fix numpy deprecation

zm711 · Dec 6, 2023 · 864163d · 864163d
1 parent 6d69f3e
commit 864163d
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diff --git a/src/spikeanalysis/spike_data.py b/src/spikeanalysis/spike_data.py
@@ -779,6 +779,8 @@ def _isolation_distance(self, pc_feat: np.array, labels: np.array, this_id: int)
             md_other = np.sort(cdist(pc_other_clusters, mean_this_cluster, "mahalanobis", VI=cov_matrix))
 
             # md_self = cdist(pc_this_cluster,mean_this_cluster,"mahalanobis", VI=cov_matrix)
+            if len(md_other.shape) > 1:
+                md_other = np.squeeze(md_other)
 
             isolation_dist = (md_other[n_spikes - 1]) ** 2
         else:

diff --git a/test/test_spike_data.py b/test/test_spike_data.py
@@ -327,7 +327,6 @@ def test_generate_qcmetrics(spikes, tmp_path):
     spikes.pc_feat = pc_feat
     spikes.CACHING = True
     spikes.generate_qcmetrics()
-
     assert isinstance(spikes.isolation_distances, np.ndarray)
     assert len(spikes.isolation_distances) == 2
     assert isinstance(spikes.silhouette_scores, np.ndarray)