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update tests
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@alessandratrapani
alessandratrapani committed Jan 24, 2025
1 parent b5a259c commit 10cba71
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Showing 3 changed files with 30 additions and 32 deletions.
20 changes: 10 additions & 10 deletions src/pynwb/ndx_microscopy/testing/_mock.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -154,7 +154,7 @@ def mock_PlanarMicroscopySeries(
*,
microscope: ndx_microscopy.Microscope,
excitation_light_path: ndx_microscopy.ExcitationLightPath,
imaging_space: ndx_microscopy.PlanarImagingSpace,
planar_imaging_space: ndx_microscopy.PlanarImagingSpace,
emission_light_path: ndx_microscopy.EmissionLightPath,
name: Optional[str] = None,
description: str = "A mock instance of a PlanarMicroscopySeries type to be used for rapid testing.",
Expand Down Expand Up @@ -192,7 +192,7 @@ def mock_PlanarMicroscopySeries(
description=description,
microscope=microscope,
excitation_light_path=excitation_light_path,
imaging_space=imaging_space,
planar_imaging_space=planar_imaging_space,
emission_light_path=emission_light_path,
data=series_data,
unit=unit,
Expand All @@ -209,7 +209,7 @@ def mock_VariableDepthMicroscopySeries(
*,
microscope: ndx_microscopy.Microscope,
excitation_light_path: ndx_microscopy.ExcitationLightPath,
imaging_space: ndx_microscopy.PlanarImagingSpace,
planar_imaging_space: ndx_microscopy.PlanarImagingSpace,
emission_light_path: ndx_microscopy.EmissionLightPath,
name: Optional[str] = None,
description: str = "A mock instance of a VariableDepthMicroscopySeries type to be used for rapid testing.",
Expand Down Expand Up @@ -254,7 +254,7 @@ def mock_VariableDepthMicroscopySeries(
description=description,
microscope=microscope,
excitation_light_path=excitation_light_path,
imaging_space=imaging_space,
planar_imaging_space=planar_imaging_space,
emission_light_path=emission_light_path,
data=series_data,
depth_per_frame_in_um=depth_per_frame_in_um,
Expand All @@ -272,7 +272,7 @@ def mock_VolumetricMicroscopySeries(
*,
microscope: ndx_microscopy.Microscope,
excitation_light_path: ndx_microscopy.ExcitationLightPath,
imaging_space: ndx_microscopy.VolumetricImagingSpace,
volumetric_imaging_space: ndx_microscopy.VolumetricImagingSpace,
emission_light_path: ndx_microscopy.EmissionLightPath,
name: Optional[str] = None,
description: str = "A mock instance of a VolumetricMicroscopySeries type to be used for rapid testing.",
Expand Down Expand Up @@ -310,7 +310,7 @@ def mock_VolumetricMicroscopySeries(
description=description,
microscope=microscope,
excitation_light_path=excitation_light_path,
imaging_space=imaging_space,
volumetric_imaging_space=volumetric_imaging_space,
emission_light_path=emission_light_path,
data=series_data,
unit=unit,
Expand All @@ -326,7 +326,7 @@ def mock_VolumetricMicroscopySeries(
def mock_MultiChannelMicroscopyVolume(
*,
microscope: ndx_microscopy.Microscope,
imaging_space: ndx_microscopy.VolumetricImagingSpace,
volumetric_imaging_space: ndx_microscopy.VolumetricImagingSpace,
excitation_light_paths: pynwb.base.VectorData,
emission_light_paths: pynwb.base.VectorData,
name: Optional[str] = None,
Expand All @@ -343,7 +343,7 @@ def mock_MultiChannelMicroscopyVolume(
name=series_name,
description=description,
microscope=microscope,
imaging_space=imaging_space,
volumetric_imaging_space=volumetric_imaging_space,
excitation_light_paths=excitation_light_paths,
emission_light_paths=emission_light_paths,
data=imaging_data,
Expand Down Expand Up @@ -424,7 +424,7 @@ def mock_MicroscopyResponseSeriesContainer(
def mock_VariableDepthMultiChannelMicroscopyVolume(
*,
microscope: ndx_microscopy.Microscope,
imaging_space: ndx_microscopy.VolumetricImagingSpace,
volumetric_imaging_space: ndx_microscopy.VolumetricImagingSpace,
excitation_light_paths: pynwb.base.VectorData,
emission_light_paths: pynwb.base.VectorData,
name: Optional[str] = None,
Expand Down Expand Up @@ -454,7 +454,7 @@ def mock_VariableDepthMultiChannelMicroscopyVolume(
name=series_name,
description=description,
microscope=microscope,
imaging_space=imaging_space,
volumetric_imaging_space=volumetric_imaging_space,
excitation_light_paths=excitation_light_paths,
emission_light_paths=emission_light_paths,
data=imaging_data,
Expand Down
20 changes: 10 additions & 10 deletions src/pynwb/tests/test_constructors.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -90,13 +90,13 @@ def test_constructor_microscopy_image_segmentation_with_plane_segmentation():
def test_constructor_planar_microscopy_series():
microscope = mock_Microscope()
excitation_light_path = mock_ExcitationLightPath()
imaging_space = mock_PlanarImagingSpace()
planar_imaging_space = mock_PlanarImagingSpace()
emission_light_path = mock_EmissionLightPath()

planar_microscopy_series = mock_PlanarMicroscopySeries(
microscope=microscope,
excitation_light_path=excitation_light_path,
imaging_space=imaging_space,
planar_imaging_space=planar_imaging_space ,
emission_light_path=emission_light_path,
)
assert (
Expand All @@ -108,13 +108,13 @@ def test_constructor_planar_microscopy_series():
def test_constructor_variable_depth_microscopy_series():
microscope = mock_Microscope()
excitation_light_path = mock_ExcitationLightPath()
imaging_space = mock_PlanarImagingSpace()
planar_imaging_space = mock_PlanarImagingSpace()
emission_light_path = mock_EmissionLightPath()

variable_depth_microscopy_series = mock_VariableDepthMicroscopySeries(
microscope=microscope,
excitation_light_path=excitation_light_path,
imaging_space=imaging_space,
planar_imaging_space =planar_imaging_space ,
emission_light_path=emission_light_path,
)
assert (
Expand All @@ -126,13 +126,13 @@ def test_constructor_variable_depth_microscopy_series():
def test_constructor_volumetric_microscopy_series():
microscope = mock_Microscope()
excitation_light_path = mock_ExcitationLightPath()
imaging_space = mock_VolumetricImagingSpace()
volumetric_imaging_space = mock_VolumetricImagingSpace()
emission_light_path = mock_EmissionLightPath()

volumetric_microscopy_series = mock_VolumetricMicroscopySeries(
microscope=microscope,
excitation_light_path=excitation_light_path,
imaging_space=imaging_space,
volumetric_imaging_space=volumetric_imaging_space,
emission_light_path=emission_light_path,
)
assert (
Expand Down Expand Up @@ -182,7 +182,7 @@ def test_constructor_microscopy_response_series_container():

def test_constructor_multi_channel_microscopy_volume():
microscope = mock_Microscope()
imaging_space = mock_VolumetricImagingSpace()
volumetric_imaging_space = mock_VolumetricImagingSpace()
excitation_light_paths = [mock_ExcitationLightPath()]
emission_light_paths = [mock_EmissionLightPath()]

Expand All @@ -201,7 +201,7 @@ def test_constructor_multi_channel_microscopy_volume():
)
multichannel_microscopy_volume = mock_MultiChannelMicroscopyVolume(
microscope=microscope,
imaging_space=imaging_space,
volumetric_imaging_space=volumetric_imaging_space,
excitation_light_paths=excitation_light_paths_used_by_volume,
emission_light_paths=emission_light_paths_used_by_volume,
)
Expand All @@ -213,7 +213,7 @@ def test_constructor_multi_channel_microscopy_volume():

def test_constructor_variable_depth_multi_channel_microscopy_volume():
microscope = mock_Microscope()
imaging_space = mock_VolumetricImagingSpace()
volumetric_imaging_space = mock_VolumetricImagingSpace()
excitation_light_paths = [mock_ExcitationLightPath()]
emission_light_paths = [mock_EmissionLightPath()]

Expand All @@ -232,7 +232,7 @@ def test_constructor_variable_depth_multi_channel_microscopy_volume():
)
variable_depth_multi_channel_microscopy_volume = mock_VariableDepthMultiChannelMicroscopyVolume(
microscope=microscope,
imaging_space=imaging_space,
volumetric_imaging_space=volumetric_imaging_space,
excitation_light_paths=excitation_light_paths_used_by_volume,
emission_light_paths=emission_light_paths_used_by_volume,
)
Expand Down
22 changes: 10 additions & 12 deletions src/pynwb/tests/test_roundtrip.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -52,7 +52,7 @@ def test_roundtrip(self):
)
nwbfile.add_lab_meta_data(lab_meta_data=excitation_light_path)

imaging_space = mock_PlanarImagingSpace(name="PlanarImagingSpace")
planar_imaging_space = mock_PlanarImagingSpace(name="PlanarImagingSpace")

photodetector = mock_Photodetector()
nwbfile.add_device(devices=photodetector)
Expand All @@ -69,7 +69,7 @@ def test_roundtrip(self):
name="PlanarMicroscopySeries",
microscope=microscope,
excitation_light_path=excitation_light_path,
imaging_space=imaging_space,
planar_imaging_space=planar_imaging_space,
emission_light_path=emission_light_path,
)
nwbfile.add_acquisition(nwbdata=planar_microscopy_series)
Expand All @@ -83,7 +83,6 @@ def test_roundtrip(self):
self.assertContainerEqual(microscope, read_nwbfile.devices["Microscope"])

self.assertContainerEqual(excitation_light_path, read_nwbfile.lab_meta_data["ExcitationLightPath"])
self.assertContainerEqual(imaging_space, read_nwbfile.lab_meta_data["PlanarImagingSpace"])
self.assertContainerEqual(emission_light_path, read_nwbfile.lab_meta_data["EmissionLightPath"])

self.assertContainerEqual(planar_microscopy_series, read_nwbfile.acquisition["PlanarMicroscopySeries"])
Expand Down Expand Up @@ -118,7 +117,7 @@ def test_roundtrip(self):
nwbfile.add_device(devices=emission_filter)

# Create imaging space
imaging_space = mock_PlanarImagingSpace(name="PlanarImagingSpace")
planar_imaging_space = mock_PlanarImagingSpace(name="PlanarImagingSpace")

# Create light paths
emission_light_path = mock_EmissionLightPath(
Expand All @@ -138,7 +137,7 @@ def test_roundtrip(self):
name="PlanarMicroscopySeries",
microscope=microscope,
excitation_light_path=excitation_light_path,
imaging_space=imaging_space,
planar_imaging_space=planar_imaging_space,
emission_light_path=emission_light_path,
)
nwbfile.add_acquisition(nwbdata=planar_microscopy_series)
Expand Down Expand Up @@ -174,7 +173,7 @@ def test_roundtrip(self):
)
nwbfile.add_lab_meta_data(lab_meta_data=excitation_light_path)

imaging_space = mock_VolumetricImagingSpace(name="VolumetricImagingSpace")
volumetric_imaging_space = mock_VolumetricImagingSpace(name="VolumetricImagingSpace")

photodetector = mock_Photodetector()
nwbfile.add_device(devices=photodetector)
Expand All @@ -191,7 +190,7 @@ def test_roundtrip(self):
name="VolumetricMicroscopySeries",
microscope=microscope,
excitation_light_path=excitation_light_path,
imaging_space=imaging_space,
volumetric_imaging_space=volumetric_imaging_space,
emission_light_path=emission_light_path,
)
nwbfile.add_acquisition(nwbdata=volumetric_microscopy_series)
Expand All @@ -205,7 +204,6 @@ def test_roundtrip(self):
self.assertContainerEqual(microscope, read_nwbfile.devices["Microscope"])

self.assertContainerEqual(excitation_light_path, read_nwbfile.lab_meta_data["ExcitationLightPath"])
self.assertContainerEqual(imaging_space, read_nwbfile.lab_meta_data["VolumetricImagingSpace"])
self.assertContainerEqual(emission_light_path, read_nwbfile.lab_meta_data["EmissionLightPath"])

self.assertContainerEqual(
Expand Down Expand Up @@ -239,7 +237,7 @@ def test_roundtrip(self):
)
nwbfile.add_lab_meta_data(lab_meta_data=excitation_light_path)

imaging_space = mock_PlanarImagingSpace(name="PlanarImagingSpace")
planar_imaging_space = mock_PlanarImagingSpace(name="PlanarImagingSpace")

photodetector = mock_Photodetector()
nwbfile.add_device(devices=photodetector)
Expand All @@ -256,7 +254,7 @@ def test_roundtrip(self):
name="VariableDepthMicroscopySeries",
microscope=microscope,
excitation_light_path=excitation_light_path,
imaging_space=imaging_space,
planar_imaging_space=planar_imaging_space,
emission_light_path=emission_light_path,
)
nwbfile.add_acquisition(nwbdata=variable_depth_microscopy_series)
Expand Down Expand Up @@ -292,7 +290,7 @@ def test_roundtrip(self):
microscope = mock_Microscope(name="Microscope")
nwbfile.add_device(devices=microscope)

imaging_space = mock_VolumetricImagingSpace(name="VolumetricImagingSpace")
volumetric_imaging_space = mock_VolumetricImagingSpace(name="VolumetricImagingSpace")

excitation_light_paths = list()
excitation_source = mock_ExcitationSource()
Expand Down Expand Up @@ -334,7 +332,7 @@ def test_roundtrip(self):
multi_channel_microscopy_volume = mock_MultiChannelMicroscopyVolume(
name="MultiChannelMicroscopyVolume",
microscope=microscope,
imaging_space=imaging_space,
volumetric_imaging_space=volumetric_imaging_space,
excitation_light_paths=excitation_light_paths_used_by_volume,
emission_light_paths=emission_light_paths_used_by_volume,
)
Expand Down

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