Merge branch 'dev' into inspect_on_dandisets

Author: CodyCBakerPhD

nwbinspector/checks/ophys.py

@@ -1,10 +1,12 @@
 """Check functions specific to optical electrophysiology neurodata types."""
-from pynwb.ophys import RoiResponseSeries, PlaneSegmentation
+from pynwb.ophys import RoiResponseSeries, PlaneSegmentation, OpticalChannel, ImagingPlane
 
 from hdmf.utils import get_data_shape
 
 from ..register_checks import register_check, Importance, InspectorMessage
 
+MIN_LAMBDA = 10.0  # trigger warnings for wavelength values less than this value
+
 
 @register_check(importance=Importance.CRITICAL, neurodata_type=RoiResponseSeries)
 def check_roi_response_series_dims(roi_response_series: RoiResponseSeries):
@@ -32,18 +34,15 @@ def check_roi_response_series_link_to_plane_segmentation(roi_response_series: Ro
         return InspectorMessage(message="rois field does not point to a PlaneSegmentation table.")
 
 
-# @nwbinspector_check(severity=2, neurodata_type=pynwb.TimeSeries)
-# def check_ophys(nwbfile):
-#     opto_sites = list(all_of_type(nwbfile, pynwb.ogen.OptogeneticStimulusSite))
-#     opto_series = list(all_of_type(nwbfile, pynwb.ogen.OptogeneticSeries))
-#     for site in opto_sites:
-#         if not site.description:
-#             error_code = "A101"
-#             print(
-#                 "%s: '%s' %s is missing text for attribute 'description'"
-# % (error_code, site.name, type(site).__name__)
-#             )
-#         if not site.location:
-#             error_code = "A101"
-#             print("%s: '%s' %s is missing text for attribute 'location'"
-# % (error_code, site.name, type(site).__name__))
+@register_check(importance=Importance.BEST_PRACTICE_VIOLATION, neurodata_type=OpticalChannel)
+def check_emission_lambda_in_nm(optical_channel: OpticalChannel):
+    """Check that emission lambda is in feasible range for unit nanometers."""
+    if optical_channel.emission_lambda < MIN_LAMBDA:
+        return InspectorMessage(f"emission lambda of {optical_channel.emission_lambda} should be in units of nm.")
+
+
+@register_check(importance=Importance.BEST_PRACTICE_VIOLATION, neurodata_type=ImagingPlane)
+def check_excitation_lambda_in_nm(imaging_plane: ImagingPlane):
+    """Check that emission lambda is in feasible range for unit nanometers."""
+    if imaging_plane.excitation_lambda < MIN_LAMBDA:
+        return InspectorMessage(f"excitation lambda of {imaging_plane.excitation_lambda} should be in units of nm.")

tests/unit_tests/test_ophys.py

@@ -4,12 +4,15 @@
 
 import numpy as np
 from pynwb import NWBFile
-from pynwb.ophys import OpticalChannel, ImageSegmentation, RoiResponseSeries
+from pynwb.device import Device
+from pynwb.ophys import OpticalChannel, ImageSegmentation, RoiResponseSeries, ImagingPlane
 from hdmf.common.table import DynamicTableRegion, DynamicTable
 
 from nwbinspector.checks.ophys import (
     check_roi_response_series_dims,
     check_roi_response_series_link_to_plane_segmentation,
+    check_excitation_lambda_in_nm,
+    check_emission_lambda_in_nm,
 )
 from nwbinspector.register_checks import InspectorMessage, Importance
 
@@ -167,3 +170,60 @@ def test_pass_check_roi_response_series_link_to_plane_segmentation(self):
         )
 
         assert check_roi_response_series_link_to_plane_segmentation(roi_resp_series) is None
+
+
+def test_check_excitation_lambda_in_nm():
+
+    device = Device(
+        name="Microscope", description="My two-photon microscope", manufacturer="The best microscope manufacturer"
+    )
+    optical_channel = OpticalChannel(name="OpticalChannel", description="an optical channel", emission_lambda=500.0)
+    imaging_plane = ImagingPlane(
+        name="ImagingPlane",
+        optical_channel=optical_channel,
+        imaging_rate=30.0,
+        description="a very interesting part of the brain",
+        device=device,
+        excitation_lambda=1.0,
+        indicator="GFP",
+        location="V1",
+        grid_spacing=[0.01, 0.01],
+        grid_spacing_unit="meters",
+        origin_coords=[1.0, 2.0, 3.0],
+        origin_coords_unit="meters",
+    )
+
+    assert check_excitation_lambda_in_nm(imaging_plane).message == "excitation lambda of 1.0 should be in units of nm."
+
+
+def test_pass_check_excitation_lambda_in_nm():
+    device = Device(
+        name="Microscope", description="My two-photon microscope", manufacturer="The best microscope manufacturer"
+    )
+    optical_channel = OpticalChannel(name="OpticalChannel", description="an optical channel", emission_lambda=500.0)
+    imaging_plane = ImagingPlane(
+        name="ImagingPlane",
+        optical_channel=optical_channel,
+        imaging_rate=30.0,
+        description="a very interesting part of the brain",
+        device=device,
+        excitation_lambda=300.0,
+        indicator="GFP",
+        location="V1",
+        grid_spacing=[0.01, 0.01],
+        grid_spacing_unit="meters",
+        origin_coords=[1.0, 2.0, 3.0],
+        origin_coords_unit="meters",
+    )
+
+    assert check_excitation_lambda_in_nm(imaging_plane) is None
+
+
+def test_check_emission_lambda_in_nm():
+    optical_channel = OpticalChannel(name="OpticalChannel", description="an optical channel", emission_lambda=5.0)
+    assert check_emission_lambda_in_nm(optical_channel).message == "emission lambda of 5.0 should be in units of nm."
+
+
+def test_pass_check_emission_lambda_in_nm():
+    optical_channel = OpticalChannel(name="OpticalChannel", description="an optical channel", emission_lambda=500.0)
+    assert check_emission_lambda_in_nm(optical_channel) is None