Add MockSegmentationInterface (#1067)

Co-authored-by: Szonja Weigl <[email protected]>
Co-authored-by: Paul Adkisson <[email protected]>

CHANGELOG.md

@@ -33,6 +33,7 @@
 * Added `get_stream_names` to `OpenEphysRecordingInterface`: [PR #1039](https://github.com/catalystneuro/neuroconv/pull/1039)
 * Most data interfaces and converters now use Pydantic to validate their inputs, including existence of file and folder paths. [PR #1022](https://github.com/catalystneuro/neuroconv/pull/1022)
 * All remaining data interfaces and converters now use Pydantic to validate their inputs, including existence of file and folder paths. [PR #1055](https://github.com/catalystneuro/neuroconv/pull/1055)
+* Added a mock for segmentation extractors interfaces in ophys: `MockSegmentationInterface`  [PR #1067](https://github.com/catalystneuro/neuroconv/pull/1067)
 * Added automated EFS volume creation and mounting to the `submit_aws_job` helper function. [PR #1018](https://github.com/catalystneuro/neuroconv/pull/1018)
 
 
@@ -44,6 +45,8 @@
 * Improved device metadata of `IntanRecordingInterface` by adding the type of controller used [PR #1059](https://github.com/catalystneuro/neuroconv/pull/1059)
 
 
+
+
 ## v0.6.1 (August 30, 2024)
 
 ### Bug fixes

src/neuroconv/datainterfaces/ophys/basesegmentationextractorinterface.py

@@ -18,8 +18,9 @@ class BaseSegmentationExtractorInterface(BaseExtractorInterface):
 
     ExtractorModuleName = "roiextractors"
 
-    def __init__(self, **source_data):
+    def __init__(self, verbose: bool = False, **source_data):
         super().__init__(**source_data)
+        self.verbose = verbose
         self.segmentation_extractor = self.get_extractor()(**source_data)
 
     def get_metadata_schema(self) -> dict:

src/neuroconv/tools/testing/mock_interfaces.py

@@ -14,6 +14,9 @@
 from ...datainterfaces.ophys.baseimagingextractorinterface import (
     BaseImagingExtractorInterface,
 )
+from ...datainterfaces.ophys.basesegmentationextractorinterface import (
+    BaseSegmentationExtractorInterface,
+)
 from ...utils import ArrayType, get_schema_from_method_signature
 
 
@@ -216,3 +219,74 @@ def get_metadata(self, photon_series_type: Optional[Literal["OnePhotonSeries", "
         metadata = super().get_metadata(photon_series_type=photon_series_type)
         metadata["NWBFile"]["session_start_time"] = session_start_time
         return metadata
+
+
+class MockSegmentationInterface(BaseSegmentationExtractorInterface):
+    """A mock segmentation interface for testing purposes."""
+
+    ExtractorModuleName = "roiextractors.testing"
+    ExtractorName = "generate_dummy_segmentation_extractor"
+
+    def __init__(
+        self,
+        num_rois: int = 10,
+        num_frames: int = 30,
+        num_rows: int = 25,
+        num_columns: int = 25,
+        sampling_frequency: float = 30.0,
+        has_summary_images: bool = True,
+        has_raw_signal: bool = True,
+        has_dff_signal: bool = True,
+        has_deconvolved_signal: bool = True,
+        has_neuropil_signal: bool = True,
+        seed: int = 0,
+        verbose: bool = False,
+    ):
+        """
+        Parameters
+        ----------
+        num_rois : int, optional
+            number of regions of interest, by default 10.
+        num_frames : int, optional
+            description, by default 30.
+        num_rows : int, optional
+            number of rows in the hypothetical video from which the data was extracted, by default 25.
+        num_columns : int, optional
+            number of columns in the hypothetical video from which the data was extracted, by default 25.
+        sampling_frequency : float, optional
+            sampling frequency of the hypothetical video from which the data was extracted, by default 30.0.
+        has_summary_images : bool, optional
+            whether the dummy segmentation extractor has summary images or not (mean and correlation).
+        has_raw_signal : bool, optional
+            whether a raw fluorescence signal is desired in the object, by default True.
+        has_dff_signal : bool, optional
+            whether a relative (df/f) fluorescence signal is desired in the object, by default True.
+        has_deconvolved_signal : bool, optional
+            whether a deconvolved signal is desired in the object, by default True.
+        has_neuropil_signal : bool, optional
+            whether a neuropil signal is desired in the object, by default True.
+        seed: int, default 0
+            seed for the random number generator, by default 0
+        verbose : bool, optional
+            controls verbosity, by default False.
+        """
+
+        super().__init__(
+            num_rois=num_rois,
+            num_frames=num_frames,
+            num_rows=num_rows,
+            num_columns=num_columns,
+            sampling_frequency=sampling_frequency,
+            has_summary_images=has_summary_images,
+            has_raw_signal=has_raw_signal,
+            has_dff_signal=has_dff_signal,
+            has_deconvolved_signal=has_deconvolved_signal,
+            has_neuropil_signal=has_neuropil_signal,
+            verbose=verbose,
+        )
+
+    def get_metadata(self) -> dict:
+        session_start_time = datetime.now().astimezone()
+        metadata = super().get_metadata()
+        metadata["NWBFile"]["session_start_time"] = session_start_time
+        return metadata

tests/test_ophys/test_ophys_interfaces.py

@@ -1,9 +1,19 @@
 from neuroconv.tools.testing.data_interface_mixins import (
     ImagingExtractorInterfaceTestMixin,
+    SegmentationExtractorInterfaceTestMixin,
+)
+from neuroconv.tools.testing.mock_interfaces import (
+    MockImagingInterface,
+    MockSegmentationInterface,
 )
-from neuroconv.tools.testing.mock_interfaces import MockImagingInterface
 
 
 class TestMockImagingInterface(ImagingExtractorInterfaceTestMixin):
     data_interface_cls = MockImagingInterface
     interface_kwargs = dict()
+
+
+class TestMockSegmentationInterface(SegmentationExtractorInterfaceTestMixin):
+
+    data_interface_cls = MockSegmentationInterface
+    interface_kwargs = dict()