minor fixes

catalystneuro · Dec 19, 2024 · cd590bf · cd590bf
1 parent 8b90262
commit cd590bf
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Showing 2 changed files with 15 additions and 9 deletions.
diff --git a/spec/ndx-microscopy.extensions.yaml b/spec/ndx-microscopy.extensions.yaml
@@ -10,12 +10,15 @@ groups:
         required: false
 
   - neurodata_type_def: ExcitationLightPath
-    neurodata_type_inc: NWBContainer
+    neurodata_type_inc: LabMetaData
     doc: Excitation light path that illuminates an imaging space.
     attributes:
       - name: excitation_wavelength_in_nm
         dtype: numeric
         doc: Excitation wavelength of light, in nanometers.
+      - name: description
+        dtype: text
+        doc: Description of the excitation light path.
     links:
       - name: excitation_source
         target_type: ExcitationSource
@@ -27,12 +30,15 @@ groups:
         required: false
 
   - neurodata_type_def: EmissionLightPath
-    neurodata_type_inc: NWBContainer
+    neurodata_type_inc: LabMetaData
     doc: Emission light path from an imaging space.
     attributes:
       - name: emission_wavelength_in_nm
         dtype: numeric
         doc: Emission wavelength of light, in nanometers.
+      - name: description
+        dtype: text
+        doc: Description of the emission light path.
     links:
       - name: photodetector
         target_type: Photodetector

diff --git a/src/pynwb/tests/test_roundtrip.py b/src/pynwb/tests/test_roundtrip.py
@@ -39,7 +39,7 @@ def test_roundtrip(self):
         excitation_light_path = mock_ExcitationLightPath(name="ExcitationLightPath")
         nwbfile.add_lab_meta_data(lab_meta_data=excitation_light_path)
 
-        imaging_space = mock_PlanarImagingSpace(name="PlanarImagingSpace", microscope=microscope)
+        imaging_space = mock_PlanarImagingSpace(name="PlanarImagingSpace")
         nwbfile.add_lab_meta_data(lab_meta_data=imaging_space)  # Would prefer .add_imaging_spacec()
 
         emission_light_path = mock_EmissionLightPath(name="EmissionLightPath")
@@ -87,7 +87,7 @@ def test_roundtrip(self):
         excitation_light_path = mock_ExcitationLightPath(name="ExcitationLightPath")
         nwbfile.add_lab_meta_data(lab_meta_data=excitation_light_path)
 
-        imaging_space = mock_VolumetricImagingSpace(name="VolumetricImagingSpace", microscope=microscope)
+        imaging_space = mock_VolumetricImagingSpace(name="VolumetricImagingSpace")
         nwbfile.add_lab_meta_data(lab_meta_data=imaging_space)  # Would prefer .add_imaging_spacec()
 
         emission_light_path = mock_EmissionLightPath(name="EmissionLightPath")
@@ -137,7 +137,7 @@ def test_roundtrip(self):
         excitation_light_path = mock_ExcitationLightPath(name="ExcitationLightPath")
         nwbfile.add_lab_meta_data(lab_meta_data=excitation_light_path)
 
-        imaging_space = mock_PlanarImagingSpace(name="PlanarImagingSpace", microscope=microscope)
+        imaging_space = mock_PlanarImagingSpace(name="PlanarImagingSpace")
         nwbfile.add_lab_meta_data(lab_meta_data=imaging_space)  # Would prefer .add_imaging_space()
 
         emission_light_path = mock_EmissionLightPath(name="EmissionLightPath")
@@ -184,7 +184,7 @@ def test_roundtrip(self):
         microscope = mock_Microscope(name="Microscope")
         nwbfile.add_device(devices=microscope)
 
-        imaging_space = mock_VolumetricImagingSpace(name="VolumetricImagingSpace", microscope=microscope)
+        imaging_space = mock_VolumetricImagingSpace(name="VolumetricImagingSpace")
         nwbfile.add_lab_meta_data(lab_meta_data=imaging_space)  # Would prefer .add_imaging_space()
 
         excitation_light_paths = list()
@@ -198,7 +198,7 @@ def test_roundtrip(self):
         emission_light_paths.append(emission_light_path_0)
 
         # TODO: It might be more convenient in Python to have a custom constructor that takes in a list of
-        # light sources and optical channels and does the VectorData wrapping internally
+        # excitation light paths and emission light paths and does the VectorData wrapping internally
         excitation_light_paths_used_by_volume = pynwb.base.VectorData(
             name="excitation_light_paths",
             description="Light sources used by this MultiChannelVolume.",
@@ -253,7 +253,7 @@ def test_roundtrip(self):
         microscope = mock_Microscope(name="Microscope")
         nwbfile.add_device(devices=microscope)
 
-        imaging_space = mock_PlanarImagingSpace(name="PlanarImagingSpace", microscope=microscope)
+        imaging_space = mock_PlanarImagingSpace(name="PlanarImagingSpace")
         nwbfile.add_lab_meta_data(lab_meta_data=imaging_space)  # Would prefer .add_imaging_space()
 
         plane_segmentation_1 = mock_MicroscopyPlaneSegmentation(
@@ -298,7 +298,7 @@ def test_roundtrip(self):
         microscope = mock_Microscope(name="Microscope")
         nwbfile.add_device(devices=microscope)
 
-        imaging_space = mock_PlanarImagingSpace(name="PlanarImagingSpace", microscope=microscope)
+        imaging_space = mock_PlanarImagingSpace(name="PlanarImagingSpace")
         nwbfile.add_lab_meta_data(lab_meta_data=imaging_space)  # Would prefer .add_imaging_space()
 
         microscopy_plane_segmentations = mock_MicroscopyPlaneSegmentation(