Merge branch 'main' into channel-ids-sortingview

src/spikeinterface/extractors/neoextractors/alphaomega.py

@@ -25,14 +25,30 @@ class AlphaOmegaRecordingExtractor(NeoBaseRecordingExtractor):
         If there are several streams, specify the stream name you want to load.
     all_annotations : bool, default: False
         Load exhaustively all annotations from neo.
+    use_names_as_ids : bool, default: False
+        Determines the format of the channel IDs used by the extractor. If set to True, the channel IDs will be the
+        names from NeoRawIO. If set to False, the channel IDs will be the ids provided by NeoRawIO.
     """
 
     NeoRawIOClass = "AlphaOmegaRawIO"
 
-    def __init__(self, folder_path, lsx_files=None, stream_id="RAW", stream_name=None, all_annotations=False):
+    def __init__(
+        self,
+        folder_path,
+        lsx_files=None,
+        stream_id="RAW",
+        stream_name=None,
+        all_annotations: bool = False,
+        use_names_as_ids: bool = False,
+    ):
         neo_kwargs = self.map_to_neo_kwargs(folder_path, lsx_files)
         NeoBaseRecordingExtractor.__init__(
-            self, stream_id=stream_id, stream_name=stream_name, all_annotations=all_annotations, **neo_kwargs
+            self,
+            stream_id=stream_id,
+            stream_name=stream_name,
+            all_annotations=all_annotations,
+            use_names_as_ids=use_names_as_ids,
+            **neo_kwargs,
         )
         self._kwargs.update(dict(folder_path=str(Path(folder_path).absolute()), lsx_files=lsx_files))
 

src/spikeinterface/extractors/neoextractors/axona.py

@@ -19,13 +19,21 @@ class AxonaRecordingExtractor(NeoBaseRecordingExtractor):
         The file path to load the recordings from.
     all_annotations : bool, default: False
         Load exhaustively all annotations from neo.
+    use_names_as_ids : bool, default: False
+        Determines the format of the channel IDs used by the extractor. If set to True, the channel IDs will be the
+        names from NeoRawIO. If set to False, the channel IDs will be the ids provided by NeoRawIO.
     """
 
     NeoRawIOClass = "AxonaRawIO"
 
-    def __init__(self, file_path, all_annotations=False):
+    def __init__(self, file_path: str | Path, all_annotations: bool = False, use_names_as_ids: bool = False):
         neo_kwargs = self.map_to_neo_kwargs(file_path)
-        NeoBaseRecordingExtractor.__init__(self, all_annotations=all_annotations, **neo_kwargs)
+        NeoBaseRecordingExtractor.__init__(
+            self,
+            all_annotations=all_annotations,
+            use_names_as_ids=use_names_as_ids,
+            **neo_kwargs,
+        )
         self._kwargs.update({"file_path": str(Path(file_path).absolute())})
 
     @classmethod

src/spikeinterface/extractors/neoextractors/biocam.py

@@ -29,6 +29,9 @@ class BiocamRecordingExtractor(NeoBaseRecordingExtractor):
         If there are several streams, specify the stream name you want to load.
     all_annotations : bool, default: False
         Load exhaustively all annotations from neo.
+    use_names_as_ids : bool, default: False
+        Determines the format of the channel IDs used by the extractor. If set to True, the channel IDs will be the
+        names from NeoRawIO. If set to False, the channel IDs will be the ids provided by NeoRawIO.
     """
 
     NeoRawIOClass = "BiocamRawIO"
@@ -40,11 +43,17 @@ def __init__(
         electrode_width=None,
         stream_id=None,
         stream_name=None,
-        all_annotations=False,
+        all_annotations: bool = False,
+        use_names_as_ids: bool = False,
     ):
         neo_kwargs = self.map_to_neo_kwargs(file_path)
         NeoBaseRecordingExtractor.__init__(
-            self, stream_id=stream_id, stream_name=stream_name, all_annotations=all_annotations, **neo_kwargs
+            self,
+            stream_id=stream_id,
+            stream_name=stream_name,
+            all_annotations=all_annotations,
+            use_names_as_ids=use_names_as_ids,
+            **neo_kwargs,
         )
 
         # load probe from probeinterface

src/spikeinterface/extractors/neoextractors/blackrock.py

@@ -27,7 +27,8 @@ class BlackrockRecordingExtractor(NeoBaseRecordingExtractor):
     all_annotations : bool, default: False
         Load exhaustively all annotations from neo.
     use_names_as_ids : bool, default: False
-        If False, use default IDs inherited from Neo. If True, use channel names as IDs.
+        Determines the format of the channel IDs used by the extractor. If set to True, the channel IDs will be the
+        names from NeoRawIO. If set to False, the channel IDs will be the ids provided by NeoRawIO.
 
     """
 
@@ -38,8 +39,8 @@ def __init__(
         file_path,
         stream_id=None,
         stream_name=None,
-        all_annotations=False,
-        use_names_as_ids=False,
+        all_annotations: bool = False,
+        use_names_as_ids: bool = False,
     ):
         neo_kwargs = self.map_to_neo_kwargs(file_path)
         neo_kwargs["load_nev"] = False  # Avoid loading spikes release in neo 0.12.0

src/spikeinterface/extractors/neoextractors/ced.py

@@ -25,14 +25,24 @@ class CedRecordingExtractor(NeoBaseRecordingExtractor):
         If there are several streams, specify the stream name you want to load.
     all_annotations : bool, default: False
         Load exhaustively all annotations from neo.
+    use_names_as_ids : bool, default: False
+        Determines the format of the channel IDs used by the extractor. If set to True, the channel IDs will be the
+        names from NeoRawIO. If set to False, the channel IDs will be the ids provided by NeoRawIO.
     """
 
     NeoRawIOClass = "CedRawIO"
 
-    def __init__(self, file_path, stream_id=None, stream_name=None, all_annotations=False):
+    def __init__(
+        self, file_path, stream_id=None, stream_name=None, all_annotations: bool = False, use_names_as_ids: bool = False
+    ):
         neo_kwargs = self.map_to_neo_kwargs(file_path)
         NeoBaseRecordingExtractor.__init__(
-            self, stream_id=stream_id, stream_name=stream_name, all_annotations=all_annotations, **neo_kwargs
+            self,
+            stream_id=stream_id,
+            stream_name=stream_name,
+            all_annotations=all_annotations,
+            use_names_as_ids=use_names_as_ids,
+            **neo_kwargs,
         )
         self._kwargs.update(dict(file_path=str(Path(file_path).absolute())))
         self.extra_requirements.append("neo[ced]")

src/spikeinterface/extractors/neoextractors/edf.py

@@ -24,14 +24,29 @@ class EDFRecordingExtractor(NeoBaseRecordingExtractor):
         If there are several streams, specify the stream name you want to load.
     all_annotations: bool, default: False
         Load exhaustively all annotations from neo.
+    use_names_as_ids : bool, default: False
+        Determines the format of the channel IDs used by the extractor. If set to True, the channel IDs will be the
+        names from NeoRawIO. If set to False, the channel IDs will be the ids provided by NeoRawIO.
     """
 
     NeoRawIOClass = "EDFRawIO"
 
-    def __init__(self, file_path, stream_id=None, stream_name=None, all_annotations=False):
+    def __init__(
+        self,
+        file_path,
+        stream_id=None,
+        stream_name=None,
+        all_annotations: bool = False,
+        use_names_as_ids: bool = False,
+    ):
         neo_kwargs = {"filename": str(file_path)}
         NeoBaseRecordingExtractor.__init__(
-            self, stream_id=stream_id, stream_name=stream_name, all_annotations=all_annotations, **neo_kwargs
+            self,
+            stream_id=stream_id,
+            stream_name=stream_name,
+            all_annotations=all_annotations,
+            use_names_as_ids=use_names_as_ids,
+            **neo_kwargs,
         )
         self._kwargs.update({"file_path": str(Path(file_path).absolute())})
         self.extra_requirements.append("neo[edf]")

src/spikeinterface/extractors/neoextractors/intan.py

@@ -28,7 +28,11 @@ class IntanRecordingExtractor(NeoBaseRecordingExtractor):
         check we perform is that timestamps are continuous. Setting this to True will ignore this check and set
         the attribute `discontinuous_timestamps` to True in the underlying neo object.
     use_names_as_ids : bool, default: False
-        If False, use default IDs inherited from Neo. If True, use channel names as IDs.
+        Determines the format of the channel IDs used by the extractor. If set to True, the channel IDs will be the
+        names from NeoRawIO. If set to False, the channel IDs will be the ids provided by NeoRawIO.
+
+        In Intan the ids provided by NeoRawIO are the hardware channel ids while the names are custom names given by
+        the user
 
 
     """

src/spikeinterface/extractors/neoextractors/maxwell.py

@@ -30,6 +30,9 @@ class MaxwellRecordingExtractor(NeoBaseRecordingExtractor):
         If there are several streams, specify the stream name you want to load.
     all_annotations : bool, default: False
         Load exhaustively all annotations from neo.
+    use_names_as_ids : bool, default: False
+        Determines the format of the channel IDs used by the extractor. If set to True, the channel IDs will be the
+    names from NeoRawIO. If set to False, the channel IDs will be the ids provided by NeoRawIO.
     rec_name : str, default: None
         When the file contains several recordings you need to specify the one
         you want to extract. (rec_name='rec0000').
@@ -50,6 +53,7 @@ def __init__(
         all_annotations=False,
         rec_name=None,
         install_maxwell_plugin=False,
+        use_names_as_ids: bool = False,
     ):
         if install_maxwell_plugin:
             self.install_maxwell_plugin()
@@ -61,6 +65,7 @@ def __init__(
             stream_name=stream_name,
             block_index=block_index,
             all_annotations=all_annotations,
+            use_names_as_ids=use_names_as_ids,
             **neo_kwargs,
         )
 

src/spikeinterface/extractors/neoextractors/mcsraw.py

@@ -28,18 +28,30 @@ class MCSRawRecordingExtractor(NeoBaseRecordingExtractor):
         If there are several blocks, specify the block index you want to load.
     all_annotations : bool, default: False
         Load exhaustively all annotations from neo.
+    use_names_as_ids : bool, default: False
+        Determines the format of the channel IDs used by the extractor. If set to True, the channel IDs will be the
+        names from NeoRawIO. If set to False, the channel IDs will be the ids provided by NeoRawIO.
     """
 
     NeoRawIOClass = "RawMCSRawIO"
 
-    def __init__(self, file_path, stream_id=None, stream_name=None, block_index=None, all_annotations=False):
+    def __init__(
+        self,
+        file_path,
+        stream_id=None,
+        stream_name=None,
+        block_index=None,
+        all_annotations=False,
+        use_names_as_ids: bool = False,
+    ):
         neo_kwargs = self.map_to_neo_kwargs(file_path)
         NeoBaseRecordingExtractor.__init__(
             self,
             stream_id=stream_id,
             stream_name=stream_name,
             block_index=block_index,
             all_annotations=all_annotations,
+            use_names_as_ids=use_names_as_ids,
             **neo_kwargs,
         )
         self._kwargs.update(dict(file_path=str(Path(file_path).absolute())))

src/spikeinterface/extractors/neoextractors/mearec.py

@@ -38,13 +38,21 @@ class MEArecRecordingExtractor(NeoBaseRecordingExtractor):
         The file path to load the recordings from.
     all_annotations : bool, default: False
         Load exhaustively all annotations from neo.
+    use_names_as_ids : bool, default: False
+        Determines the format of the channel IDs used by the extractor. If set to True, the channel IDs will be the
+        names from NeoRawIO. If set to False, the channel IDs will be the ids provided by NeoRawIO.
     """
 
     NeoRawIOClass = "MEArecRawIO"
 
-    def __init__(self, file_path: Union[str, Path], all_annotations: bool = False):
+    def __init__(self, file_path: Union[str, Path], all_annotations: bool = False, use_names_as_ids: bool = False):
         neo_kwargs = self.map_to_neo_kwargs(file_path)
-        NeoBaseRecordingExtractor.__init__(self, all_annotations=all_annotations, **neo_kwargs)
+        NeoBaseRecordingExtractor.__init__(
+            self,
+            all_annotations=all_annotations,
+            use_names_as_ids=use_names_as_ids,
+            **neo_kwargs,
+        )
 
         self.extra_requirements.append("mearec")
 

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):

src/spikeinterface/extractors/neoextractors/neuralynx.py

@@ -29,6 +29,9 @@ class NeuralynxRecordingExtractor(NeoBaseRecordingExtractor):
     exclude_filename : list[str], default: None
         List of filename to exclude from the loading.
         For example, use `exclude_filename=["events.nev"]` to skip loading the event file.
+    use_names_as_ids : bool, default: False
+        Determines the format of the channel IDs used by the extractor. If set to True, the channel IDs will be the
+        names from NeoRawIO. If set to False, the channel IDs will be the ids provided by NeoRawIO.
     strict_gap_mode : bool, default: False
         See neo documentation.
         Detect gaps using strict mode or not.
@@ -44,16 +47,22 @@ class NeuralynxRecordingExtractor(NeoBaseRecordingExtractor):
 
     def __init__(
         self,
-        folder_path,
+        folder_path: str | Path,
         stream_id=None,
         stream_name=None,
         all_annotations=False,
         exclude_filename=None,
         strict_gap_mode=False,
+        use_names_as_ids: bool = False,
     ):
         neo_kwargs = self.map_to_neo_kwargs(folder_path, exclude_filename, strict_gap_mode)
         NeoBaseRecordingExtractor.__init__(
-            self, stream_id=stream_id, stream_name=stream_name, all_annotations=all_annotations, **neo_kwargs
+            self,
+            stream_id=stream_id,
+            stream_name=stream_name,
+            all_annotations=all_annotations,
+            use_names_as_ids=use_names_as_ids,
+            **neo_kwargs,
         )
         self._kwargs.update(
             dict(folder_path=str(Path(folder_path).absolute()), exclude_filename=exclude_filename),

src/spikeinterface/extractors/neoextractors/neuroexplorer.py

@@ -45,14 +45,24 @@ class NeuroExplorerRecordingExtractor(NeoBaseRecordingExtractor):
         If there are several streams, specify the stream name you want to load.
     all_annotations : bool, default: False
         Load exhaustively all annotations from neo.
+    use_names_as_ids : bool, default: False
+        Determines the format of the channel IDs used by the extractor. If set to True, the channel IDs will be the
+        names from NeoRawIO. If set to False, the channel IDs will be the ids provided by NeoRawIO.
     """
 
     NeoRawIOClass = "NeuroExplorerRawIO"
 
-    def __init__(self, file_path, stream_id=None, stream_name=None, all_annotations=False):
+    def __init__(
+        self, file_path, stream_id=None, stream_name=None, all_annotations: bool = False, use_names_as_ids: bool = False
+    ):
         neo_kwargs = {"filename": str(file_path)}
         NeoBaseRecordingExtractor.__init__(
-            self, stream_id=stream_id, stream_name=stream_name, all_annotations=all_annotations, **neo_kwargs
+            self,
+            stream_id=stream_id,
+            stream_name=stream_name,
+            all_annotations=all_annotations,
+            use_names_as_ids=use_names_as_ids,
+            **neo_kwargs,
         )
         self._kwargs.update({"file_path": str(Path(file_path).absolute())})
         self.extra_requirements.append("neo[edf]")