it seems like the spikesorting table now needs a keyword in SpikeSortingParameters called "whiten", but when the clusterless thresholder checks for this keyword it does not expect it and so gives an error
---------------------------------------------------------------------------
TypeError Traceback (most recent call last)
Cell In [26], line 54
52 position_info_param_name = "default_decoding"
53 # want to skip tet 100 and 101,
---> 54 populate_spike_threshold(recording_keys[2:3],
55 mark_param_name=mark_param_name,
56 position_info_param_name=position_info_param_name )
Cell In [26], line 14, in populate_spike_threshold(spikesorting_selection_keys, mark_param_name, position_info_param_name)
1 def populate_spike_threshold(
2 spikesorting_selection_keys: list,
3 mark_param_name='default',
(...)
8 # either do spike sorting or marks - not both
9 ## Populate spike sorting
10 SpikeSortingSelection().insert(
11 spikesorting_selection_keys,
12 skip_duplicates=True,
13 )
---> 14 SpikeSorting.populate(spikesorting_selection_keys)
16 ## Skip any curation
17 curation_keys = [Curation.insert_curation(
18 key) for key in spikesorting_selection_keys]
File ~/anaconda3/envs/spyglass2/lib/python3.9/site-packages/datajoint/autopopulate.py:230, in AutoPopulate.populate(self, suppress_errors, return_exception_objects, reserve_jobs, order, limit, max_calls, display_progress, processes, make_kwargs, *restrictions)
226 if processes == 1:
227 for key in (
228 tqdm(keys, desc=self.__class__.__name__) if display_progress else keys
229 ):
--> 230 error = self._populate1(key, jobs, **populate_kwargs)
231 if error is not None:
232 error_list.append(error)
File ~/anaconda3/envs/spyglass2/lib/python3.9/site-packages/datajoint/autopopulate.py:281, in AutoPopulate._populate1(self, key, jobs, suppress_errors, return_exception_objects, make_kwargs)
279 self.__class__._allow_insert = True
280 try:
--> 281 make(dict(key), **(make_kwargs or {}))
282 except (KeyboardInterrupt, SystemExit, Exception) as error:
283 try:
File ~/spyglass/src/spyglass/spikesorting/spikesorting_sorting.py:201, in SpikeSorting.make(self, key)
197 if sorter == "clusterless_thresholder":
198 # Detect peaks for clusterless decoding
199 # need to remove tempdir
200 sorter_params.pop("tempdir", None)
--> 201 detected_spikes = detect_peaks(recording, **sorter_params)
202 sorting = si.NumpySorting.from_times_labels(
203 times_list=detected_spikes["sample_ind"],
204 labels_list=np.zeros(len(detected_spikes), dtype=np.int),
205 sampling_frequency=recording.get_sampling_frequency(),
206 )
207 else:
File ~/spikeinterface/src/spikeinterface/sortingcomponents/peak_detection.py:80, in detect_peaks(recording, method, pipeline_nodes, gather_mode, folder, names, **kwargs)
77 mp_context = method_class.preferred_mp_context
79 # prepare args
---> 80 method_args = method_class.check_params(recording, **method_kwargs)
82 extra_margin = 0
83 if pipeline_nodes is None:
TypeError: check_params() got an unexpected keyword argument 'whiten'
edeno
commented
1 year ago
it seems like the spikesorting table now needs a keyword in SpikeSortingParameters called "whiten", but when the clusterless thresholder checks for this keyword it does not expect it and so gives an error