From be2f35bb6caf61f102395b44ae95f8d958490732 Mon Sep 17 00:00:00 2001 From: olivier Date: Tue, 27 Feb 2024 10:58:19 +0000 Subject: [PATCH] blacked --- src/spikeinterface/extractors/alfsortingextractor.py | 7 ++++--- .../extractors/tests/test_alfsortingextractor.py | 10 +++++----- 2 files changed, 9 insertions(+), 8 deletions(-) diff --git a/src/spikeinterface/extractors/alfsortingextractor.py b/src/spikeinterface/extractors/alfsortingextractor.py index 7f618a027f..b259c59361 100644 --- 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 index 6d4a342f5f..8556e4158b 100644 --- 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