add tests for PupilTracking

src/neuroconv/datainterfaces/behavior/facemap/facemapdatainterface.py

@@ -87,7 +87,8 @@
 
     def add_eye_tracking(self, nwbfile: NWBFile, metadata: DeepDict):
 
-        timestamps = self.get_timestamps()
+        if self.timestamps is None:
+            self.timestamps = self.get_timestamps() 
 
         with h5py.File(self.source_data["mat_file_path"], "r") as file:
 
@@ -100,7 +101,7 @@
                 data=file["proc"]["pupil"]["com"][:].T,
                 reference_frame=eye_tracking_metadata["reference_frame"],
                 unit=eye_tracking_metadata["unit"],
-                timestamps=timestamps,
+                timestamps=self.timestamps,
             )
 
             eye_tracking = EyeTracking(name="EyeTracking", spatial_series=eye_com)
@@ -237,7 +238,7 @@
                 series_ref = series_ref[0]
                 mask_ref = mask_ref[0]
 
                 # skipping the first ROI because it referes to "running" mask, from Facemap doc
                 mask_coordinates = file[file["proc"]["locROI"][n][0]]
                 y1 = int(np.round(mask_coordinates[0][0]) - 1)  # correct matlab indexing
                 x1 = int(np.round(mask_coordinates[1][0]) - 1)  # correct matlab indexing

tests/test_on_data/test_behavior_interfaces.py

@@ -14,7 +14,7 @@
 from numpy.testing import assert_array_equal
 from parameterized import param, parameterized
 from pynwb import NWBHDF5IO
-from pynwb.behavior import EyeTracking, Position, SpatialSeries
+from pynwb.behavior import EyeTracking, Position, SpatialSeries, PupilTracking
 
 from neuroconv import NWBConverter
 from neuroconv.datainterfaces import (
@@ -752,31 +752,49 @@ class TestFacemapInterface(DataInterfaceTestMixin, TemporalAlignmentMixin, unitt
 
     @classmethod
     def setUpClass(cls):
-        cls.eye_com_name = "eye_center_of_mass"
+
+        cls.eye_tracking_module = "EyeTracking"
         cls.eye_com_expected_metadata = dict(
-            name=cls.eye_com_name,
+            name="eye_center_of_mass",
             description="The position of the eye measured in degrees.",
             reference_frame="unknown",
             unit="degrees",
         )
 
+        cls.pupil_tracking_module = "PupilTracking"
+        cls.pupil_area_expected_metadata = dict(
+            name="pupil_area",
+            description="Area of pupil.",
+            unit="unknown",
+        )
+        cls.pupil_area_raw__expected_metadata = dict(
+            name="pupil_area_raw",
+            description="Raw unprocessed area of pupil.",
+            unit="unknown",
+        ) 
+
         with h5py.File(cls.interface_kwargs["mat_file_path"], "r") as file:
             cls.eye_com_test_data = file["proc"]["pupil"]["com"][:].T
 
-        cls.eye_tracking_module = "EyeTracking"
-
     def check_extracted_metadata(self, metadata: dict):
 
         self.assertIn(self.eye_tracking_module, metadata["Behavior"])
         self.assertEqual(self.eye_com_expected_metadata, metadata["Behavior"]["EyeTracking"])
 
+        self.assertIn(self.pupil_tracking_module, metadata["Behavior"])
+        self.assertEqual(self.pupil_area_expected_metadata, metadata["Behavior"]["PupilTracking"]["area"])
+        self.assertEqual(self.pupil_area_raw__expected_metadata, metadata["Behavior"]["PupilTracking"]["area_raw"])
+
     def check_read_nwb(self, nwbfile_path: str):
         with NWBHDF5IO(path=nwbfile_path, mode="r", load_namespaces=True) as io:
             nwbfile = io.read()
             self.assertIn("behavior", nwbfile.processing)
             self.assertIn(self.eye_tracking_module, nwbfile.processing["behavior"].data_interfaces)
             eye_tracking_container = nwbfile.processing["behavior"].data_interfaces[self.eye_tracking_module]
             self.assertIsInstance(eye_tracking_container, EyeTracking)
+            self.assertIn(self.pupil_tracking_module, nwbfile.processing["behavior"].data_interfaces)
+            pupil_tracking_container = nwbfile.processing["behavior"].data_interfaces[self.pupil_tracking_module]
+            self.assertIsInstance(pupil_tracking_container, PupilTracking)
 
 
 if __name__ == "__main__":