python 3.7.7
Here's my PIP list.
PIP_List.txt

[samuelgarcia]

Hi @MingChingChiang
Could you do this
sorting_TDC = ss.run_tridesclous(recording, output_folder='tmp_TDC', raise_error=True)
and copy/paste the error message ?

[MingChingChiang]

Sure! I got these error messages:

Traceback (most recent call last):
File "/usr/local/lib/python3.7/site-packages/IPython/core/interactiveshell.py", line 3331, in run_code
exec(code_obj, self.user_global_ns, self.user_ns)
File "", line 2, in
sorting_TDC = ss.run_tridesclous(recording, output_folder=tmp_TDC, raise_error=True)
File "/Users/Ming-Ching/Documents/Python_Project/SI/venv/lib/python3.7/site-packages/spikesorters-0.3.0-py3.7.egg/spikesorters/sorterlist.py", line 230, in run_tridesclous
return run_sorter('tridesclous', *args, **kwargs)
File "/Users/Ming-Ching/Documents/Python_Project/SI/venv/lib/python3.7/site-packages/spikesorters-0.3.0-py3.7.egg/spikesorters/sorterlist.py", line 79, in run_sorter
parallel=parallel, verbose=verbose, delete_output_folder=delete_output_folder)
File "/Users/Ming-Ching/Documents/Python_Project/SI/venv/lib/python3.7/site-packages/spikesorters-0.3.0-py3.7.egg/spikesorters/tridesclous/tridesclous.py", line 53, in init
BaseSorter.init(self, **kargs)
File "/Users/Ming-Ching/Documents/Python_Project/SI/venv/lib/python3.7/site-packages/spikesorters-0.3.0-py3.7.egg/spikesorters/basesorter.py", line 48, in init
Please install it with: \n{} """.format(self.sorter_name, self.installation_mesg)
AssertionError: This sorter tridesclous is not installed.
Please install it with:
>>> pip install https://github.com/tridesclous/tridesclous/archive/master.zip
More information on tridesclous at:
* https://github.com/tridesclous/tridesclous
* https://tridesclous.readthedocs.io

[samuelgarcia]

what happen if you do
import tridesclous
in ipython ?

[MingChingChiang]

It returns:
Traceback (most recent call last):
File "/usr/local/lib/python3.7/site-packages/IPython/core/interactiveshell.py", line 3331, in run_code
exec(code_obj, self.user_global_ns, self.user_ns)
File "", line 1, in
import tridesclous
File "/Applications/PyCharm.app/Contents/plugins/python/helpers/pydev/_pydev_bundle/pydev_import_hook.py", line 21, in do_import
module = self._system_import(name, *args, **kwargs)
ModuleNotFoundError: No module named 'tridesclous'
I'll try reinstalling my iPython into my virtualenv again to see whether I can fix the problem...

[samuelgarcia]

Very strange that you have it in the pip list but not being able to import.
Which method did you used for installing tridesclous pip install tridesclous?

[MingChingChiang]

Yes, I used pip install tridesclous for installation.
The other strange thing is that after I created a new environment with python==3.7.6 and reinstall everything, including spikeinterface and tridesclous, everything just worked fine.
Not sure whether the python version has such strong impacts or not...
But at least I learned that avoid using python 3.7.7 or higher version for spikeinterface might be a better option.

Very strange that you have it in the pip list but not being able to import.
Which method did you used for installing tridesclous pip install tridesclous?