Merge pull request #3150 from h-mayorquin/close_nwb

Improved conditions for closing nwb when using hdf5 backend

src/spikeinterface/extractors/nwbextractors.py

@@ -401,7 +401,40 @@ def _retrieve_electrodes_indices_from_electrical_series_backend(open_file, elect
     return electrodes_indices
 
 
-class NwbRecordingExtractor(BaseRecording):
+class _BaseNWBExtractor:
+    "A class for common methods for NWB extractors."
+
+    def _close_hdf5_file(self):
+        has_hdf5_backend = hasattr(self, "_file")
+        if has_hdf5_backend:
+            import h5py
+
+            main_file_id = self._file.id
+            open_object_ids_main = h5py.h5f.get_obj_ids(main_file_id, types=h5py.h5f.OBJ_ALL)
+            for object_id in open_object_ids_main:
+                object_name = h5py.h5i.get_name(object_id).decode("utf-8")
+                try:
+                    object_id.close()
+                except:
+                    import warnings
+
+                    warnings.warn(f"Error closing object {object_name}")
+
+    def __del__(self):
+        # backend mode
+        if hasattr(self, "_file"):
+            if hasattr(self._file, "store"):
+                self._file.store.close()
+            else:
+                self._close_hdf5_file()
+        # pynwb mode
+        elif hasattr(self, "_nwbfile"):
+            io = self._nwbfile.get_read_io()
+            if io is not None:
+                io.close()
+
+
+class NwbRecordingExtractor(BaseRecording, _BaseNWBExtractor):
     """Load an NWBFile as a RecordingExtractor.
 
     Parameters
@@ -623,19 +656,6 @@ def __init__(
             "file": file,
         }
 
-    def __del__(self):
-        # backend mode
-        if hasattr(self, "_file"):
-            if hasattr(self._file, "store"):
-                self._file.store.close()
-            else:
-                self._file.close()
-        # pynwb mode
-        elif hasattr(self, "_nwbfile"):
-            io = self._nwbfile.get_read_io()
-            if io is not None:
-                io.close()
-
     def _fetch_recording_segment_info_pynwb(self, file, cache, load_time_vector, samples_for_rate_estimation):
         self._nwbfile = read_nwbfile(
             backend=self.backend,
@@ -949,7 +969,7 @@ def get_traces(self, start_frame, end_frame, channel_indices):
         return traces
 
 
-class NwbSortingExtractor(BaseSorting):
+class NwbSortingExtractor(BaseSorting, _BaseNWBExtractor):
     """Load an NWBFile as a SortingExtractor.
     Parameters
     ----------
@@ -1105,19 +1125,6 @@ def __init__(
             "t_start": self.t_start,
         }
 
-    def __del__(self):
-        # backend mode
-        if hasattr(self, "_file"):
-            if hasattr(self._file, "store"):
-                self._file.store.close()
-            else:
-                self._file.close()
-        # pynwb mode
-        elif hasattr(self, "_nwbfile"):
-            io = self._nwbfile.get_read_io()
-            if io is not None:
-                io.close()
-
     def _fetch_sorting_segment_info_pynwb(
         self, unit_table_path: str = None, samples_for_rate_estimation: int = 1000, cache: bool = False
     ):