From c8b5dfd23c41247880a7156349d4ebd10e047c93 Mon Sep 17 00:00:00 2001 From: Cody Baker Date: Wed, 26 Jun 2024 12:26:39 -0400 Subject: [PATCH 1/3] fix intercompatability --- spec/ndx-microscopy.extensions.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/spec/ndx-microscopy.extensions.yaml b/spec/ndx-microscopy.extensions.yaml index da3d397..8d03861 100644 --- a/spec/ndx-microscopy.extensions.yaml +++ b/spec/ndx-microscopy.extensions.yaml @@ -313,8 +313,8 @@ groups: doc: Link to a Microscope object containing metadata about the device used to acquire this imaging data. target_type: Microscope - name: light_source - doc: Link to a LightSource object containing metadata about the device used to illuminate the imaging space. - target_type: LightSource + doc: Link to a MicroscopyLightSource object containing metadata about the device used to illuminate the imaging space. + target_type: MicroscopyLightSource # TODO: figure out best way to link to list of optical channels - name: optical_channels doc: Link to an ordered list of MicroscopyOpticalChannel objects containing metadata about the indicator and From ad6b5e74adf681bb4ac9c191629ead857d79ba62 Mon Sep 17 00:00:00 2001 From: Cody Baker Date: Wed, 26 Jun 2024 12:30:14 -0400 Subject: [PATCH 2/3] fix light sources --- spec/ndx-microscopy.extensions.yaml | 5 +++-- src/pynwb/ndx_microscopy/testing/_mock.py | 4 ++-- 2 files changed, 5 insertions(+), 4 deletions(-) diff --git a/spec/ndx-microscopy.extensions.yaml b/spec/ndx-microscopy.extensions.yaml index 8d03861..c5fb049 100644 --- a/spec/ndx-microscopy.extensions.yaml +++ b/spec/ndx-microscopy.extensions.yaml @@ -312,8 +312,9 @@ groups: - name: microscope doc: Link to a Microscope object containing metadata about the device used to acquire this imaging data. target_type: Microscope - - name: light_source - doc: Link to a MicroscopyLightSource object containing metadata about the device used to illuminate the imaging space. + # TODO: figure out best way to link to list of light sources + - name: light_sources + doc: Link to an ordered list of MicroscopyLightSource objects containing metadata about the excitation method. target_type: MicroscopyLightSource # TODO: figure out best way to link to list of optical channels - name: optical_channels diff --git a/src/pynwb/ndx_microscopy/testing/_mock.py b/src/pynwb/ndx_microscopy/testing/_mock.py index 6a32364..4a09dfb 100644 --- a/src/pynwb/ndx_microscopy/testing/_mock.py +++ b/src/pynwb/ndx_microscopy/testing/_mock.py @@ -291,7 +291,7 @@ def mock_VolumetricMicroscopySeries( def mock_MultiChannelMicroscopyVolume( *, microscope: ndx_microscopy.Microscope, - light_source: ndx_microscopy.LightSource, + light_sources: ndx_microscopy.MicroscopyLightSource, imaging_space: ndx_microscopy.VolumetricImagingSpace, optical_channels: List[ndx_microscopy.MicroscopyOpticalChannel], name: Optional[str] = None, @@ -308,7 +308,7 @@ def mock_MultiChannelMicroscopyVolume( name=series_name, description=description, microscope=microscope, - light_source=light_source, + light_sources=light_source[0], # TODO: figure out how to specify list imaging_space=imaging_space, optical_channels=optical_channels[0], # TODO: figure out how to specify list data=imaging_data, From 8b69db4fb9318e1d3a9c1dfa34aaf6ac40611e9e Mon Sep 17 00:00:00 2001 From: Cody Baker Date: Wed, 26 Jun 2024 13:06:41 -0400 Subject: [PATCH 3/3] fix --- src/pynwb/ndx_microscopy/testing/_mock.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/pynwb/ndx_microscopy/testing/_mock.py b/src/pynwb/ndx_microscopy/testing/_mock.py index 4a09dfb..12cf5eb 100644 --- a/src/pynwb/ndx_microscopy/testing/_mock.py +++ b/src/pynwb/ndx_microscopy/testing/_mock.py @@ -291,7 +291,7 @@ def mock_VolumetricMicroscopySeries( def mock_MultiChannelMicroscopyVolume( *, microscope: ndx_microscopy.Microscope, - light_sources: ndx_microscopy.MicroscopyLightSource, + light_sources: List[ndx_microscopy.MicroscopyLightSource], imaging_space: ndx_microscopy.VolumetricImagingSpace, optical_channels: List[ndx_microscopy.MicroscopyOpticalChannel], name: Optional[str] = None, @@ -308,7 +308,7 @@ def mock_MultiChannelMicroscopyVolume( name=series_name, description=description, microscope=microscope, - light_sources=light_source[0], # TODO: figure out how to specify list + light_sources=light_sources[0], # TODO: figure out how to specify list imaging_space=imaging_space, optical_channels=optical_channels[0], # TODO: figure out how to specify list data=imaging_data,