Add MicroscopyStaticImageContainer and related mock functions

Author: alessandratrapani

spec/ndx-microscopy.extensions.yaml

@@ -245,10 +245,17 @@ groups:
         quantity: "?"
 
   - neurodata_type_def: MicroscopyStaticImage
-    neurodata_type_inc: Image --> bisogna usare per forza container
+    neurodata_type_inc: NWBDataInterface
     doc:
       Abstract class to contain static imaging data acquired from an optical channel in a microscope while a light source illuminates the
       imaging space.
+    attributes:
+      - name: name
+        dtype: text
+        doc: Name of the static image.
+      - name: description
+        dtype: text
+        doc: Description of the static image.
     links:
       - name: microscopy_rig
         doc: Link to a MicroscopyRig object containing metadata about the microscopy rig used to acquire this imaging data.
@@ -303,6 +310,15 @@ groups:
           VolumetricImagingSpace object containing metadata about the region of physical space this imaging data
           was recorded from.
 
+  - neurodata_type_def: MicroscopyStaticImageContainer
+    neurodata_type_inc: NWBDataInterface
+    default_name: MicroscopyStaticImageContainer
+    doc: A container of many MicroscopyStaticImage objects.
+    groups:
+      - neurodata_type_inc: MicroscopyStaticImage
+        doc: MicroscopyStaticImage object containing imaging data for a single channel scan.
+        quantity: "+"
+
   - neurodata_type_def: MicroscopySeries
     neurodata_type_inc: TimeSeries
     doc:
@@ -371,29 +387,22 @@ groups:
     default_name: MultiPlaneMicroscopyContainer
     doc:
       Imaging data acquired over several depths, regularly or irregularly spaced; for instance, when using an
-      electrically tunable lens. Each depth scan is stored in a separate PlanarMicroscopySeries or PlanarMicroscopyStaticImage object.
+      electrically tunable lens. Each depth scan is stored in a separate PlanarMicroscopySeries object.
     groups:
       - neurodata_type_inc: PlanarMicroscopySeries
         doc: PlanarMicroscopySeries object(s) containing imaging data for a single depth scan.
-        quantity: "*"
-      - neurodata_type_inc: PlanarMicroscopyStaticImage
-        doc: PlanarMicroscopyStaticImage object(s) containing imaging data for a single depth scan.
-        quantity: "*"
+        quantity: "+"
 
   - neurodata_type_def: MultiChannelMicroscopyContainer
     neurodata_type_inc: NWBDataInterface
     default_name: MultiChannelMicroscopyContainer
     doc:
       Imaging data acquired over several channels; for instance, when using multiple excitation wavelengths
-      or multiple indicators. Each channel is stored in a separate PlanarMicroscopySeries, VolumetricMicroscopySeries,
-      PlanarMicroscopyStaticImage or VolumetricMicroscopyStaticImage.
+      or multiple indicators. Each channel is stored in a separate PlanarMicroscopySeries or VolumetricMicroscopySeries.
     groups:
       - neurodata_type_inc: MicroscopySeries
         doc: MicroscopySeries object containing imaging data for a single channel scan.
-        quantity: "*"
-      - neurodata_type_inc: MicroscopyStaticImage
-        doc: MicroscopyStaticImage object containing imaging data for a single channel scan.
-        quantity: "*"
+        quantity: "+"
 
   - neurodata_type_def: SegmentationContainer
     neurodata_type_inc: NWBDataInterface

spec/ndx-microscopy.namespace.yaml

@@ -20,11 +20,12 @@ namespaces:
           - VectorData
           - VectorIndex
           - DynamicTableRegion
-          - ImageSeries
       - namespace: ndx-ophys-devices
         neurodata_types:
           - ExcitationSource
           - Indicator
+          - ViralVectorInjection
+          - ViralVector
           - OpticalFilter
           - Photodetector
           - DichroicMirror

src/pynwb/ndx_microscopy/__init__.py

@@ -58,6 +58,7 @@
 MicroscopyStaticImage = get_class("MicroscopyStaticImage", extension_name)
 PlanarMicroscopyStaticImage = get_class("PlanarMicroscopyStaticImage", extension_name)
 VolumetricMicroscopyStaticImage = get_class("VolumetricMicroscopyStaticImage", extension_name)
+MicroscopyStaticImageContainer = get_class("MicroscopyStaticImageContainer", extension_name)
 MicroscopySeries = get_class("MicroscopySeries", extension_name)
 PlanarMicroscopySeries = get_class("PlanarMicroscopySeries", extension_name)
 VolumetricMicroscopySeries = get_class("VolumetricMicroscopySeries", extension_name)
@@ -97,6 +98,7 @@
     "MicroscopyStaticImage",
     "PlanarMicroscopyStaticImage",
     "VolumetricMicroscopyStaticImage",
+    "MicroscopyStaticImageContainer",
     "MultiPlaneMicroscopyContainer",
     "MultiChannelMicroscopyContainer",
     "MicroscopyResponseSeries",

src/pynwb/ndx_microscopy/testing/_mock.py

@@ -419,17 +419,29 @@ def mock_PlanarMicroscopyStaticImage(
     return planar_microscopy_static_image
 
 
+def mock_MicroscopyStaticImageContainer(
+    *,
+    microscopy_static_images: Optional[List[ndx_microscopy.MicroscopyStaticImage]] = None,
+    name: Optional[str] = None,
+) -> ndx_microscopy.MicroscopyStaticImageContainer:
+    container_name = name or name_generator("MicroscopyStaticImageContainer")
+
+    microscopy_static_image_container = ndx_microscopy.MicroscopyStaticImageContainer(
+        name=container_name,
+        microscopy_static_images=microscopy_static_images,
+    )
+    return microscopy_static_image_container
+
+
 def mock_MultiPlaneMicroscopyContainer(
     *,
     planar_microscopy_series: Optional[List[ndx_microscopy.PlanarMicroscopySeries]] = None,
-    planar_microscopy_static_images: Optional[List[ndx_microscopy.PlanarMicroscopyStaticImage]] = None,
     name: Optional[str] = None,
 ) -> ndx_microscopy.MultiPlaneMicroscopyContainer:
     container_name = name or name_generator("MultiPlaneMicroscopyContainer")
     multi_plane_microscopy_container = ndx_microscopy.MultiPlaneMicroscopyContainer(
         name=container_name,
         planar_microscopy_series=planar_microscopy_series,
-        planar_microscopy_static_images=planar_microscopy_static_images,
     )
 
     return multi_plane_microscopy_container
@@ -438,15 +450,13 @@ def mock_MultiPlaneMicroscopyContainer(
 def mock_MultiChannelMicroscopyContainer(
     *,
     microscopy_series: Optional[List[ndx_microscopy.MicroscopySeries]] = None,
-    microscopy_static_images: Optional[List[ndx_microscopy.MicroscopyStaticImage]] = None,
     name: Optional[str] = None,
 ) -> ndx_microscopy.MultiChannelMicroscopyContainer:
     container_name = name or name_generator("MultiChannelMicroscopyContainer")
 
     multi_channel_microscopy_container = ndx_microscopy.MultiChannelMicroscopyContainer(
         name=container_name,
         microscopy_series=microscopy_series,
-        microscopy_static_images=microscopy_static_images,
     )
     return multi_channel_microscopy_container
 

src/pynwb/tests/test_constructors.py

@@ -1,6 +1,10 @@
 """Test in-memory Python API constructors for the ndx-microscopy extension."""
 
-from ndx_microscopy.testing._mock import mock_PlanarMicroscopyStaticImage, mock_VolumetricMicroscopyStaticImage
+from ndx_microscopy.testing._mock import (
+    mock_MicroscopyStaticImageContainer,
+    mock_PlanarMicroscopyStaticImage,
+    mock_VolumetricMicroscopyStaticImage,
+)
 import pytest
 
 from ndx_microscopy.testing import (
@@ -73,7 +77,7 @@ def test_constructor_microscopy_experiment_metadata():
     indicator = mock_Indicator(name="Indicator1", viral_vector_injection=viral_vector_injection)
     microscopy_rig = mock_MicroscopyRig()
 
-    microscopy_experiment_metadata = MicroscopyExperimentMetadata(
+    _ = MicroscopyExperimentMetadata(
         viral_vectors=[viral_vector],
         viral_vector_injections=[viral_vector_injection],
         indicators=[indicator],
@@ -220,7 +224,7 @@ def test_constructor_planar_microscopy_static_image():
     )
 
 
-def test_constructor_multi_plane_microscopy_container_with_series():
+def test_constructor_multi_plane_microscopy_container():
     from ndx_ophys_devices.testing import mock_Indicator
 
     microscopy_channel = mock_MicroscopyChannel(indicator=mock_Indicator(name="Indicator1"))
@@ -239,26 +243,7 @@ def test_constructor_multi_plane_microscopy_container_with_series():
     assert multi_plane_microscopy_container.name == "MultiPlaneMicroscopyContainer"
 
 
-def test_constructor_multi_plane_microscopy_container_with_static_images():
-    from ndx_ophys_devices.testing import mock_Indicator
-
-    microscopy_channel = mock_MicroscopyChannel(indicator=mock_Indicator(name="Indicator1"))
-    microscopy_rig = mock_MicroscopyRig()
-    planar_imaging_space = mock_PlanarImagingSpace()
-
-    planar_microscopy_static_image = mock_PlanarMicroscopyStaticImage(
-        microscopy_rig=microscopy_rig,
-        microscopy_channel=microscopy_channel,
-        planar_imaging_space=planar_imaging_space,
-    )
-
-    multi_plane_microscopy_container = mock_MultiPlaneMicroscopyContainer(
-        planar_microscopy_static_images=[planar_microscopy_static_image]
-    )
-    assert multi_plane_microscopy_container.name == "MultiPlaneMicroscopyContainer"
-
-
-def test_constructor_multi_channel_microscopy_container_with_series():
+def test_constructor_multi_channel_microscopy_container():
     from ndx_ophys_devices.testing import mock_Indicator
 
     microscopy_channel = mock_MicroscopyChannel(indicator=mock_Indicator(name="Indicator1"))
@@ -276,7 +261,7 @@ def test_constructor_multi_channel_microscopy_container_with_series():
     assert multi_channel_microscopy_container.name == "MultiChannelMicroscopyContainer"
 
 
-def test_constructor_multi_channel_microscopy_container_with_static_images():
+def test_constructor_microscopy_static_images_container():
     from ndx_ophys_devices.testing import mock_Indicator
 
     microscopy_channel = mock_MicroscopyChannel(indicator=mock_Indicator(name="Indicator1"))
@@ -288,10 +273,10 @@ def test_constructor_multi_channel_microscopy_container_with_static_images():
         planar_imaging_space=planar_imaging_space,
     )
 
-    multi_channel_microscopy_container = mock_MultiChannelMicroscopyContainer(
+    microscopy_static_image_container = mock_MicroscopyStaticImageContainer(
         microscopy_static_images=[planar_microscopy_static_image]
     )
-    assert multi_channel_microscopy_container.name == "MultiChannelMicroscopyContainer"
+    assert microscopy_static_image_container.name == "MicroscopyStaticImageContainer"
 
 
 def test_constructor_volumetric_microscopy_series():