[pre-commit.ci] auto fixes from pre-commit.com hooks

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SpikeInterface · Oct 9, 2023 · fa82f10 · fa82f10
1 parent ed44aaf
commit fa82f10
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Showing 3 changed files with 16 additions and 9 deletions.
diff --git a/src/spikeinterface/sorters/internal/spyking_circus2.py b/src/spikeinterface/sorters/internal/spyking_circus2.py
@@ -88,7 +88,6 @@ def _run_from_folder(cls, sorter_output_folder, params, verbose):
         selection_params["n_peaks"] = params["selection"]["n_peaks_per_channel"] * num_channels
         selection_params["n_peaks"] = max(selection_params["min_n_peaks"], selection_params["n_peaks"])
 
-
         selection_params.update({"noise_levels": noise_levels})
         selected_peaks = select_peaks(
             peaks, method="smart_sampling_amplitudes", select_per_channel=False, **selection_params

diff --git a/src/spikeinterface/sortingcomponents/clustering/random_projections.py b/src/spikeinterface/sortingcomponents/clustering/random_projections.py
@@ -20,7 +20,12 @@
 from spikeinterface.core import extract_waveforms
 from spikeinterface.sortingcomponents.waveforms.savgol_denoiser import SavGolDenoiser
 from spikeinterface.sortingcomponents.features_from_peaks import RandomProjectionsFeature
-from spikeinterface.core.node_pipeline import run_node_pipeline, ExtractDenseWaveforms, ExtractSparseWaveforms, PeakRetriever
+from spikeinterface.core.node_pipeline import (
+    run_node_pipeline,
+    ExtractDenseWaveforms,
+    ExtractSparseWaveforms,
+    PeakRetriever,
+)
 
 
 class RandomProjectionClustering:
@@ -43,7 +48,7 @@ class RandomProjectionClustering:
         "ms_before": 1,
         "ms_after": 1,
         "random_seed": 42,
-        "noise_levels" : None,
+        "noise_levels": None,
         "smoothing_kwargs": {"window_length_ms": 0.25},
         "shared_memory": True,
         "tmp_folder": None,
@@ -86,13 +91,16 @@ def main_function(cls, recording, peaks, params):
         else:
             tmp_folder = Path(params["tmp_folder"]).absolute()
 
-
         tmp_folder.mkdir(parents=True, exist_ok=True)
 
         node0 = PeakRetriever(recording, peaks)
         node1 = ExtractSparseWaveforms(
-            recording, parents=[node0], return_output=False, ms_before=params["ms_before"], ms_after=params["ms_after"],
-            radius_um=params['radius_um']
+            recording,
+            parents=[node0],
+            return_output=False,
+            ms_before=params["ms_before"],
+            ms_after=params["ms_after"],
+            radius_um=params["radius_um"],
         )
 
         node2 = SavGolDenoiser(recording, parents=[node0, node1], return_output=False, **params["smoothing_kwargs"])
@@ -131,7 +139,7 @@ def sigmoid(x, L, x0, k, b):
             projections=projections,
             radius_um=params["radius_um"],
             sigmoid=None,
-            sparse=True
+            sparse=True,
         )
 
         pipeline_nodes = [node0, node1, node2, node3]

diff --git a/src/spikeinterface/sortingcomponents/features_from_peaks.py b/src/spikeinterface/sortingcomponents/features_from_peaks.py
@@ -186,7 +186,7 @@ def __init__(
         projections=None,
         sigmoid=None,
         radius_um=None,
-        sparse=True
+        sparse=True,
     ):
         PipelineNode.__init__(self, recording, return_output=return_output, parents=parents)
 
@@ -216,7 +216,7 @@ def compute(self, traces, peaks, waveforms):
             (chan_inds,) = np.nonzero(self.neighbours_mask[main_chan])
             local_projections = self.projections[chan_inds, :]
             if self.sparse:
-                wf_ptp = np.ptp(waveforms[idx][:, :, :len(chan_inds)], axis=1)
+                wf_ptp = np.ptp(waveforms[idx][:, :, : len(chan_inds)], axis=1)
             else:
                 wf_ptp = np.ptp(waveforms[idx][:, :, chan_inds], axis=1)