Waveform extraction: AttributeError: 'KiloSortSortingExtractor' object has no attribute 'get_probegroup'

[mtehrani-code]

Still working with the Cambridge NeuroTech, November 2023 tutorial.

In the waveform extraction step, I type:

we = si.create_sorting_analyzer(recording_saved, sorting, folder=base_folder / "waveforms_dense", sparse=False, overwrite=True, **job_kwargs) print(we)

And I get this error:

AttributeError Traceback (most recent call last) Cell In[109], line 1 ----> 1 we = si.create_sorting_analyzer(recording_saved, sorting, folder=base_folder / "waveforms_dense", 2 sparse=False, overwrite=True, **job_kwargs) 3 print(we)

File ~\Documents\GitHub\spikeinterface\src\spikeinterface\core\sortinganalyzer.py:121, in create_sorting_analyzer(sorting, recording, format, folder, sparse, sparsity, overwrite, **sparsity_kwargs) 118 else: 119 sparsity = None --> 121 sorting_analyzer = SortingAnalyzer.create(sorting, recording, format=format, folder=folder, sparsity=sparsity) 123 return sorting_analyzer

File ~\Documents\GitHub\spikeinterface\src\spikeinterface\core\sortinganalyzer.py:221, in SortingAnalyzer.create(cls, sorting, recording, format, folder, sparsity) 219 assert sorting.sampling_frequency == recording.sampling_frequency 220 # check that multiple probes are non-overlapping --> 221 all_probes = recording.get_probegroup().probes 222 check_probe_do_not_overlap(all_probes) 224 if format == "memory":

AttributeError: 'KiloSortSortingExtractor' object has no attribute 'get_probegroup'

I'm replacing "extract_waveforms" with "create_sorting_analyzer" as was suggested in the update.

Please help!

[alejoe91]

The create_sorting_analyzer takes a sorting object first and then a recording, not the other way around!

[mtehrani-code]

Okay. When I swap those, this is what I get:

SortingAnalyzer: 49 channels - 120 units - 1 segments - memory - has recording Loaded 0 extensions:

No processing happens...Shouldn't there be an output file like a 'waveforms' folder somewhere?

[alejoe91]

No, this only creates a sorting analyzer, that can be used to compute extensions. Note that the waveform extraction step has been deprecated