diff --git a/README.md b/README.md index 347baaf..148426c 100644 --- a/README.md +++ b/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 diff --git a/spec/ndx-microscopy.extensions.yaml b/spec/ndx-microscopy.extensions.yaml index 8c63255..dd0279f 100644 --- a/spec/ndx-microscopy.extensions.yaml +++ b/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. diff --git a/src/pynwb/ndx_microscopy/__init__.py b/src/pynwb/ndx_microscopy/__init__.py index 97fcb51..d5f989b 100644 --- a/src/pynwb/ndx_microscopy/__init__.py +++ b/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", diff --git a/src/pynwb/ndx_microscopy/testing/_mock.py b/src/pynwb/ndx_microscopy/testing/_mock.py index 5b2467c..60944e2 100644 --- a/src/pynwb/ndx_microscopy/testing/_mock.py +++ b/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 diff --git a/src/pynwb/tests/test_constructors.py b/src/pynwb/tests/test_constructors.py index 4c99c34..f6054ff 100644 --- a/src/pynwb/tests/test_constructors.py +++ b/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 diff --git a/src/pynwb/tests/test_roundtrip.py b/src/pynwb/tests/test_roundtrip.py index 6778919..a7b1330 100644 --- a/src/pynwb/tests/test_roundtrip.py +++ b/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