Add ophys devices from ndx-ophys-devices #22
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alessandratrapani
changed the base branch from
main
to
use_updated_ndx_template
alessandratrapani
changed the base branch from
use_updated_ndx_template
to
main
* update to new template * add ndx-ophys-devices as requirement * Import ndx-ophys-devices first * minor fixes --------- Co-authored-by: rly <[email protected]>
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@pauladkisson Sorry for the messy PR. I'll try to explain what I did here:
Basically, I am asking you to review the following files that contain those 3 changes:
All the other files have already been reviewed in #26, where we updated the base template for the extension and fixed the import of ndx-ophys-device (#23). In a follow-up PR, I will make the ExcitationLightPath, the EmissionLightPath, and the ImagingSpace inherit from a general NWBContainer instead of LabMetadata. In other PR I will update the documentation |
| - neurodata_type_def: MicroscopyLightSource | ||
| neurodata_type_inc: Device | ||
| doc: Light source used to illuminate an imaging space. | ||
| - neurodata_type_def: ExcitationLightPath |
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zoomQ: ExcitationLightPath is new to me, could you explain what its purpose is?
| - name: description | ||
| doc: Description or other notes about the channel. | ||
| dtype: text | ||
| - neurodata_type_def: EmissionLightPath |
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ZoomQ: EmissionLightPath is new to me, could you explain what its purpose is?
| - name: emission_filter | ||
| target_type: OpticalFilter | ||
| doc: Link to OpticalFilter object which contains metadata about the optical filter in this emission light path. It can be either a BandOpticalFilter (e.g., 'Bandpass', 'Bandstop', 'Longpass', 'Shortpass') or a EdgeOpticalFilter (Longpass or Shortpass). | ||
| quantity: '?' | ||
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| - neurodata_type_def: ImagingSpace |
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This basically replaces ImagingPlane right?
| - name: emission_filter | ||
| target_type: OpticalFilter | ||
| doc: Link to OpticalFilter object which contains metadata about the optical filter in this emission light path. It can be either a BandOpticalFilter (e.g., 'Bandpass', 'Bandstop', 'Longpass', 'Shortpass') or a EdgeOpticalFilter (Longpass or Shortpass). | ||
| quantity: '?' |
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Is there a dichroic mirror in the light path of these microscopes? If so we should probably include it right?
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| def test_constructor_microscope(): | ||
| ndx_microscopy.testing.mock_Microscope() | ||
| mock_Microscope() |
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These tests really should have some assertions to check that the information is propagating properly.
For example, for the microscope,
def test_constructor_microscope():
microscope = mock_Microscope()
assert microscope.description == "A mock instance of a Microscope type to be used for rapid testing."| imaging_space=imaging_space, | ||
| optical_channel=optical_channel, | ||
| emission_light_path=emission_light_path, | ||
| ) | ||
| nwbfile.add_acquisition(nwbdata=planar_microscopy_series) |
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What happens if you add a PlanarMicroscopySeries to acquisition, but forget to add one of its devices?
I ask bc I've made this mistake and sometimes it fails ungracefully (ex. write works but read fails).
In this PR I added neurodatatypes from ndx-ophys-devices:
Entity relationship diagram for ndx-ophys-devices objects in ndx-microscopy
%%{init: {'theme': 'base', 'themeVariables': {'primaryColor': '#ffffff', 'primaryBorderColor': '#144E73', 'lineColor': '#D96F32'}}}%% classDiagram direction TB class DeviceModel { <<Device>> -------------------------------------- attributes -------------------------------------- model : text, optional } class ExcitationLightPath { <<LabMetaData>> -------------------------------------- attributes -------------------------------------- excitation_wavelength_in_nm : numeric description : text -------------------------------------- links -------------------------------------- excitation_source : ExcitationSource, optional excitation_filter : OpticalFilter, optional } class EmissionLightPath { <<LabMetaData>> -------------------------------------- attributes -------------------------------------- emission_wavelength_in_nm : numeric description : text -------------------------------------- groups -------------------------------------- indicator : Indicator -------------------------------------- links -------------------------------------- photodetector : Photodetector, optional emission_filter : OpticalFilter, optional } class ExcitationSource { <<DeviceModel>> -------------------------------------- attributes -------------------------------------- illumination_type : text excitation_wavelength_in_nm : float power_in_W : float, optional intensity_in_W_per_m2 : float, optional exposure_time_in_s : float, optional } class PulsedExcitationSource { <<ExcitationSource>> -------------------------------------- attributes -------------------------------------- peak_power_in_W : float, optional peak_pulse_energy_in_J : float, optional pulse_rate_in_Hz : float, optional } class OpticalFilter { <<DeviceModel>> -------------------------------------- attributes -------------------------------------- filter_type : text } class BandOpticalFilter { <<OpticalFilter>> -------------------------------------- attributes -------------------------------------- center_wavelength_in_nm : float bandwidth_in_nm : float } class EdgeOpticalFilter { <<OpticalFilter>> -------------------------------------- attributes -------------------------------------- cut_wavelength_in_nm : float slope_in_percent_cut_wavelength : float, optional slope_starting_transmission_in_percent : float, optional slope_ending_transmission_in_percent : float, optional } class Photodetector { <<DeviceModel>> -------------------------------------- attributes -------------------------------------- detector_type : text detected_wavelength_in_nm : float gain : float, optional gain_unit : text, optional } class Indicator { <<NWBContainer>> -------------------------------------- attributes -------------------------------------- label : text description : text, optional manufacturer : text, optional injection_brain_region : text, optional injection_coordinates_in_mm : float[3], optional } DeviceModel <|-- ExcitationSource : extends DeviceModel <|-- OpticalFilter : extends DeviceModel <|-- Photodetector : extends ExcitationSource <|-- PulsedExcitationSource : extends OpticalFilter <|-- BandOpticalFilter : extends OpticalFilter <|-- EdgeOpticalFilter : extends ExcitationLightPath ..> ExcitationSource : links ExcitationLightPath ..> OpticalFilter : links EmissionLightPath ..> Photodetector : links EmissionLightPath ..> OpticalFilter : links EmissionLightPath *-- Indicator : containsEntity relationship diagram for ndx-microscopy
%%{init: {'theme': 'base', 'themeVariables': {'primaryColor': '#ffffff', 'primaryBorderColor': '#144E73', 'lineColor': '#D96F32'}}}%% classDiagram direction BT class MicroscopySeries { <<TimeSeries>> -------------------------------------- links -------------------------------------- microscope : Microscope excitation_light_path : ExcitationLightPath emission_light_path : EmissionLightPath } class PlanarMicroscopySeries { <<MicroscopySeries>> -------------------------------------- datasets -------------------------------------- data : numeric, frame x height x width -------------------------------------- links -------------------------------------- imaging_space : PlanarImagingSpace } class VariableDepthMicroscopySeries { <<PlanarMicroscopySeries>> -------------------------------------- datasets -------------------------------------- depth_per_frame_in_um : numeric, length of frames } class VolumetricMicroscopySeries { <<MicroscopySeries>> -------------------------------------- datasets -------------------------------------- data : numeric, frame x height x width x depth -------------------------------------- links -------------------------------------- imaging_space : VolumetricImagingSpace } class MultiChannelMicroscopyVolume { <<NWBDataInterface>> -------------------------------------- attributes -------------------------------------- description : text, optional unit : text conversion : float32, optional, default=1.0 offset : float32, optional, default=0.0 -------------------------------------- datasets -------------------------------------- data : numeric, height x width x depth x emission_light_paths excitation_light_paths : ExcitationLightPath[] emission_light_paths : EmissionLightPath[] -------------------------------------- links -------------------------------------- imaging_space : VolumetricImagingSpace microscope : Microscope } class ImagingSpace { <<LabMetaData>> -------------------------------------- datasets -------------------------------------- description : text origin_coordinates : float64[3], optional --> unit : text, default="micrometers" -------------------------------------- attributes -------------------------------------- location : text, optional } class PlanarImagingSpace { <<ImagingSpace>> -------------------------------------- datasets -------------------------------------- grid_spacing_in_um : float64[2], optional -------------------------------------- attributes -------------------------------------- reference_frame : text, optional } class VolumetricImagingSpace { <<ImagingSpace>> -------------------------------------- datasets -------------------------------------- grid_spacing_in_um : float64[3], optional -------------------------------------- attributes -------------------------------------- reference_frame : text, optional } class ExcitationLightPath { <<LabMetaData>> -------------------------------------- attributes -------------------------------------- excitation_wavelength_in_nm : numeric description : text -------------------------------------- links -------------------------------------- excitation_source : ExcitationSource, optional excitation_filter : OpticalFilter, optional } class EmissionLightPath { <<LabMetaData>> -------------------------------------- attributes -------------------------------------- emission_wavelength_in_nm : numeric description : text -------------------------------------- groups -------------------------------------- indicator : Indicator -------------------------------------- links -------------------------------------- photodetector : Photodetector, optional emission_filter : OpticalFilter, optional } class Microscope { <<Device>> -------------------------------------- attributes -------------------------------------- model : text, optional } PlanarMicroscopySeries *-- MicroscopySeries : extends PlanarMicroscopySeries -- PlanarImagingSpace : links VariableDepthMicroscopySeries *-- PlanarMicroscopySeries : extends VolumetricMicroscopySeries *-- MicroscopySeries : extends VolumetricMicroscopySeries -- VolumetricImagingSpace : links MultiChannelMicroscopyVolume -- VolumetricImagingSpace : links PlanarImagingSpace *-- ImagingSpace : extends VolumetricImagingSpace *-- ImagingSpace : extends MicroscopySeries ..> Microscope : links MicroscopySeries ..> ExcitationLightPath : links MicroscopySeries ..> EmissionLightPath : links