Rename spikeinterface api to add_nwb (#1015)

catalystneuro · Aug 20, 2024 · 60ca62f · 60ca62f
1 parent 5a74e09
commit 60ca62f
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Showing 6 changed files with 592 additions and 175 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -2,6 +2,7 @@
 
 ### Deprecations
 * Deprecated  `WaveformExtractor` usage. [PR #821](https://github.com/catalystneuro/neuroconv/pull/821)
+* Changed the spikeinterface.tool functions (e.g. `add_recording`, `add_sorting`) to have `_to_nwbfile` as suffix  [PR #1015](https://github.com/catalystneuro/neuroconv/pull/1015)
 * Deprecated use of `compression` and `compression_options` in `VideoInterface` [PR #1005](https://github.com/catalystneuro/neuroconv/pull/1005)
 * `get_schema_from_method_signature` has been deprecated; please use `get_json_schema_from_method_signature` instead. [PR #1016](https://github.com/catalystneuro/neuroconv/pull/1016)
 

diff --git a/src/neuroconv/datainterfaces/ecephys/baserecordingextractorinterface.py b/src/neuroconv/datainterfaces/ecephys/baserecordingextractorinterface.py
@@ -349,7 +349,7 @@ def add_to_nwbfile(
                 Dictionary of keyword arguments to be passed directly to tqdm.
                 See https://github.com/tqdm/tqdm#parameters for options.
         """
-        from ...tools.spikeinterface import add_recording
+        from ...tools.spikeinterface import add_recording_to_nwbfile
 
         if stub_test or self.subset_channels is not None:
             recording = self.subset_recording(stub_test=stub_test)
@@ -359,7 +359,7 @@ def add_to_nwbfile(
         if metadata is None:
             metadata = self.get_metadata()
 
-        add_recording(
+        add_recording_to_nwbfile(
             recording=recording,
             nwbfile=nwbfile,
             metadata=metadata,

diff --git a/src/neuroconv/datainterfaces/ecephys/basesortingextractorinterface.py b/src/neuroconv/datainterfaces/ecephys/basesortingextractorinterface.py
@@ -263,17 +263,17 @@ def add_channel_metadata_to_nwb(self, nwbfile: NWBFile, metadata: Optional[DeepD
         This function adds metadata to the `nwbfile` in-place, meaning the `nwbfile` object is modified directly.
         """
         from ...tools.spikeinterface import (
-            add_devices,
-            add_electrode_groups,
-            add_electrodes,
+            add_devices_to_nwbfile,
+            add_electrode_groups_to_nwbfile,
+            add_electrodes_to_nwbfile,
         )
 
         if hasattr(self, "generate_recording_with_channel_metadata"):
             recording = self.generate_recording_with_channel_metadata()
 
-            add_devices(nwbfile=nwbfile, metadata=metadata)
-            add_electrode_groups(recording=recording, nwbfile=nwbfile, metadata=metadata)
-            add_electrodes(recording=recording, nwbfile=nwbfile, metadata=metadata)
+            add_devices_to_nwbfile(nwbfile=nwbfile, metadata=metadata)
+            add_electrode_groups_to_nwbfile(recording=recording, nwbfile=nwbfile, metadata=metadata)
+            add_electrodes_to_nwbfile(recording=recording, nwbfile=nwbfile, metadata=metadata)
 
     def add_to_nwbfile(
         self,
@@ -309,7 +309,7 @@ def add_to_nwbfile(
             The name of the units table. If write_as=='units', then units_name must also be 'units'.
         units_description : str, default: 'Autogenerated by neuroconv.'
         """
-        from ...tools.spikeinterface import add_sorting
+        from ...tools.spikeinterface import add_sorting_to_nwbfile
 
         metadata_copy = deepcopy(metadata)
         if write_ecephys_metadata:
@@ -335,7 +335,7 @@ def add_to_nwbfile(
                         value=value,
                     )
 
-        add_sorting(
+        add_sorting_to_nwbfile(
             sorting_extractor,
             nwbfile=nwbfile,
             property_descriptions=property_descriptions,

diff --git a/src/neuroconv/tools/spikeinterface/__init__.py b/src/neuroconv/tools/spikeinterface/__init__.py
@@ -7,11 +7,21 @@
     add_sorting,
     add_units_table,
     add_sorting_analyzer,
-    check_if_recording_traces_fit_into_memory,
-    get_nwb_metadata,
     write_recording,
     write_sorting,
     write_sorting_analyzer,
     add_waveforms,
     write_waveforms,
+    add_devices_to_nwbfile,
+    add_electrical_series_to_nwbfile,
+    add_electrode_groups_to_nwbfile,
+    add_electrodes_to_nwbfile,
+    add_recording_to_nwbfile,
+    add_sorting_to_nwbfile,
+    add_units_table_to_nwbfile,
+    add_sorting_analyzer_to_nwbfile,
+    write_recording_to_nwbfile,
+    write_sorting_to_nwbfile,
+    write_sorting_analyzer_to_nwbfile,
+    check_if_recording_traces_fit_into_memory,
 )