add Minian data interface

src/neuroconv/datainterfaces/__init__.py

@@ -81,6 +81,7 @@
 from .ophys.micromanagertiff.micromanagertiffdatainterface import (
     MicroManagerTiffImagingInterface,
 )
+from .ophys.minian.miniandatainterface import MinianSegmentationInterface
 from .ophys.miniscope.miniscopeimagingdatainterface import MiniscopeImagingInterface
 from .ophys.sbx.sbxdatainterface import SbxImagingInterface
 from .ophys.scanimage.scanimageimaginginterfaces import (
@@ -151,6 +152,7 @@
     MicroManagerTiffImagingInterface,
     MiniscopeImagingInterface,
     TDTFiberPhotometryInterface,
+    MinianSegmentationInterface,
     # Behavior
     VideoInterface,
     AudioInterface,

src/neuroconv/datainterfaces/ophys/minian/miniandatainterface.py

@@ -0,0 +1,59 @@
+from typing import Optional
+
+from pynwb import NWBFile
+from roiextractors.extraction_tools import PathType
+
+from ..basesegmentationextractorinterface import BaseSegmentationExtractorInterface
+
+
+class MinianSegmentationInterface(BaseSegmentationExtractorInterface):
+    """Data interface for MinianSegmentationExtractor."""
+
+    display_name = "Minian Segmentation"
+    associated_suffixes = (".zarr",)
+    info = "Interface for Minian segmentation data."
+
+    @classmethod
+    def get_source_schema(cls) -> dict:
+        source_metadata = super().get_source_schema()
+        source_metadata["properties"]["folder_path"]["description"] = "Path to .zarr output."
+        return source_metadata
+
+    def __init__(self, folder_path: PathType, verbose: bool = True):
+        """
+
+        Parameters
+        ----------
+        folder_path : PathType
+            Path to .zarr path.
+        verbose : bool, default True
+            Whether to print progress
+        """
+        super().__init__(folder_path=folder_path)
+        self.verbose = verbose
+
+    def add_to_nwbfile(
+        self,
+        nwbfile: NWBFile,
+        metadata: Optional[dict] = None,
+        stub_test: bool = False,
+        stub_frames: int = 100,
+        include_background_segmentation: bool = True,
+        include_roi_centroids: bool = True,
+        include_roi_acceptance: bool = False,
+        mask_type: Optional[str] = "image",  # Literal["image", "pixel", "voxel"]
+        plane_segmentation_name: Optional[str] = None,
+        iterator_options: Optional[dict] = None,
+    ):
+        super().add_to_nwbfile(
+            nwbfile=nwbfile,
+            metadata=metadata,
+            stub_test=stub_test,
+            stub_frames=stub_frames,
+            include_background_segmentation=include_background_segmentation,
+            include_roi_centroids=include_roi_centroids,
+            include_roi_acceptance=include_roi_acceptance,
+            mask_type=mask_type,
+            plane_segmentation_name=plane_segmentation_name,
+            iterator_options=iterator_options,
+        )

tests/test_on_data/ophys/test_segmentation_interfaces.py

@@ -4,6 +4,7 @@
     CaimanSegmentationInterface,
     CnmfeSegmentationInterface,
     ExtractSegmentationInterface,
+    MinianSegmentationInterface,
     Suite2pSegmentationInterface,
 )
 from neuroconv.tools.testing.data_interface_mixins import (
@@ -204,3 +205,47 @@ class TestSuite2pSegmentationInterfaceWithStubTest(SegmentationExtractorInterfac
     )
     save_directory = OUTPUT_PATH
     conversion_options = dict(stub_test=True)
+
+
+class TestMinianSegmentationInterface(SegmentationExtractorInterfaceTestMixin):
+    data_interface_cls = MinianSegmentationInterface
+    interface_kwargs = dict(folder_path=OPHYS_DATA_PATH / "segmentation_datasets" / "minian")
+    save_directory = OUTPUT_PATH
+
+    @pytest.fixture(
+        params=[
+            {"mask_type": "image", "include_background_segmentation": True},
+            {"mask_type": "pixel", "include_background_segmentation": True},
+            {"mask_type": "voxel", "include_background_segmentation": True},
+            # {"mask_type": None, "include_background_segmentation": True}, # Uncomment when https://github.com/catalystneuro/neuroconv/issues/530 is resolved
+            {"include_roi_centroids": False, "include_background_segmentation": True},
+            {"include_roi_acceptance": False, "include_background_segmentation": True},
+            {"include_background_segmentation": False},
+        ],
+        ids=[
+            "mask_type_image",
+            "mask_type_pixel",
+            "mask_type_voxel",
+            "exclude_roi_centroids",
+            "exclude_roi_acceptance",
+            "exclude_background_segmentation",
+        ],
+    )
+    def setup_interface(self, request):
+
+        test_id = request.node.callspec.id
+        self.test_name = test_id
+        self.interface_kwargs = self.interface_kwargs
+        self.conversion_options = request.param
+        self.interface = self.data_interface_cls(**self.interface_kwargs)
+
+        return self.interface, self.test_name
+
+
+class TestMinianSegmentationInterfaceWithStubTest(SegmentationExtractorInterfaceTestMixin):
+    data_interface_cls = MinianSegmentationInterface
+    interface_kwargs = dict(
+        folder_path=OPHYS_DATA_PATH / "segmentation_datasets" / "minian",
+    )
+    save_directory = OUTPUT_PATH
+    conversion_options = dict(stub_test=True)