Merge branch 'main' into add_roi_response_series

README.md

@@ -63,8 +63,7 @@ classDiagram
         --------------------------------------
         data : numeric, frame x height x width
         --> unit : text
-        depth_per_frame : numeric, length of frames
-        -- > unit : text, default="micrometers"
+        depth_per_frame_in_um : numeric, length of frames
 
         --------------------------------------
         links

spec/ndx-microscopy.extensions.yaml

@@ -473,7 +473,6 @@ groups:
       - null
     - name: depth_per_frame_in_um
       doc: Depth in micrometers of each frame in the data array.
-        These values offset the 'z' value of the `origin_coordinates` of the linked `imaging_space` object.
       dtype: numeric
       dims:
       - depths
@@ -508,6 +507,7 @@ groups:
         was recorded from.
       target_type: VolumetricImagingSpace
 
+
   - neurodata_type_def: MicroscopyResponseSeries
     neurodata_type_inc: TimeSeries
     doc: ROI responses extracted from optical imaging.

src/pynwb/ndx_microscopy/__init__.py

@@ -34,9 +34,11 @@
 VolumetricMicroscopySeries = get_class("VolumetricMicroscopySeries", extension_name)
 MultiChannelMicroscopyVolume = get_class("MultiChannelMicroscopyVolume", extension_name)
 VariableDepthMultiChannelMicroscopyVolume = get_class("VariableDepthMultiChannelMicroscopyVolume", extension_name)
+
 MicroscopyResponseSeries = get_class("MicroscopyResponseSeries", extension_name)
 MicroscopyResponseSeriesContainer = get_class("MicroscopyResponseSeriesContainer", extension_name)
 
+
 __all__ = [
     "Microscope",
     "MicroscopyLightSource",

src/pynwb/ndx_microscopy/testing/_mock.py

@@ -233,6 +233,7 @@ def mock_VariableDepthMicroscopySeries(
 ) -> ndx_microscopy.VariableDepthMicroscopySeries:
     series_name = name or name_generator("VariableDepthMicroscopySeries")
     series_data = data if data is not None else np.ones(shape=(15, 5, 5))
+
     depth_per_frame_in_um = (
         depth_per_frame_in_um
         if depth_per_frame_in_um is not None
@@ -379,6 +380,7 @@ def mock_VariableDepthMultiChannelMicroscopyVolume(
     series_name = name or name_generator("MultiChannelMicroscopyVolume")
 
     series_data = data if data is not None else np.ones(shape=(15, 5, 5))
+
     volume_depth_per_frame_in_um = (
         depth_per_frame_in_um
         if depth_per_frame_in_um is not None

src/pynwb/tests/test_constructors.py

@@ -151,9 +151,7 @@ def test_constructor_variable_depth_multi_channel_microscopy_volume():
         optical_channels=optical_channels_used_by_volume,
     )
 
-
 # TODO: add constructor tests for MicroscopyResponseSeries
 
-
 if __name__ == "__main__":
     pytest.main()  # Required since not a typical package structure

src/pynwb/tests/test_roundtrip.py

@@ -282,5 +282,6 @@ def test_roundtrip(self):
 
 # TODO: add roundtrip test for MicroscopyResponseSeries
 
+
 if __name__ == "__main__":
     pytest.main()  # Required since not a typical package structure