Create specs #1
Create specs #1
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FYI I highly recommend using The 'code' for it can then live in the README or some other |
Not to mention the current extension is a lot more modular than most others - I'd recommend separate ER diagrams per related group; e.g., you could define a base |
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Overall looks good - made first round of comments |
Yes, thank you for the suggestion. I was planning to do it in Mermaid once I finished this first step. I started with draw.io because it was a simple copy-paste from previous diagrams, and I just wanted to have a reference for this specific PR. |
README.md
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| attributes | ||
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| microscopy_type : text, optional | ||
| doi : text, optional |
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All microscopes have a DOI? I don't think I've ever seen that in the methods/supplemental section
How would I look it up for a particular microscope?
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It was meant to be there just for custom microscopes. I remember we discussed this a while ago, but I am also not totally convinced that this is something needed.
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Would a home-built microscope have a manufacturer or model number?
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probably not 😑, I need to change this 😅
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Where are we at on this? Does the base PyNWB device has the manufacturer then you add the model to the new BaseModel?
Is this still a TODO? |
| OpticalFilter *-- DeviceModel : extends | ||
| BandOpticalFilter *-- OpticalFilter : extends | ||
| EdgeOpticalFilter *-- OpticalFilter : extends | ||
| DichroicMirror *-- DeviceModel : extends |
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Did you intend to duplicate the OpticalFilter and below in both the ophys and fiber photometry?
I think just including it in the separate block above is sufficient unless you also showed how those filters interact as metadata with the other extensions data series (which I think would be better in the respective extensions)
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Yes! Agree I can simplify it like this
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I am correcting this in #2
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1 question about simplifying the ER diagrams, otherwise looks good! |
TODO:
Entity relationship diagrams
Indicator and Effector
%%{init: {'theme': 'base', 'themeVariables': {'primaryColor': '#ffffff', "primaryBorderColor': '#144E73', 'lineColor': '#D96F32'}}}%% classDiagram direction BT class Indicator{ <<NWBContainer>> -------------------------------------- attributes -------------------------------------- label : text description : text, optional manufacturer : text, optional injection_brain_region : text, optional injection_coordinates_in_mm : numeric, length 3, optional } class Effector{ <<NWBContainer>> -------------------------------------- attributes -------------------------------------- label : text description : text, optional manufacturer : text, optional injection_brain_region : text, optional injection_coordinates_in_mm : numeric, length 3, optional }Optical Filters
%%{init: {'theme': 'base', 'themeVariables': {'primaryColor': '#ffffff', "primaryBorderColor': '#144E73', 'lineColor': '#D96F32'}}}%% classDiagram direction BT class DeviceModel{ <<Device>> -------------------------------------- attributes -------------------------------------- model : text, optional } class DichroicMirror{ <<DeviceModel>> -------------------------------------- attributes -------------------------------------- cut_on_wavelength_in_nm : numeric, optional cut_off_wavelength_in_nm : numeric, optional reflection_band_in_nm : numeric, optional transmission_band_in_nm : numeric, optional angle_of_incidence_in_degrees : numeric, optional } class OpticalFilter{ <<DeviceModel>> -------------------------------------- attributes -------------------------------------- filter_type : text, optional } class BandOpticalFilter{ <<OpticalFilter>> -------------------------------------- attributes -------------------------------------- center_wavelength_in_nm : numeric bandwidth_in_nm : numeric } class EdgeOpticalFilter{ <<OpticalFilter>> -------------------------------------- attributes -------------------------------------- cut_wavelength_in_nm : numeric slope_in_percent_cut_wavelength : numeric, optional slope_starting_transmission_in_percent : numeric, optional slope_ending_transmission_in_percent : numeric, optional } DichroicMirror *-- DeviceModel : extends OpticalFilter *-- DeviceModel : extends BandOpticalFilter *-- OpticalFilter : extends EdgeOpticalFilter *-- OpticalFilter : extendsOther devices in the optical setup
%%{init: {'theme': 'base', 'themeVariables': {'primaryColor': '#ffffff', "primaryBorderColor': '#144E73', 'lineColor': '#D96F32'}}}%% classDiagram direction BT class DeviceModel{ <<Device>> -------------------------------------- attributes -------------------------------------- model : text, optional } class ExcitationSource{ <<DeviceModel>> -------------------------------------- attributes -------------------------------------- illumination_type : text, optional excitation_wavelength_in_nm : numeric, optional power_in_W : numeric, optional intensity_in_W_per_m2 : numeric, optional exposure_time_in_s : numeric, optional } class PulsedExcitationSource{ <<DeviceModel>> -------------------------------------- attributes -------------------------------------- peak_power_in_W : numeric, optional peak_pulse_energy_in_J : numeric, optional pulse_rate_in_Hz : numeric, optional } class Photodetector{ <<DeviceModel>> -------------------------------------- attributes -------------------------------------- detector_type : text, optional detected_wavelength_in_nm : numeric, optional gain : numeric, optional gain_unit : text, false } class ObjectiveLens{ <<DeviceModel>> -------------------------------------- attributes -------------------------------------- numerical_aperture : numeric, optional magnification : numeric, optional } class OpticalFiber{ <<DeviceModel>> -------------------------------------- attributes -------------------------------------- numerical_aperture : numeric, optional core_diameter_in_um : numeric, optional } ExcitationSource *-- DeviceModel : extends PulsedExcitationSource *-- ExcitationSource : extends Photodetector *-- DeviceModel : extends ObjectiveLens *-- DeviceModel : extends OpticalFilter *-- DeviceModel : extends BandOpticalFilter *-- OpticalFilter : extends EdgeOpticalFilter *-- OpticalFilter : extends DichroicMirror *-- DeviceModel : extends OpticalFiber *-- DeviceModel : extends