Create specs (#1)

* create specs * add test * minor fix * fix typos * restructure testing * minor fix * create DeviceModel * add OpticalFilter as base calss for BandOpticalFilter and EdgeOpticalFilter * add a example for magnification field * minor fixes * add mermaid entity relationship diagram * add pulsed excitation source * add tests for DeviceModel, OpticalFilter and PulsedExcitationSource * update Entity relationship diagram * Update spec/ndx-ophys-devices.extensions.yaml Co-authored-by: Cody Baker <[email protected]> * separate diagrams * fix illumination_type doc * define indicator and effector as nwbcontainer * minor fix * remove Microscope object * remove Microscope object * remmove tetrode series from example.ipynb * minor fixes * change dichroic mirror attribute from bandwidth to band --------- Co-authored-by: Cody Baker <[email protected]>
catalystneuro · Aug 27, 2024 · 3a5dc62 · 3a5dc62
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diff --git a/README.md b/README.md
@@ -13,3 +13,211 @@ This is an NWB extension for storing metadata of devices used in optical experim
 
 ---
 This extension was created using [ndx-template](https://github.com/nwb-extensions/ndx-template).
+
+## Entity relationship diagrams
+
+#### Indicator and Effector
+
+```mermaid
+%%{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
+
+```mermaid
+%%{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 : extends
+```
+#### Devices in the microscopy setup
+```mermaid
+%%{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
+    }
+    
+    ExcitationSource *-- DeviceModel : extends
+    PulsedExcitationSource *-- ExcitationSource : extends
+    Photodetector *-- DeviceModel : extends
+    ObjectiveLens *-- DeviceModel : extends
+    OpticalFilter *-- DeviceModel : extends
+    BandOpticalFilter *-- OpticalFilter : extends
+    EdgeOpticalFilter *-- OpticalFilter : extends
+    DichroicMirror *-- DeviceModel : extends
+```
+#### Devices in the fiber photometry setup
+```mermaid
+%%{init: {'theme': 'base', 'themeVariables': {'primaryColor': '#ffffff', "primaryBorderColor': '#144E73', 'lineColor': '#D96F32'}}}%%
+classDiagram
+    direction BT
+    class DeviceModel{
+        <<Device>>
+        --------------------------------------
+        attributes
+        --------------------------------------
+        model : text, optional
+    }
+    class OpticalFiber{
+        <<DeviceModel>>
+        --------------------------------------
+        attributes
+        --------------------------------------
+        numerical_aperture : numeric, optional
+        core_diameter_in_um : numeric, 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
+    }
+    ExcitationSource *-- DeviceModel : extends
+    PulsedExcitationSource *-- ExcitationSource : extends
+    Photodetector *-- DeviceModel : extends
+    OpticalFiber *-- DeviceModel : extends
+    DichroicMirror *-- DeviceModel : extends
+    OpticalFilter *-- DeviceModel : extends
+    BandOpticalFilter *-- OpticalFilter : extends
+    EdgeOpticalFilter *-- OpticalFilter : extends
+```
+
+## Contributing
+
+Add a comment on how to contribute to this extension