Add optional parameters to OpticalSeries constructor (#2023)

Co-authored-by: Steph Prince <[email protected]> Co-authored-by: Ryan Ly <[email protected]>
NeurodataWithoutBorders · Feb 20, 2025 · 5564f82 · 5564f82
1 parent f3b3306
commit 5564f82
Show file tree

Hide file tree

Showing 4 changed files with 69 additions and 6 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -5,6 +5,9 @@
 ### Enhancements and minor changes
 - Added `__all__` to modules. @bendichter [#2021](https://github.com/NeurodataWithoutBorders/pynwb/pull/2021)
 - Added `pynwb.read_nwb` convenience method to simplify reading an NWBFile written with any backend @h-mayorquin [#1994](https://github.com/NeurodataWithoutBorders/pynwb/pull/1994)
+
+### Bug fixes
+- Made distance, orientation, and field_of_view optional in OpticalSeries to match schema @bendichter [#2023](https://github.com/NeurodataWithoutBorders/pynwb/pull/2023)
 - Added support for NWB schema 2.8.0. @rly [#2001](https://github.com/NeurodataWithoutBorders/pynwb/pull/2001)
   - Removed `SpatialSeries.bounds` field that was not functional. This will be fixed in a future release. @rly [#1907](https://github.com/NeurodataWithoutBorders/pynwb/pull/1907), [#1996](https://github.com/NeurodataWithoutBorders/pynwb/pull/1996)
   - Added support for `NWBFile.was_generated_by` field. @stephprince [#1924](https://github.com/NeurodataWithoutBorders/pynwb/pull/1924)

diff --git a/src/pynwb/image.py b/src/pynwb/image.py
@@ -331,12 +331,26 @@ class OpticalSeries(ImageSeries):
                      'orientation')
 
     @docval(*get_docval(ImageSeries.__init__, 'name'),  # required
-            {'name': 'distance', 'type': float, 'doc': 'Distance from camera/monitor to target/eye.'},  # required
-            {'name': 'field_of_view', 'type': ('array_data', 'data', 'TimeSeries'), 'shape': ((2, ), (3, )),  # required
-             'doc': 'Width, height and depth of image, or imaged area (meters).'},
-            {'name': 'orientation', 'type': str,  # required
-             'doc': 'Description of image relative to some reference frame (e.g., which way is up). '
-                    'Must also specify frame of reference.'},
+            {
+                "name": "distance",
+                "type": float,
+                "doc": "Distance from camera/monitor to target/eye.",
+                "default": None,
+            },
+            {
+                "name": "field_of_view",
+                "type": ("array_data", "data", "TimeSeries"),
+                "shape": ((2,), (3,)),
+                "doc": "Width, height and depth of image, or imaged area (meters).",
+                "default": None,
+            },
+            {
+                "name": "orientation",
+                "type": str,
+                "doc": "Description of image relative to some reference frame (e.g., which way is up). "
+                "Must also specify frame of reference.",
+                "default": None,
+            },
             {'name': 'data', 'type': ('array_data', 'data'), 'shape': ([None] * 3, [None, None, None, 3]),
              'doc': ('Images presented to subject, either grayscale or RGB. May be 3D or 4D. The first dimension must '
                      'be time (frame). The second and third dimensions represent x and y. The optional fourth '

diff --git a/tests/integration/hdf5/test_image.py b/tests/integration/hdf5/test_image.py
@@ -53,3 +53,35 @@ def addContainer(self, nwbfile):
     def getContainer(self, nwbfile):
         """ Return the test OpticalSeries from the given NWBFile """
         return nwbfile.stimulus['OpticalSeries']
+
+
+class TestOpticalSeriesOptionalFieldsIO(NWBH5IOMixin, TestCase):
+    """Test reading/writing OpticalSeries with optional fields omitted"""
+
+    def setUpContainer(self):
+        """ Return a test OpticalSeries with optional fields set to None """
+        self.dev1 = Device('dev1')
+        self.optical_series = OpticalSeries(
+            name='OpticalSeries',
+            data=np.ones((10, 3, 3)),
+            unit='m',
+            format='raw',
+            timestamps=np.arange(10.),
+            device=self.dev1,
+        )
+        return self.optical_series
+
+    def addContainer(self, nwbfile):
+        """ Add the test OpticalSeries to the given NWBFile """
+        nwbfile.add_device(self.dev1)
+        nwbfile.add_stimulus(self.optical_series)
+
+    def getContainer(self, nwbfile):
+        """ Return the test OpticalSeries from the given NWBFile """
+        return nwbfile.stimulus['OpticalSeries']
+
+    def test_optional_fields(self):
+        """Test that optional fields are None when omitted"""
+        self.assertIsNone(self.optical_series.distance)
+        self.assertIsNone(self.optical_series.field_of_view)
+        self.assertIsNone(self.optical_series.orientation)
diff --git a/tests/unit/test_image.py b/tests/unit/test_image.py
@@ -404,6 +404,20 @@ def test_init(self):
         self.assertEqual(ts.format, 'external')
 
 
+    def test_init_all_optional_fields_none(self):
+        """Test that OpticalSeries can be created with all optional fields set to None."""
+        ts = OpticalSeries(
+            name="test_ts",
+            unit="unit",
+            external_file=["external_file"],
+            starting_frame=[0],
+            format="external",
+            timestamps=[1.0, 2.0],
+        )
+        self.assertIsNone(ts.distance)
+        self.assertIsNone(ts.field_of_view)
+        self.assertIsNone(ts.orientation)
+
 class TestImageSubtypes(TestCase):
 
     def test_grayscale_image(self):