search

SpikeInterface / spikeinterface-dockerfiles

Collection of spike sorters Docker files
MIT License
8 stars 9 forks source link

error on getting results from sorter #23

Closed vncntprvst closed 2 years ago

vncntprvst commented 2 years ago

When sorting purely with containers (no specific sorters installed in the environment), I get an error with some sorters when retrieving the results with sorting = SorterClass.get_result_from_folder(output_folder) (this code line)

e.g., with Tridesclous, calling:

sorting_TDC = ss.run_tridesclous(recording,
                                 output_folder="tridesclous_output",
                                 docker_image="spikeinterface/tridesclous-base:1.6.5")

returns

Exception has occurred: AssertionError       
To use the TridesclousSortingExtractor install tridesclous: 
pip install tridesclous

Here's the call stack: image

This doesn't happen with all sorters (e.g, Spyking Circus is fine). I haven't been able to track down the cause yet.

vncntprvst commented 2 years ago

This error comes from the way the SortingExtractor class is written for that particular sorter. TridesclousSortingExtractor has assert HAVE_TDC, while SpykingCircusSortingExtractor only asserts HAVE_H5PY. Is it possible to go around this?

vncntprvst commented 2 years ago

See comment and explanation in the related issue: https://github.com/SpikeInterface/spikeinterface/issues/640