get basic roundtrip tests

src/pynwb/tests/test_roundtrip.py

@@ -0,0 +1,164 @@
+"""Test roundtrip (write and read back) of the Python API for the ndx-microscopy extension."""
+
+from pynwb.testing import TestCase as pynwb_TestCase
+from pynwb.testing.mock.file import mock_NWBFile
+
+import pynwb
+from ndx_microscopy.testing import (
+    mock_LightSource,
+    mock_Microscope,
+    mock_MicroscopyOpticalChannel,
+    mock_PlanarImagingSpace,
+    mock_PlanarMicroscopySeries,
+    mock_VariableDepthMicroscopySeries,
+    mock_VolumetricImagingSpace,
+    mock_VolumetricMicroscopySeries,
+)
+
+
+class TestPlanarMicroscopySeriesSimpleRoundtrip(pynwb_TestCase):
+    """Simple roundtrip test for PlanarMicroscopySeries."""
+
+    def setUp(self):
+        self.nwbfile_path = "test.nwb"
+
+    def tearDown(self):
+        pynwb.testing.remove_test_file(self.nwbfile_path)
+
+    def test_roundtrip(self):
+        nwbfile = mock_NWBFile()
+
+        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_PlanarImagingSpace(name="PlanarImagingSpace", microscope=microscope)
+        nwbfile.add_lab_meta_data(lab_meta_data=imaging_space)  # Would prefer .add_imaging_spacec()
+
+        optical_channel = mock_MicroscopyOpticalChannel(name="MicroscopyOpticalChannel")
+        nwbfile.add_lab_meta_data(lab_meta_data=optical_channel)
+
+        planar_microscopy_series = mock_PlanarMicroscopySeries(
+            name="PlanarMicroscopySeries",
+            microscope=microscope,
+            light_source=light_source,
+            imaging_space=imaging_space,
+            optical_channel=optical_channel,
+        )
+        nwbfile.add_acquisition(nwbdata=planar_microscopy_series)
+
+        with pynwb.NWBHDF5IO(path=self.nwbfile_path, mode="w") as io:
+            io.write(nwbfile)
+
+        with pynwb.NWBHDF5IO(path=self.nwbfile_path, mode="r", load_namespaces=True) as io:
+            read_nwbfile = io.read()
+
+            self.assertContainerEqual(microscope, read_nwbfile.devices["Microscope"])
+            self.assertContainerEqual(light_source, read_nwbfile.devices["LightSource"])
+
+            self.assertContainerEqual(imaging_space, read_nwbfile.lab_meta_data["PlanarImagingSpace"])
+            self.assertContainerEqual(optical_channel, read_nwbfile.lab_meta_data["MicroscopyOpticalChannel"])
+
+            self.assertContainerEqual(planar_microscopy_series, read_nwbfile.acquisition["PlanarMicroscopySeries"])
+
+
+class TestVolumetricMicroscopySeriesSimpleRoundtrip(pynwb_TestCase):
+    """Simple roundtrip test for VolumetricMicroscopySeries."""
+
+    def setUp(self):
+        self.nwbfile_path = "test.nwb"
+
+    def tearDown(self):
+        pynwb.testing.remove_test_file(self.nwbfile_path)
+
+    def test_roundtrip(self):
+        nwbfile = mock_NWBFile()
+
+        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_spacec()
+
+        optical_channel = mock_MicroscopyOpticalChannel(name="MicroscopyOpticalChannel")
+        nwbfile.add_lab_meta_data(lab_meta_data=optical_channel)
+
+        volumetric_microscopy_series = mock_VolumetricMicroscopySeries(
+            name="VolumetricMicroscopySeries",
+            microscope=microscope,
+            light_source=light_source,
+            imaging_space=imaging_space,
+            optical_channel=optical_channel,
+        )
+        nwbfile.add_acquisition(nwbdata=volumetric_microscopy_series)
+
+        with pynwb.NWBHDF5IO(path=self.nwbfile_path, mode="w") as io:
+            io.write(nwbfile)
+
+        with pynwb.NWBHDF5IO(path=self.nwbfile_path, mode="r", load_namespaces=True) as io:
+            read_nwbfile = io.read()
+
+            self.assertContainerEqual(microscope, read_nwbfile.devices["Microscope"])
+            self.assertContainerEqual(light_source, 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(
+                volumetric_microscopy_series, read_nwbfile.acquisition["VolumetricMicroscopySeries"]
+            )
+
+
+class TestVariableDepthMicroscopySeriesSimpleRoundtrip(pynwb_TestCase):
+    """Simple roundtrip test for VariableDepthMicroscopySeries."""
+
+    def setUp(self):
+        self.nwbfile_path = "test.nwb"
+
+    def tearDown(self):
+        pynwb.testing.remove_test_file(self.nwbfile_path)
+
+    def test_roundtrip(self):
+        nwbfile = mock_NWBFile()
+
+        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_PlanarImagingSpace(name="PlanarImagingSpace", microscope=microscope)
+        nwbfile.add_lab_meta_data(lab_meta_data=imaging_space)  # Would prefer .add_imaging_spacec()
+
+        optical_channel = mock_MicroscopyOpticalChannel(name="MicroscopyOpticalChannel")
+        nwbfile.add_lab_meta_data(lab_meta_data=optical_channel)
+
+        variable_depth_microscopy_series = mock_VariableDepthMicroscopySeries(
+            name="VariableDepthMicroscopySeries",
+            microscope=microscope,
+            light_source=light_source,
+            imaging_space=imaging_space,
+            optical_channel=optical_channel,
+        )
+        nwbfile.add_acquisition(nwbdata=variable_depth_microscopy_series)
+
+        with pynwb.NWBHDF5IO(path=self.nwbfile_path, mode="w") as io:
+            io.write(nwbfile)
+
+        with pynwb.NWBHDF5IO(path=self.nwbfile_path, mode="r", load_namespaces=True) as io:
+            read_nwbfile = io.read()
+
+            self.assertContainerEqual(microscope, read_nwbfile.devices["Microscope"])
+            self.assertContainerEqual(light_source, read_nwbfile.devices["LightSource"])
+
+            self.assertContainerEqual(imaging_space, read_nwbfile.lab_meta_data["PlanarImagingSpace"])
+            self.assertContainerEqual(optical_channel, read_nwbfile.lab_meta_data["MicroscopyOpticalChannel"])
+
+            self.assertContainerEqual(
+                variable_depth_microscopy_series, read_nwbfile.acquisition["VariableDepthMicroscopySeries"]
+            )