Merge branch 'all_previous_prs_and_variable_depth_static' into swap_t…

…o_um

spec/ndx-microscopy.extensions.yaml

@@ -393,19 +393,22 @@ groups:
       - null
       - null
       - null
+    - name: light_sources
+      doc: Reference to a list of MicroscopyLightSource objects containing metadata about the excitation methods.
+      neurodata_type_inc: VectorData
+      dtype:
+        reftype: object
+        target_type: MicroscopyLightSource
+    - name: optical_channels
+      doc: Reference to an ordered list of MicroscopyOpticalChannel objects containing metadata about the indicator and filters used to collect this data.
+      neurodata_type_inc: VectorData
+      dtype:
+        reftype: object
+        target_type: MicroscopyOpticalChannel
     links:
     - name: microscope
       doc: Link to a Microscope object containing metadata about the device used to acquire this imaging data.
       target_type: Microscope
-      # TODO: figure out best way to link to list of light sources
-    - name: light_sources
-      doc: Link to an ordered list of MicroscopyLightSource objects containing metadata about the excitation method.
-      target_type: MicroscopyLightSource
-    # TODO: figure out best way to link to list of optical channels
-    - name: optical_channels
-      doc: Link to an ordered list of MicroscopyOpticalChannel objects containing metadata about the indicator and
-        filters used to collect this data.
-      target_type: MicroscopyOpticalChannel
     - name: imaging_space
       doc: Link to VolumetricImagingSpace object containing metadata about the region of physical space this imaging data
         was recorded from.

src/pynwb/ndx_microscopy/testing/_mock.py

@@ -2,6 +2,7 @@
 from typing import Iterable, List, Optional, Tuple
 
 import numpy as np
+import pynwb.base
 from pynwb.testing.mock.utils import name_generator
 
 import ndx_microscopy
@@ -322,9 +323,9 @@ def mock_VolumetricMicroscopySeries(
 def mock_MultiChannelMicroscopyVolume(
     *,
     microscope: ndx_microscopy.Microscope,
-    light_sources: List[ndx_microscopy.MicroscopyLightSource],
     imaging_space: ndx_microscopy.VolumetricImagingSpace,
-    optical_channels: List[ndx_microscopy.MicroscopyOpticalChannel],
+    light_sources: pynwb.base.VectorData,
+    optical_channels: pynwb.base.VectorData,
     name: Optional[str] = None,
     description: str = "This is a mock instance of a MultiChannelMicroscopyVolume type to be used for rapid testing.",
     data: Optional[np.ndarray] = None,
@@ -339,9 +340,9 @@ def mock_MultiChannelMicroscopyVolume(
         name=series_name,
         description=description,
         microscope=microscope,
-        light_sources=light_sources[0],  # TODO: figure out how to specify list
         imaging_space=imaging_space,
-        optical_channels=optical_channels[0],  # TODO: figure out how to specify list
+        light_sources=light_sources,
+        optical_channels=optical_channels,
         data=imaging_data,
         unit=unit,
         conversion=conversion,

src/pynwb/tests/test_constructors.py

@@ -2,6 +2,7 @@
 
 import pytest
 
+import pynwb
 from ndx_microscopy.testing import (
     mock_Microscope,
     mock_MicroscopyImageSegmentation,
@@ -103,15 +104,26 @@ def test_constructor_volumetric_microscopy_series():
 
 def test_constructor_multi_channel_microscopy_volume():
     microscope = mock_Microscope()
-    light_source = mock_LightSource()
     imaging_space = mock_VolumetricImagingSpace(microscope=microscope)
-    optical_channel = mock_MicroscopyOpticalChannel()
+    light_sources = [mock_MicroscopyLightSource()]
+    optical_channels = [mock_MicroscopyOpticalChannel()]
 
+    light_sources_used_by_volume = pynwb.base.VectorData(
+        name="light_sources", description="Light sources used by this MultiChannelVolume.", data=light_sources
+    )
+    optical_channels_used_by_volume = pynwb.base.VectorData(
+        name="optical_channels",
+        description=(
+            "Optical channels ordered to correspond to the third axis (e.g., [0, 0, :, 0]) "
+            "of the data for this MultiChannelVolume."
+        ),
+        data=optical_channels,
+    )
     mock_MultiChannelMicroscopyVolume(
         microscope=microscope,
-        light_source=light_source,
         imaging_space=imaging_space,
-        optical_channels=[optical_channel],
+        light_sources=light_sources_used_by_volume,
+        optical_channels=optical_channels_used_by_volume,
     )
 
 

src/pynwb/tests/test_roundtrip.py

@@ -21,7 +21,7 @@ class TestPlanarMicroscopySeriesSimpleRoundtrip(pynwb_TestCase):
     """Simple roundtrip test for PlanarMicroscopySeries."""
 
     def setUp(self):
-        self.nwbfile_path = "test.nwb"
+        self.nwbfile_path = "test_planar_microscopy_series_roundtrip.nwb"
 
     def tearDown(self):
         pynwb.testing.remove_test_file(self.nwbfile_path)
@@ -69,7 +69,7 @@ class TestVolumetricMicroscopySeriesSimpleRoundtrip(pynwb_TestCase):
     """Simple roundtrip test for VolumetricMicroscopySeries."""
 
     def setUp(self):
-        self.nwbfile_path = "test.nwb"
+        self.nwbfile_path = "test_volumetric_microscopy_series_roundtrip.nwb"
 
     def tearDown(self):
         pynwb.testing.remove_test_file(self.nwbfile_path)
@@ -119,7 +119,7 @@ class TestVariableDepthMicroscopySeriesSimpleRoundtrip(pynwb_TestCase):
     """Simple roundtrip test for VariableDepthMicroscopySeries."""
 
     def setUp(self):
-        self.nwbfile_path = "test.nwb"
+        self.nwbfile_path = "test_variable_depth_microscopy_series_roundtrip.nwb"
 
     def tearDown(self):
         pynwb.testing.remove_test_file(self.nwbfile_path)
@@ -169,7 +169,7 @@ class TestMultiChannelMicroscopyVolumeSimpleRoundtrip(pynwb_TestCase):
     """Simple roundtrip test for MultiChannelMicroscopyVolume."""
 
     def setUp(self):
-        self.nwbfile_path = "test.nwb"
+        self.nwbfile_path = "test_multi_channel_microscopy_volume_roundtrip.nwb"
 
     def tearDown(self):
         pynwb.testing.remove_test_file(self.nwbfile_path)
@@ -180,21 +180,38 @@ def test_roundtrip(self):
         microscope = mock_Microscope(name="Microscope")
         nwbfile.add_device(devices=microscope)
 
-        light_source = mock_LightSource(name="LightSource")
-        nwbfile.add_device(devices=light_source)
-
         imaging_space = mock_VolumetricImagingSpace(name="VolumetricImagingSpace", microscope=microscope)
         nwbfile.add_lab_meta_data(lab_meta_data=imaging_space)  # Would prefer .add_imaging_space()
 
-        optical_channel = mock_MicroscopyOpticalChannel(name="MicroscopyOpticalChannel")
-        nwbfile.add_lab_meta_data(lab_meta_data=optical_channel)
+        light_sources = list()
+        light_source_0 = mock_MicroscopyLightSource(name="LightSource")
+        nwbfile.add_device(devices=light_source_0)
+        light_sources.append(light_source_0)
+
+        optical_channels = list()
+        optical_channel_0 = mock_MicroscopyOpticalChannel(name="MicroscopyOpticalChannel")
+        nwbfile.add_lab_meta_data(lab_meta_data=optical_channel_0)
+        optical_channels.append(optical_channel_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
+        light_sources_used_by_volume = pynwb.base.VectorData(
+            name="light_sources", description="Light sources used by this MultiChannelVolume.", data=light_sources
+        )
+        optical_channels_used_by_volume = pynwb.base.VectorData(
+            name="optical_channels",
+            description=(
+                "Optical channels ordered to correspond to the third axis (e.g., [0, 0, :, 0]) "
+                "of the data for this MultiChannelVolume."
+            ),
+            data=optical_channels,
+        )
         multi_channel_microscopy_volume = mock_MultiChannelMicroscopyVolume(
             name="MultiChannelMicroscopyVolume",
             microscope=microscope,
-            light_source=light_source,
             imaging_space=imaging_space,
-            optical_channels=[optical_channel],
+            light_sources=light_sources_used_by_volume,
+            optical_channels=optical_channels_used_by_volume,
         )
         nwbfile.add_acquisition(nwbdata=multi_channel_microscopy_volume)
 
@@ -205,14 +222,17 @@ def test_roundtrip(self):
             read_nwbfile = io.read()
 
             self.assertContainerEqual(microscope, read_nwbfile.devices["Microscope"])
-            self.assertContainerEqual(light_source, read_nwbfile.devices["LightSource"])
+            self.assertContainerEqual(light_source_0, read_nwbfile.devices["LightSource"])
 
             self.assertContainerEqual(imaging_space, read_nwbfile.lab_meta_data["VolumetricImagingSpace"])
-            self.assertContainerEqual(optical_channel, read_nwbfile.lab_meta_data["MicroscopyOpticalChannel"])
+            self.assertContainerEqual(optical_channel_0, read_nwbfile.lab_meta_data["MicroscopyOpticalChannel"])
 
             self.assertContainerEqual(
                 multi_channel_microscopy_volume, read_nwbfile.acquisition["MultiChannelMicroscopyVolume"]
             )
 
 
 # TODO: add roundtrip for planesegmentation, imagesegmentation, etc.
+
+if __name__ == "__main__":
+    pytest.main()  # Required since not a typical package structure