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complete tests
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@CodyCBakerPhD
CodyCBakerPhD committed Aug 27, 2024
1 parent 3d66f79 commit 5110cd8
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Showing 3 changed files with 110 additions and 45 deletions.
26 changes: 22 additions & 4 deletions src/pynwb/ndx_microscopy/testing/_mock.py
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Original file line number Diff line number Diff line change
Expand Up @@ -382,17 +382,35 @@ def mock_MicroscopyResponseSeries(
number_of_rois = len(table_region.data)
series_data = data if data is not None else np.ones(shape=(number_of_frames, number_of_rois))

if timestamps is None:
series_starting_time = starting_time or 0.0
series_rate = rate or 10.0
series_timestamps = None
else:
if starting_time is not None or rate is not None:
warnings.warn(
message=(
"Timestamps were provided in addition to either rate or starting_time! "
"Please specify only timestamps, or both starting_time and rate. Timestamps will take precedence."
),
stacklevel=2,
)

series_starting_time = None
series_rate = None
series_timestamps = timestamps

microscopy_response_series = ndx_microscopy.MicroscopyResponseSeries(
name=series_name,
description=description,
table_region=table_region,
data=data,
data=series_data,
unit=unit,
conversion=conversion,
offset=offset,
starting_time=starting_time,
rate=rate,
timestamps=timestamps,
starting_time=series_starting_time,
rate=series_rate,
timestamps=series_timestamps,
)

return microscopy_response_series
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6 changes: 4 additions & 2 deletions src/pynwb/tests/test_constructors.py
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Original file line number Diff line number Diff line change
Expand Up @@ -117,9 +117,11 @@ def test_constructor_microscopy_response_series_container():
table=plane_segmentation,
)

microscopy_response_series = [ndx_microscopy.testing.mock_MicroscopyResponseSeries(table_region=table_region)]
microscopy_response_series = ndx_microscopy.testing.mock_MicroscopyResponseSeries(table_region=table_region)

ndx_microscopy.testing.mock_MicroscopyResponseSeriesContainer(microscopy_response_series=microscopy_response_series)
ndx_microscopy.testing.mock_MicroscopyResponseSeriesContainer(
microscopy_response_series=[microscopy_response_series]
)


def test_constructor_multi_channel_microscopy_volume():
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123 changes: 84 additions & 39 deletions src/pynwb/tests/test_roundtrip.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,20 +4,8 @@
from pynwb.testing import TestCase as pynwb_TestCase
from pynwb.testing.mock.file import mock_NWBFile

import ndx_microscopy.testing
import pynwb
from ndx_microscopy.testing import (
mock_Microscope,
mock_MicroscopyLightSource,
mock_MicroscopyOpticalChannel,
mock_MicroscopyPlaneSegmentation,
mock_MicroscopySegmentations,
mock_MultiChannelMicroscopyVolume,
mock_PlanarImagingSpace,
mock_PlanarMicroscopySeries,
mock_VariableDepthMicroscopySeries,
mock_VolumetricImagingSpace,
mock_VolumetricMicroscopySeries,
)


class TestPlanarMicroscopySeriesSimpleRoundtrip(pynwb_TestCase):
Expand All @@ -32,19 +20,19 @@ def tearDown(self):
def test_roundtrip(self):
nwbfile = mock_NWBFile()

microscope = mock_Microscope(name="Microscope")
microscope = ndx_microscopy.testing.mock_Microscope(name="Microscope")
nwbfile.add_device(devices=microscope)

light_source = mock_MicroscopyLightSource(name="MicroscopyLightSource")
light_source = ndx_microscopy.testing.mock_MicroscopyLightSource(name="MicroscopyLightSource")
nwbfile.add_device(devices=light_source)

imaging_space = mock_PlanarImagingSpace(name="PlanarImagingSpace", microscope=microscope)
imaging_space = ndx_microscopy.testing.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")
optical_channel = ndx_microscopy.testing.mock_MicroscopyOpticalChannel(name="MicroscopyOpticalChannel")
nwbfile.add_lab_meta_data(lab_meta_data=optical_channel)

planar_microscopy_series = mock_PlanarMicroscopySeries(
planar_microscopy_series = ndx_microscopy.testing.mock_PlanarMicroscopySeries(
name="PlanarMicroscopySeries",
microscope=microscope,
light_source=light_source,
Expand Down Expand Up @@ -80,19 +68,21 @@ def tearDown(self):
def test_roundtrip(self):
nwbfile = mock_NWBFile()

microscope = mock_Microscope(name="Microscope")
microscope = ndx_microscopy.testing.mock_Microscope(name="Microscope")
nwbfile.add_device(devices=microscope)

light_source = mock_MicroscopyLightSource(name="MicroscopyLightSource")
light_source = ndx_microscopy.testing.mock_MicroscopyLightSource(name="MicroscopyLightSource")
nwbfile.add_device(devices=light_source)

imaging_space = mock_VolumetricImagingSpace(name="VolumetricImagingSpace", microscope=microscope)
imaging_space = ndx_microscopy.testing.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")
optical_channel = ndx_microscopy.testing.mock_MicroscopyOpticalChannel(name="MicroscopyOpticalChannel")
nwbfile.add_lab_meta_data(lab_meta_data=optical_channel)

volumetric_microscopy_series = mock_VolumetricMicroscopySeries(
volumetric_microscopy_series = ndx_microscopy.testing.mock_VolumetricMicroscopySeries(
name="VolumetricMicroscopySeries",
microscope=microscope,
light_source=light_source,
Expand Down Expand Up @@ -130,19 +120,19 @@ def tearDown(self):
def test_roundtrip(self):
nwbfile = mock_NWBFile()

microscope = mock_Microscope(name="Microscope")
microscope = ndx_microscopy.testing.mock_Microscope(name="Microscope")
nwbfile.add_device(devices=microscope)

light_source = mock_MicroscopyLightSource(name="MicroscopyLightSource")
light_source = ndx_microscopy.testing.mock_MicroscopyLightSource(name="MicroscopyLightSource")
nwbfile.add_device(devices=light_source)

imaging_space = mock_PlanarImagingSpace(name="PlanarImagingSpace", microscope=microscope)
imaging_space = ndx_microscopy.testing.mock_PlanarImagingSpace(name="PlanarImagingSpace", microscope=microscope)
nwbfile.add_lab_meta_data(lab_meta_data=imaging_space) # Would prefer .add_imaging_space()

optical_channel = mock_MicroscopyOpticalChannel(name="MicroscopyOpticalChannel")
optical_channel = ndx_microscopy.testing.mock_MicroscopyOpticalChannel(name="MicroscopyOpticalChannel")
nwbfile.add_lab_meta_data(lab_meta_data=optical_channel)

variable_depth_microscopy_series = mock_VariableDepthMicroscopySeries(
variable_depth_microscopy_series = ndx_microscopy.testing.mock_VariableDepthMicroscopySeries(
name="VariableDepthMicroscopySeries",
microscope=microscope,
light_source=light_source,
Expand Down Expand Up @@ -180,19 +170,21 @@ def tearDown(self):
def test_roundtrip(self):
nwbfile = mock_NWBFile()

microscope = mock_Microscope(name="Microscope")
microscope = ndx_microscopy.testing.mock_Microscope(name="Microscope")
nwbfile.add_device(devices=microscope)

imaging_space = mock_VolumetricImagingSpace(name="VolumetricImagingSpace", microscope=microscope)
imaging_space = ndx_microscopy.testing.mock_VolumetricImagingSpace(
name="VolumetricImagingSpace", microscope=microscope
)
nwbfile.add_lab_meta_data(lab_meta_data=imaging_space) # Would prefer .add_imaging_space()

light_sources = list()
light_source_0 = mock_MicroscopyLightSource(name="LightSource")
light_source_0 = ndx_microscopy.testing.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")
optical_channel_0 = ndx_microscopy.testing.mock_MicroscopyOpticalChannel(name="MicroscopyOpticalChannel")
nwbfile.add_lab_meta_data(lab_meta_data=optical_channel_0)
optical_channels.append(optical_channel_0)

Expand All @@ -209,7 +201,7 @@ def test_roundtrip(self):
),
data=optical_channels,
)
multi_channel_microscopy_volume = mock_MultiChannelMicroscopyVolume(
multi_channel_microscopy_volume = ndx_microscopy.testing.mock_MultiChannelMicroscopyVolume(
name="MultiChannelMicroscopyVolume",
microscope=microscope,
imaging_space=imaging_space,
Expand Down Expand Up @@ -247,21 +239,21 @@ def tearDown(self):
def test_roundtrip(self):
nwbfile = mock_NWBFile()

microscope = mock_Microscope(name="Microscope")
microscope = ndx_microscopy.testing.mock_Microscope(name="Microscope")
nwbfile.add_device(devices=microscope)

imaging_space = mock_PlanarImagingSpace(name="PlanarImagingSpace", microscope=microscope)
imaging_space = ndx_microscopy.testing.mock_PlanarImagingSpace(name="PlanarImagingSpace", microscope=microscope)
nwbfile.add_lab_meta_data(lab_meta_data=imaging_space) # Would prefer .add_imaging_space()

plane_segmentation_1 = mock_MicroscopyPlaneSegmentation(
plane_segmentation_1 = ndx_microscopy.testing.mock_MicroscopyPlaneSegmentation(
imaging_space=imaging_space, name="MicroscopyPlaneSegmentation1"
)
plane_segmentation_2 = mock_MicroscopyPlaneSegmentation(
plane_segmentation_2 = ndx_microscopy.testing.mock_MicroscopyPlaneSegmentation(
imaging_space=imaging_space, name="MicroscopyPlaneSegmentation2"
)
microscopy_plane_segmentations = [plane_segmentation_1, plane_segmentation_2]

segmentations = mock_MicroscopySegmentations(
segmentations = ndx_microscopy.testing.mock_MicroscopySegmentations(
name="MicroscopySegmentations", microscopy_plane_segmentations=microscopy_plane_segmentations
)
processing_module = nwbfile.create_processing_module(name="ophys", description="")
Expand All @@ -280,7 +272,60 @@ def test_roundtrip(self):
self.assertContainerEqual(segmentations, read_nwbfile.processing["ophys"]["MicroscopySegmentations"])


# TODO: add roundtrip test for MicroscopyResponseSeries
class TestMicroscopyResponseSeriesSimpleRoundtrip(pynwb_TestCase):
"""Simple roundtrip test for MicroscopyResponseSeries."""

def setUp(self):
self.nwbfile_path = "test_microscopy_response_series_roundtrip.nwb"

def tearDown(self):
pynwb.testing.remove_test_file(self.nwbfile_path)

def test_roundtrip(self):
nwbfile = mock_NWBFile()

ophys_module = nwbfile.create_processing_module(name="ophys", description="Optical neurophysiology data.")

microscope = ndx_microscopy.testing.mock_Microscope(name="Microscope")
nwbfile.add_device(devices=microscope)

imaging_space = ndx_microscopy.testing.mock_PlanarImagingSpace(device=device)
nwbfile.add_lab_meta_data(lab_meta_data=imaging_space) # Would prefer .add_imaging_space()

plane_segmentation = ndx_microscopy.testing.mock_MicroscopyPlaneSegmentation(
name="MicroscopyPlaneSegmentation", imaging_space=imaging_space
)
ophys_module.add(plane_segmentation)

number_of_rois = 10
plane_segmentation_region = pynwb.ophys.DynamicTableRegion(
name="table_region", # Name must be exactly this
description="",
data=[x for x in range(number_of_rois)],
table=plane_segmentation,
)
microscopy_response_series = ndx_microscopy.testing.mock_MicroscopyResponseSeries(
name="MicroscopyResponseSeries",
table_region=plane_segmentation_region,
)

container = ndx_microscopy.MicroscopyResponseSeriesContainer(
name="MicroscopyResponseSeriesContainer", microscopy_response_series=[microscopy_response_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(imaging_space, read_nwbfile.lab_meta_data["PlanarImagingSpace"])

self.assertContainerEqual(segmentations, read_nwbfile.processing["ophys"]["MicroscopySegmentations"])

self.assertContainerEqual(container, read_nwbfile.processing["ophys"]["MicroscopyResponseSeriesContainer"])


if __name__ == "__main__":
Expand Down

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