Merge pull request #3198 from h-mayorquin/correct_extractor_metadata_with_same_annotations

Fix naming when `all_annotations=True` in neo base extractors

Author: samuelgarcia

src/spikeinterface/extractors/neoextractors/neobaseextractor.py

@@ -206,8 +206,8 @@ def __init__(
         if stream_id is None and stream_name is None:
             if stream_channels.size > 1:
                 raise ValueError(
-                    f"This reader have several streams: \nNames: {stream_names}\nIDs: {stream_ids}. "
-                    f"Specify it with the 'stream_name' or 'stream_id' arguments"
+                    f"This reader have several streams: \nNames: {stream_names}\nIDs: {stream_ids}. \n"
+                    f"Specify it from the options above with the 'stream_name' or 'stream_id' arguments"
                 )
             else:
                 stream_id = stream_ids[0]
@@ -276,7 +276,7 @@ def __init__(
 
         self.set_property("gain_to_uV", final_gains)
         self.set_property("offset_to_uV", final_offsets)
-        if not use_names_as_ids and not all_annotations:
+        if not use_names_as_ids:
             self.set_property("channel_names", signal_channels["name"])
 
         if all_annotations:
@@ -287,13 +287,26 @@ def __init__(
             seg_ann = block_ann["segments"][0]
             sig_ann = seg_ann["signals"][self.stream_index]
 
-            # scalar annotations
-            for k, v in sig_ann.items():
-                if not k.startswith("__"):
-                    self.set_annotation(k, v)
+            scalar_annotations = {name: value for name, value in sig_ann.items() if not name.startswith("__")}
+
+            # name in neo corresponds to stream name
+            # We don't propagate the name as an annotation because that has a differnt meaning on spikeinterface
+            stream_name = scalar_annotations.pop("name", None)
+            if stream_name:
+                self.set_annotation(annotation_key="stream_name", value=stream_name)
+            for annotation_key, value in scalar_annotations.items():
+                self.set_annotation(annotation_key=annotation_key, value=value)
+
+            array_annotations = sig_ann["__array_annotations__"]
+            # We do not add this because is confusing for the user to have this repeated
+            array_annotations.pop("channel_ids", None)
+            # This is duplicated when using channel_names as ids
+            if use_names_as_ids:
+                array_annotations.pop("channel_names", None)
+
             # vector array_annotations are channel properties
-            for k, values in sig_ann["__array_annotations__"].items():
-                self.set_property(k, values)
+            for key, values in array_annotations.items():
+                self.set_property(key=key, values=values)
 
         nseg = self.neo_reader.segment_count(block_index=self.block_index)
         for segment_index in range(nseg):