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Make add_segmentation kwarg only #1687

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Merged
h-mayorquin merged 1 commit into from
Mar 9, 2026
Merged

Make add_segmentation kwarg only #1687

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1 change: 1 addition & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,7 @@
## Removals, Deprecations and Changes
* Removed deprecated wrapper functions from `roiextractors_pending_deprecation.py` (March 2026 deadline): `add_imaging_plane_to_nwbfile`, `add_image_segmentation_to_nwbfile`, `add_photon_series_to_nwbfile`, `add_plane_segmentation_to_nwbfile`, `add_background_plane_segmentation_to_nwbfile`, `add_background_fluorescence_traces_to_nwbfile`, `add_summary_images_to_nwbfile`. [PR #1680](https://github.com/catalystneuro/neuroconv/pull/1680)
* Added `*args` positional argument deprecation to `add_imaging_to_nwbfile` to enforce keyword-only arguments. Will be enforced on or after September 2026. [PR #1680](https://github.com/catalystneuro/neuroconv/pull/1680)
* Added `*args` positional argument deprecation to `add_segmentation_to_nwbfile` to enforce keyword-only arguments. Will be enforced on or after September 2026. [PR #1687](https://github.com/catalystneuro/neuroconv/pull/1687)
* Removed the deprecated `staging` parameter from `automatic_dandi_upload`. Use `sandbox` instead. [PR #1678](https://github.com/catalystneuro/neuroconv/pull/1678)
* Removed the deprecated `container_name` parameter from `ImageInterface.add_to_nwbfile` and `DeepLabCutInterface.add_to_nwbfile`. Use `metadata_key` in `__init__` instead. [PR #1678](https://github.com/catalystneuro/neuroconv/pull/1678)
* Removed the deprecated `time_series_name` parameter from `add_recording_as_time_series_to_nwbfile`. Use `metadata_key` instead. [PR #1678](https://github.com/catalystneuro/neuroconv/pull/1678)
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40 changes: 40 additions & 0 deletions src/neuroconv/tools/roiextractors/roiextractors.py
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Expand Up @@ -1911,6 +1911,7 @@ def add_segmentation_to_nwbfile(
segmentation_extractor: SegmentationExtractor,
nwbfile: NWBFile,
metadata: dict | None = None,
*args, # TODO: change to * (keyword only) on or after September 2026
plane_segmentation_name: str | None = None,
background_plane_segmentation_name: str | None = None,
include_background_segmentation: bool = False,
Expand Down Expand Up @@ -1950,6 +1951,45 @@ def add_segmentation_to_nwbfile(
NWBFile
The NWBFile with the added segmentation data.
"""
# TODO: Remove this block in September 2026 or after when positional arguments are no longer supported.
if args:
parameter_names = [
"plane_segmentation_name",
"background_plane_segmentation_name",
"include_background_segmentation",
"include_roi_centroids",
"include_roi_acceptance",
"mask_type",
"iterator_options",
]
num_positional_args_before_args = 3 # segmentation_extractor, nwbfile, metadata
if len(args) > len(parameter_names):
raise TypeError(
f"add_segmentation_to_nwbfile() takes at most {len(parameter_names) + num_positional_args_before_args} positional arguments but "
f"{len(args) + num_positional_args_before_args} were given. "
"Note: Positional arguments are deprecated and will be removed in September 2026 or after. Please use keyword arguments."
)
positional_values = dict(zip(parameter_names, args))
passed_as_positional = list(positional_values.keys())
warnings.warn(
f"Passing arguments positionally to add_segmentation_to_nwbfile is deprecated "
f"and will be removed in September 2026 or after. "
f"The following arguments were passed positionally: {passed_as_positional}. "
"Please use keyword arguments instead.",
FutureWarning,
stacklevel=2,
)
plane_segmentation_name = positional_values.get("plane_segmentation_name", plane_segmentation_name)
background_plane_segmentation_name = positional_values.get(
"background_plane_segmentation_name", background_plane_segmentation_name
)
include_background_segmentation = positional_values.get(
"include_background_segmentation", include_background_segmentation
)
include_roi_centroids = positional_values.get("include_roi_centroids", include_roi_centroids)
include_roi_acceptance = positional_values.get("include_roi_acceptance", include_roi_acceptance)
mask_type = positional_values.get("mask_type", mask_type)
iterator_options = positional_values.get("iterator_options", iterator_options)

# Add device:
_add_devices_to_nwbfile_old_list_format(nwbfile=nwbfile, metadata=metadata)
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