Add to_nwbfile to methods in roi extractors (#1027)

catalystneuro · Aug 25, 2024 · 727228c · 727228c
1 parent bd1493c
commit 727228c
Show file tree

Hide file tree

Showing 7 changed files with 645 additions and 235 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -6,6 +6,8 @@
 * 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)
 * `neuroconv.utils.FilePathType` and `neuroconv.utils.FolderPathType` have been deprecated; please use `pydantic.FilePath` and `pydantic.DirectoryPath` instead. [PR #1017](https://github.com/catalystneuro/neuroconv/pull/1017)
+* Changed the roiextractors.tool function (e.g. `add_imaging` and `add_segmentation`) to have the `_to_nwbfile` suffix [PR #1027][PR #1017](https://github.com/catalystneuro/neuroconv/pull/1027)
+
 
 ### Features
 * Added MedPCInterface for operant behavioral output files. [PR #883](https://github.com/catalystneuro/neuroconv/pull/883)

diff --git a/src/neuroconv/datainterfaces/ophys/baseimagingextractorinterface.py b/src/neuroconv/datainterfaces/ophys/baseimagingextractorinterface.py
@@ -147,15 +147,15 @@ def add_to_nwbfile(
         stub_test: bool = False,
         stub_frames: int = 100,
     ):
-        from ...tools.roiextractors import add_imaging
+        from ...tools.roiextractors import add_imaging_to_nwbfile
 
         if stub_test:
             stub_frames = min([stub_frames, self.imaging_extractor.get_num_frames()])
             imaging_extractor = self.imaging_extractor.frame_slice(start_frame=0, end_frame=stub_frames)
         else:
             imaging_extractor = self.imaging_extractor
 
-        add_imaging(
+        add_imaging_to_nwbfile(
             imaging=imaging_extractor,
             nwbfile=nwbfile,
             metadata=metadata,

diff --git a/src/neuroconv/datainterfaces/ophys/basesegmentationextractorinterface.py b/src/neuroconv/datainterfaces/ophys/basesegmentationextractorinterface.py
@@ -165,15 +165,15 @@ def add_to_nwbfile(
         -------
 
         """
-        from ...tools.roiextractors import add_segmentation
+        from ...tools.roiextractors import add_segmentation_to_nwbfile
 
         if stub_test:
             stub_frames = min([stub_frames, self.segmentation_extractor.get_num_frames()])
             segmentation_extractor = self.segmentation_extractor.frame_slice(start_frame=0, end_frame=stub_frames)
         else:
             segmentation_extractor = self.segmentation_extractor
 
-        add_segmentation(
+        add_segmentation_to_nwbfile(
             segmentation_extractor=segmentation_extractor,
             nwbfile=nwbfile,
             metadata=metadata,

diff --git a/src/neuroconv/datainterfaces/ophys/miniscope/miniscopeimagingdatainterface.py b/src/neuroconv/datainterfaces/ophys/miniscope/miniscopeimagingdatainterface.py
@@ -93,7 +93,7 @@ def add_to_nwbfile(
     ):
         from ndx_miniscope.utils import add_miniscope_device
 
-        from ....tools.roiextractors import add_photon_series
+        from ....tools.roiextractors import add_photon_series_to_nwbfile
 
         miniscope_timestamps = self.get_original_timestamps()
         imaging_extractor = self.imaging_extractor
@@ -108,7 +108,7 @@ def add_to_nwbfile(
         device_metadata = metadata["Ophys"]["Device"][0]
         add_miniscope_device(nwbfile=nwbfile, device_metadata=device_metadata)
 
-        add_photon_series(
+        add_photon_series_to_nwbfile(
             imaging=imaging_extractor,
             nwbfile=nwbfile,
             metadata=metadata,

diff --git a/src/neuroconv/tools/roiextractors/__init__.py b/src/neuroconv/tools/roiextractors/__init__.py
@@ -1,6 +1,20 @@
 from .roiextractors import (
+    check_if_imaging_fits_into_memory,
+    get_nwb_imaging_metadata,
+    get_nwb_segmentation_metadata,
     add_background_fluorescence_traces,
     add_background_plane_segmentation,
+    add_devices_to_nwbfile,
+    add_fluorescence_traces_to_nwbfile,
+    add_image_segmentation_to_nwbfile,
+    add_imaging_to_nwbfile,
+    add_imaging_plane_to_nwbfile,
+    add_photon_series_to_nwbfile,
+    add_plane_segmentation_to_nwbfile,
+    add_segmentation_to_nwbfile,
+    add_summary_images_to_nwbfile,
+    write_imaging_to_nwbfile,
+    write_segmentation_to_nwbfile,
     add_devices,
     add_fluorescence_traces,
     add_image_segmentation,
@@ -10,9 +24,6 @@
     add_plane_segmentation,
     add_segmentation,
     add_summary_images,
-    check_if_imaging_fits_into_memory,
-    get_nwb_imaging_metadata,
-    get_nwb_segmentation_metadata,
     write_imaging,
     write_segmentation,
 )