Pull changes from upstream

kabilar · Aug 24, 2023 · 315886c · 315886c
1 parent 9c7fa45
commit 315886c
Showing 1 changed file with 8 additions and 2 deletions.
diff --git a/element_array_ephys/ephys_organoids.py b/element_array_ephys/ephys_organoids.py
@@ -649,7 +649,7 @@ def make(self, key):
             raise ValueError(f"Unknown task mode: {task_mode}")
 
         creation_time, _, _ = kilosort.extract_clustering_info(kilosort_dir)
-        self.insert1({**key, "clustering_time": creation_time})
+        self.insert1({**key, "clustering_time": creation_time, "package_version": ""})
 
 
 @schema
@@ -1092,14 +1092,20 @@ def make(self, key):
         kilosort_dir = find_full_path(get_ephys_root_data_dir(), output_dir)
 
         metric_fp = kilosort_dir / "metrics.csv"
+        rename_dict = {
+            "isi_viol": "isi_violation",
+            "num_viol": "number_violation",
+            "contam_rate": "contamination_rate",
+        }
 
         if not metric_fp.exists():
             raise FileNotFoundError(f"QC metrics file not found: {metric_fp}")
 
         metrics_df = pd.read_csv(metric_fp)
         metrics_df.set_index("cluster_id", inplace=True)
         metrics_df.replace([np.inf, -np.inf], np.nan, inplace=True)
-
+        metrics_df.columns = metrics_df.columns.str.lower()
+        metrics_df.rename(columns=rename_dict, inplace=True)
         metrics_list = [
             dict(metrics_df.loc[unit_key["unit"]], **unit_key)
             for unit_key in (CuratedClustering.Unit & key).fetch("KEY")