Merge branch 'sc2_recording_slices' of github.com:yger/spikeinterface…

… into sc2_recording_slices

src/spikeinterface/sorters/internal/spyking_circus2.py

@@ -221,13 +221,17 @@ def _run_from_folder(cls, sorter_output_folder, params, verbose):
                 np.save(clustering_folder / "prototype.npy", prototype)
             if skip_peaks:
                 detection_params["skip_after_n_peaks"] = n_peaks
-                detection_params["recording_slices"] = get_shuffled_recording_slices(recording_w, seed=params["seed"], **job_kwargs)
+                detection_params["recording_slices"] = get_shuffled_recording_slices(
+                    recording_w, seed=params["seed"], **job_kwargs
+                )
             peaks = detect_peaks(recording_w, "matched_filtering", **detection_params, **job_kwargs)
         else:
             waveforms = None
             if skip_peaks:
                 detection_params["skip_after_n_peaks"] = n_peaks
-                detection_params["recording_slices"] = get_shuffled_recording_slices(recording_w, seed=params["seed"], **job_kwargs)
+                detection_params["recording_slices"] = get_shuffled_recording_slices(
+                    recording_w, seed=params["seed"], **job_kwargs
+                )
             peaks = detect_peaks(recording_w, "locally_exclusive", **detection_params, **job_kwargs)
 
         if verbose:

src/spikeinterface/sortingcomponents/tools.py

@@ -69,7 +69,9 @@ def extract_waveform_at_max_channel(rec, peaks, ms_before=0.5, ms_after=1.5, **j
     return all_wfs
 
 
-def get_prototype_and_waveforms_from_peaks(recording, peaks, n_peaks=5000, ms_before=0.5, ms_after=0.5, seed=None, **all_kwargs):
+def get_prototype_and_waveforms_from_peaks(
+    recording, peaks, n_peaks=5000, ms_before=0.5, ms_after=0.5, seed=None, **all_kwargs
+):
     """
     Function to extract a prototype waveform from peaks.
 
@@ -100,6 +102,7 @@ def get_prototype_and_waveforms_from_peaks(recording, peaks, n_peaks=5000, ms_be
         The selected peaks used to extract waveforms.
     """
     from spikeinterface.sortingcomponents.peak_selection import select_peaks
+
     _, job_kwargs = split_job_kwargs(all_kwargs)
 
     nbefore = int(ms_before * recording.sampling_frequency / 1000.0)
@@ -118,7 +121,9 @@ def get_prototype_and_waveforms_from_peaks(recording, peaks, n_peaks=5000, ms_be
     return prototype, waveforms[:, :, 0], few_peaks
 
 
-def get_prototype_and_waveforms_from_recording(recording, n_peaks=5000, ms_before=0.5, ms_after=0.5, seed=None, **all_kwargs):
+def get_prototype_and_waveforms_from_recording(
+    recording, n_peaks=5000, ms_before=0.5, ms_after=0.5, seed=None, **all_kwargs
+):
     """
     Function to extract a prototype waveform from peaks detected on the fly.
 
@@ -148,6 +153,7 @@ def get_prototype_and_waveforms_from_recording(recording, n_peaks=5000, ms_befor
     """
     from spikeinterface.sortingcomponents.peak_detection import detect_peaks
     from spikeinterface.core.node_pipeline import ExtractSparseWaveforms
+
     detection_kwargs, job_kwargs = split_job_kwargs(all_kwargs)
 
     nbefore = int(ms_before * recording.sampling_frequency / 1000.0)
@@ -159,7 +165,7 @@ def get_prototype_and_waveforms_from_recording(recording, n_peaks=5000, ms_befor
         ms_after=ms_after,
         radius_um=0,
     )
-    
+
     pipeline_nodes = [node]
 
     recording_slices = get_shuffled_recording_slices(recording, seed=seed, **job_kwargs)
@@ -172,7 +178,7 @@ def get_prototype_and_waveforms_from_recording(recording, n_peaks=5000, ms_befor
         **detection_kwargs,
         **job_kwargs,
     )
-    
+
     rng = np.random.RandomState(seed)
     indices = rng.permutation(np.arange(len(res[0])))
 
@@ -219,9 +225,14 @@ def get_prototype_and_waveforms(
         The selected peaks used to extract waveforms.
     """
     if peaks is None:
-       return get_prototype_and_waveforms_from_peaks(recording, n_peaks, ms_before=ms_before, ms_after=ms_after, seed=seed, **all_kwargs) 
+        return get_prototype_and_waveforms_from_peaks(
+            recording, n_peaks, ms_before=ms_before, ms_after=ms_after, seed=seed, **all_kwargs
+        )
     else:
-        return get_prototype_and_waveforms_from_recording(recording, peaks, n_peaks, ms_before=ms_before, ms_after=ms_after, seed=seed, **all_kwargs)
+        return get_prototype_and_waveforms_from_recording(
+            recording, peaks, n_peaks, ms_before=ms_before, ms_after=ms_after, seed=seed, **all_kwargs
+        )
+
 
 def check_probe_for_drift_correction(recording, dist_x_max=60):
     num_channels = recording.get_num_channels()