Protect against uninitialized chunks and add anonymous zarr open

Author: alejoe91

src/spikeinterface/core/zarrextractors.py

@@ -15,6 +15,18 @@
 from .core_tools import is_path_remote
 
 
+def anononymous_zarr_open(folder_path: str | Path, mode: str = "r", storage_options: dict | None = None):
+    if is_path_remote(str(folder_path)) and storage_options is None:
+        try:
+            root = zarr.open(str(folder_path), mode="r", storage_options=storage_options)
+        except Exception as e:
+            storage_options = {"anon": True}
+            root = zarr.open(str(folder_path), mode="r", storage_options=storage_options)
+    else:
+        root = zarr.open(str(folder_path), mode="r", storage_options=storage_options)
+    return root
+
+
 class ZarrRecordingExtractor(BaseRecording):
     """
     RecordingExtractor for a zarr format
@@ -40,14 +52,7 @@ def __init__(self, folder_path: Path | str, storage_options: dict | None = None)
 
         folder_path, folder_path_kwarg = resolve_zarr_path(folder_path)
 
-        if is_path_remote(str(folder_path)) and storage_options is None:
-            try:
-                self._root = zarr.open(str(folder_path), mode="r", storage_options=storage_options)
-            except Exception as e:
-                storage_options = {"anon": True}
-                self._root = zarr.open(str(folder_path), mode="r", storage_options=storage_options)
-        else:
-            self._root = zarr.open(str(folder_path), mode="r", storage_options=storage_options)
+        self._root = anononymous_zarr_open(folder_path, mode="r", storage_options=storage_options)
 
         sampling_frequency = self._root.attrs.get("sampling_frequency", None)
         num_segments = self._root.attrs.get("num_segments", None)
@@ -93,7 +98,10 @@ def __init__(self, folder_path: Path | str, storage_options: dict | None = None)
 
             nbytes_segment = self._root[trace_name].nbytes
             nbytes_stored_segment = self._root[trace_name].nbytes_stored
-            cr_by_segment[segment_index] = nbytes_segment / nbytes_stored_segment
+            if nbytes_stored_segment > 0:
+                cr_by_segment[segment_index] = nbytes_segment / nbytes_stored_segment
+            else:
+                cr_by_segment[segment_index] = np.nan
 
             total_nbytes += nbytes_segment
             total_nbytes_stored += nbytes_stored_segment
@@ -117,7 +125,10 @@ def __init__(self, folder_path: Path | str, storage_options: dict | None = None)
         if annotations is not None:
             self.annotate(**annotations)
         # annotate compression ratios
-        cr = total_nbytes / total_nbytes_stored
+        if total_nbytes_stored > 0:
+            cr = total_nbytes / total_nbytes_stored
+        else:
+            cr = np.nan
         self.annotate(compression_ratio=cr, compression_ratio_segments=cr_by_segment)
 
         self._kwargs = {"folder_path": folder_path_kwarg, "storage_options": storage_options}
@@ -181,14 +192,7 @@ def __init__(self, folder_path: Path | str, storage_options: dict | None = None,
 
         folder_path, folder_path_kwarg = resolve_zarr_path(folder_path)
 
-        if is_path_remote(str(folder_path)) and storage_options is None:
-            try:
-                zarr_root = zarr.open(str(folder_path), mode="r", storage_options=storage_options)
-            except Exception as e:
-                storage_options = {"anon": True}
-                zarr_root = zarr.open(str(folder_path), mode="r", storage_options=storage_options)
-        else:
-            zarr_root = zarr.open(str(folder_path), mode="r", storage_options=storage_options)
+        zarr_root = anononymous_zarr_open(folder_path, mode="r", storage_options=storage_options)
 
         if zarr_group is None:
             self._root = zarr_root
@@ -267,7 +271,7 @@ def read_zarr(
     """
     # TODO @alessio : we should have something more explicit in our zarr format to tell which object it is.
     # for the futur SortingAnalyzer we will have this 2 fields!!!
-    root = zarr.open(str(folder_path), mode="r", storage_options=storage_options)
+    root = anononymous_zarr_open(folder_path, mode="r", storage_options=storage_options)
     if "channel_ids" in root.keys():
         return read_zarr_recording(folder_path, storage_options=storage_options)
     elif "unit_ids" in root.keys():