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SpikeInterface · Feb 27, 2024 · be2f35b · be2f35b
1 parent e2a8908
commit be2f35b
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Showing 2 changed files with 9 additions and 8 deletions.
diff --git a/src/spikeinterface/extractors/alfsortingextractor.py b/src/spikeinterface/extractors/alfsortingextractor.py
@@ -9,6 +9,7 @@
 
 try:
     import pandas as pd
+
     HAVE_PANDAS = True
 except:
     HAVE_PANDAS = False
@@ -43,12 +44,12 @@ def __init__(self, folder_path, sampling_frequency=30000):
         assert self.installed, self.installation_mesg
         # check correct parent folder:
         self._folder_path = Path(folder_path)
-        spikes = alfio.load_object(self._folder_path, 'spikes', short_keys=True)
-        clusters = alfio.load_object(self._folder_path, 'clusters', short_keys=True)
+        spikes = alfio.load_object(self._folder_path, "spikes", short_keys=True)
+        clusters = alfio.load_object(self._folder_path, "clusters", short_keys=True)
         total_units = clusters[next(iter(clusters))].size
         unit_ids = np.arange(total_units)  # in alf format, spikes.clusters index directly into clusters
         BaseSorting.__init__(self, unit_ids=unit_ids, sampling_frequency=sampling_frequency)
-        sorting_segment = ALFSortingSegment(spikes['clusters'], spikes["times"], sampling_frequency)
+        sorting_segment = ALFSortingSegment(spikes["clusters"], spikes["times"], sampling_frequency)
         self.add_sorting_segment(sorting_segment)
         self.extra_requirements.append("pandas")
         self.extra_requirements.append("ONE-api")

diff --git a/src/spikeinterface/extractors/tests/test_alfsortingextractor.py b/src/spikeinterface/extractors/tests/test_alfsortingextractor.py
@@ -14,8 +14,8 @@ def test_alf_sorting_extractor():
     spike_times = []
     spike_clusters = []
     for i, fr in enumerate([123, 78, 145]):
-        st = np.cumsum(- np.log(np.random.rand(int(rec_len_secs * firing_rate * 1.5))) / firing_rate)
-        st = st[:np.searchsorted(st, rec_len_secs)]
+        st = np.cumsum(-np.log(np.random.rand(int(rec_len_secs * firing_rate * 1.5))) / firing_rate)
+        st = st[: np.searchsorted(st, rec_len_secs)]
         spike_times.append(st)
         spike_clusters.append(st * 0 + i)
     spike_times = np.concatenate(spike_times)
@@ -25,9 +25,9 @@ def test_alf_sorting_extractor():
 
     with tempfile.TemporaryDirectory() as td:
         folder_path = Path(td)
-        np.save(folder_path.joinpath('spikes.times.npy'), spike_times)
-        np.save(folder_path.joinpath('spikes.clusters.npy'), spike_clusters)
-        np.save(folder_path.joinpath('clusters.channels.npy'), np.arange(3))
+        np.save(folder_path.joinpath("spikes.times.npy"), spike_times)
+        np.save(folder_path.joinpath("spikes.clusters.npy"), spike_clusters)
+        np.save(folder_path.joinpath("clusters.channels.npy"), np.arange(3))
 
         sorting = read_alf_sorting(folder_path, sampling_frequency=30000)
         assert sorting.get_unit_spike_train(0).size > 50_000