bugfixes

Former-commit-id: 14c7b6bdfe4a278930f9a58d6345f08af17c18ad

core/functions/tracks.py

@@ -229,13 +229,13 @@ def get_joinable(tracks, smooth=False, tol=0.1, window=5, degree=3) -> dict:
         savgol_on_srs = lambda x: non_uniform_savgol(x.index, x.values, window, degree)
         contig = clean.groupby(["trap"]).apply(get_contiguous_pairs)
         contig = contig.loc[contig.apply(len) > 0]
-        linear = set([k for v in contig.values for i in v for j in i for k in j])
-        smoothed_tracks = clean.loc[linear].apply(savgol_on_srs, 1)
+        flat = set([k for v in contig.values for i in v for j in i for k in j])
+        smoothed_tracks = clean.loc[flat].apply(savgol_on_srs, 1)
     else:
         contig = tracks.groupby(["trap"]).apply(get_contiguous_pairs)
         contig = contig.loc[contig.apply(len) > 0]
-        linear = set([k for v in contig.values for i in v for j in i for k in j])
-        smoothed_tracks = tracks.loc[linear].apply(lambda x: np.array(x.values), axis=1)
+        flat = set([k for v in contig.values for i in v for j in i for k in j])
+        smoothed_tracks = tracks.loc[flat].apply(lambda x: np.array(x.values), axis=1)
 
     # fetch edges from ids TODO (IF necessary, here we can compare growth rates)
     idx_to_edge = lambda preposts: [

core/processor.py

@@ -114,14 +114,15 @@ class PostProcessor:
         with h5py.File(self._filename, "r") as f:
             prev_idchanges = self._signal.get_id_changes()
 
-        changes_history = prev_idchanges + [merge_events]  # + [picks]
-        self._writer.write("/id_changes", data=changes_history)
+        changes_history = prev_idchanges + merge_events
+        self._writer.write("id_changes", data=changes_history)
         # self._writer.write(
         #     "/postprocessing/merge_events/",
         #     data=merge_events,
         #     meta={"source": "/cell_info/"},
         # )
         # changes_history += picks
+        # TODO add picks dataset
         # picks = self.picker.run(self._signal[self.targets["prepost"]["picker"][0]])
         # self._writer.write()