Create initial specs integrating devices from ndx-ophys-devices #12
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rly
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May 26, 2024
spec/ndx-microscopy.namespace.yaml
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| - namespace: | ||
| - core | ||
| - ndx-ophys-devices |
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Should be:
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| - namespace: | |
| - core | |
| - ndx-ophys-devices | |
| - namespace: core | |
| - namespace: ndx-ophys-devices |
schema should be a list of dicts with certain keys
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In general, I recommend using the API to create the specs, though I know it adds another step.
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Does ndx-ophys-devices need to be in the ndx-catalog? I got this error:
KeyError: "'ndx-ophys-devices' not a namespace"
for more information, see https://pre-commit.ci
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@alessandratrapani Two small conflicts |
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replaced by #22 |
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see catalystneuro/ndx-ophys-devices#1 for ophys devices
%%{init: {'theme': 'base', 'themeVariables': {'primaryColor': '#ffffff', "primaryBorderColor': '#144E73', 'lineColor': '#D96F32'}}}%% classDiagram direction BT class MicroscopySeries { <<TimeSeries>> -------------------------------------- datasets -------------------------------------- microscopy_table_region : DynamicTableRegion } class PlanarMicroscopySeries { <<MicroscopySeries>> -------------------------------------- datasets -------------------------------------- data : numeric, frame x height x width --> unit : text -------------------------------------- links -------------------------------------- imaging_space : PlanarImagingSpace } class VariableDepthMicroscopySeries { <<MicroscopySeries>> -------------------------------------- datasets -------------------------------------- data : numeric, frame x height x width --> unit : text depth_per_frame : numeric, length of frames -- > unit : text, default="micrometers" -------------------------------------- links -------------------------------------- imaging_space : PlanarImagingSpace } class VolumetricMicroscopySeries { <<MicroscopySeries>> -------------------------------------- datasets -------------------------------------- data : numeric, frame x height x width x depth --> unit : text -------------------------------------- links -------------------------------------- imaging_space : VolumetricImageSpace } class ImagingSpace{ <<NWBContainer>> -------------------------------------- datasets -------------------------------------- description : text origin_coordinates : numeric, length 3, optional --> unit : text, default="micrometers" -------------------------------------- attributes -------------------------------------- location : text, optional } class PlanarImagingSpace{ <<ImagingSpace>> -------------------------------------- datasets -------------------------------------- grid_spacing : numeric, length 2, optional --> unit : text, default="micrometers" -------------------------------------- attributes -------------------------------------- reference_frame : text, optional } class VolumetricImagingSpace{ <<ImagingSpace>> -------------------------------------- datasets -------------------------------------- grid_spacing : numeric, length 2, optional --> unit : text, default="micrometers" -------------------------------------- attributes -------------------------------------- reference_frame : text, optional } class MicroscopyTable{ <<DynamicTable>> -------------------------------------- datasets -------------------------------------- VectorData : - location : text, optional - coordinates : numeric, length 2, optional --> unit : text, default="micrometers" - indicator : Indicator - notes : text, optional - microscope : Microscope - excitation_source : ExcitationSource - photodetector : Photodetector - dichroic_mirror : DichroicMirror - emission_filter : OpticalFilter - excitation_filter : OpticalFilter - objective_lens : ObjectiveLens } class Microscopy{ <<LabMetaData>> -------------------------------------- groups -------------------------------------- microscopy_table : MicroscopyTable } PlanarMicroscopySeries *-- MicroscopySeries : extends PlanarMicroscopySeries -- PlanarImagingSpace : links VariableDepthMicroscopySeries *-- MicroscopySeries : extends VariableDepthMicroscopySeries -- PlanarImagingSpace : links VolumetricMicroscopySeries *-- MicroscopySeries : extends VolumetricMicroscopySeries -- VolumetricImagingSpace : links PlanarImagingSpace *-- ImagingSpace : extends VolumetricImagingSpace *-- ImagingSpace : extends MicroscopySeries ..> MicroscopyTable : reference rows Microscopy ..> MicroscopyTable : links