Create specs

README.md

@@ -13,3 +13,7 @@ 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).
+
+## Contributing
+
+Add a comment on how to contribute to this extension

spec/ndx-ophys-devices.extensions.yaml

@@ -1,8 +1,216 @@
 groups:
-- neurodata_type_def: TetrodeSeries
-  neurodata_type_inc: ElectricalSeries
-  doc: An extension of ElectricalSeries to include the tetrode ID for each time series.
+- neurodata_type_def: Indicator
+  neurodata_type_inc: Device
+  doc: Extends Device to hold metadata on the Indicator.
   attributes:
-  - name: trode_id
-    dtype: int32
-    doc: The tetrode ID.
+  - name: label
+    dtype: text
+    doc: Indicator standard notation.
+  - name: injection_location
+    dtype: text
+    doc: Injection brain region name.
+    required: false
+  - name: injection_coordinates_in_mm
+    dtype: float
+    shape:
+    - 3
+    doc: Indicator injection location in stereotactic coordinates (AP, ML, DV) mm
+      relative to Bregma.
+    required: false
+- neurodata_type_def: OpticalFiber
+  neurodata_type_inc: Device
+  doc: Extends Device to hold metadata on the Optical Fiber.
+  attributes:
+  - name: model
+    dtype: text
+    doc: Model of optical fiber.
+    required: false
+  - name: numerical_aperture
+    dtype: float
+    doc: Numerical aperture, e.g., 0.39 NA.
+    required: false
+  - name: core_diameter_in_um
+    dtype: float
+    doc: Core diameter in micrometers.
+    required: false
+- neurodata_type_def: ExcitationSource
+  neurodata_type_inc: Device
+  doc: Extends Device to hold metadata on the Excitation Source.
+  attributes:
+  - name: model
+    dtype: text
+    doc: Model of excitation source device.
+    required: false
+  - name: illumination_type
+    dtype: text
+    doc: 'Type of illumination. Suggested values: LED, LAser or more specifically
+      Gas, Metal vapor, Solid state, Dye, Semiconductor, Free electron, etc.'
+  - name: excitation_wavelength_in_nm
+    dtype: float
+    doc: Excitation wavelength of the stimulation light (nanometers).
+  - name: peak_power_in_W
+    dtype: float
+    doc: Incident power of stimulation device (in Watts).
+    required: false
+  - name: peak_pulse_energy_in_J
+    dtype: float
+    doc: If device is pulsed light source, pulse energy (in Joules).
+    required: false
+  - name: intensity_in_W_per_m2
+    dtype: float
+    doc: Intensity of the excitation in W/m^2, if known.
+    required: false
+  - name: pulse_rate_in_Hz
+    dtype: float
+    doc: If device is pulsed light source, pulse rate (in Hz) used for stimulation.
+    required: false
+  - name: exposure_time_in_s
+    dtype: float
+    doc: Exposure time of the sample (in sec).
+    required: false
+- neurodata_type_def: Photodetector
+  neurodata_type_inc: Device
+  doc: Extends Device to hold metadata on the Photodetector.
+  attributes:
+  - name: model
+    dtype: text
+    doc: Model of photodetector device.
+    required: false
+  - name: detector_type
+    dtype: text
+    doc: 'Technology used to detect the light. Suggested values: CCD, Intensified
+      CCD, Analog video, PMT, Photodiode, CMOS, EBCCD, FTIR.'
+  - name: detected_wavelength_in_nm
+    dtype: float
+    doc: Wavelength detected by photodetector.
+  - name: gain
+    dtype: float
+    doc: Gain on the photodetector.
+- neurodata_type_def: DichroicMirror
+  neurodata_type_inc: Device
+  doc: Extends Device to hold a Dichroic Mirror.
+  attributes:
+  - name: cut_on_wavelength_in_nm
+    dtype: float
+    doc: Wavelength at which the mirror starts to transmit light more than reflect.
+    required: false
+  - name: cut_off_wavelength_in_nm
+    dtype: float
+    doc: Wavelength at which transmission shifts back to reflection,for mirrors with
+      complex transmission spectra.
+    required: false
+  - name: reflection_bandwidth_in_nm
+    dtype: float
+    doc: The range of wavelengths that are primarily reflected.The start and end wavelengths
+      needs to be specified.
+    required: false
+  - name: transmission_bandwidth_in_nm
+    dtype: float
+    doc: The range of wavelengths that are primarily transmitted.The start and end
+      wavelengths needs to be specified.
+    required: false
+  - name: angle_of_incidence_in_degrees
+    dtype: float
+    doc: Intended angle at which light strikes the mirror.
+    required: false
+  - name: model
+    dtype: text
+    doc: Model of the dichroic mirror.
+    required: false
+- neurodata_type_def: BandOpticalFilter
+  neurodata_type_inc: Device
+  doc: Extends Device to hold a Band Optical Filter (Bandpass or Bandstop).
+  attributes:
+  - name: center_wavelength_in_nm
+    dtype: float
+    doc: The midpoint of the band of wavelengths that the filter transmits or blocks.
+  - name: bandwidth_in_nm
+    dtype: float
+    doc: The width of the wavelength range that the filter transmits or blocks (full
+      width at half maximum).
+  - name: filter_type
+    dtype: text
+    doc: Type of filter (e.g., 'Bandpass', 'Bandstop').
+  - name: model
+    dtype: text
+    doc: Model of the optical filter.
+    required: false
+- neurodata_type_def: EdgeOpticalFilter
+  neurodata_type_inc: Device
+  doc: Extends Device to hold an Edge Optical Filter (Longpass or Shortpass).
+  attributes:
+  - name: cut_wavelength_in_nm
+    dtype: float
+    doc: ' The wavelength at which the filter transmits half as much as its peak transmission.'
+  - name: filter_type
+    dtype: text
+    doc: Type of filter (e.g., 'Longpass', 'Shortpass').
+  - name: slope_in_percent_cut_wavelength
+    dtype: float
+    doc: The steepness of the transition from high blocking to high transmission (or
+      vice versa). Specified as a percentage of the cut wavelength.
+    required: false
+  - name: slope_starting_transmission_in_percent
+    dtype: float
+    doc: The percent transmission that defines the starting point for the slope (e.g.
+      10%).
+    required: false
+  - name: slope_ending_transmission_in_percent
+    dtype: float
+    doc: The percent transmission that defines the ending point for the slope (e.g.
+      80%).
+    required: false
+  - name: model
+    dtype: text
+    doc: Model of the optical filter.
+    required: false
+- neurodata_type_def: ObjectiveLens
+  neurodata_type_inc: Device
+  doc: Extends Device to hold a Objective lens.
+  attributes:
+  - name: model
+    dtype: text
+    doc: Model of the objective lens.
+    required: false
+  - name: numerical_aperture
+    dtype: float
+    doc: Numerical aperture, e.g., 0.39 NA.
+    required: false
+  - name: magnification
+    dtype: float
+    doc: Lens magnification.
+    required: false
+- neurodata_type_def: Effector
+  neurodata_type_inc: Device
+  doc: Extends Device to hold metadata on the Effector or Opsin.
+  attributes:
+  - name: label
+    dtype: text
+    doc: Effector standard notation.
+  - name: injection_location
+    dtype: text
+    doc: Injection brain region name.
+    required: false
+  - name: injection_coordinates_in_mm
+    dtype: float
+    shape:
+    - 3
+    doc: Indicator injection location in stereotactic coordinates (AP, ML, DV) mm
+      relative to Bregma.
+    required: false
+- neurodata_type_def: Microscope
+  neurodata_type_inc: Device
+  doc: Extends Device to hold a Microscope.
+  attributes:
+  - name: microscopy_type
+    dtype: text
+    doc: Type of microscope used to capture the image (e.g., inverted, upright, light
+      sheet, confocal, two photon).
+  - name: doi
+    dtype: text
+    doc: The publication link for custom-built microscope.
+    required: false
+  - name: model
+    dtype: text
+    doc: Model of the Microscope.
+    required: false

spec/ndx-ophys-devices.namespace.yaml

@@ -8,5 +8,7 @@ namespaces:
   name: ndx-ophys-devices
   schema:
   - namespace: core
+    neurodata_types:
+    - Device
   - source: ndx-ophys-devices.extensions.yaml
   version: 0.1.0

src/pynwb/ndx_ophys_devices/__init__.py

@@ -18,17 +18,16 @@
 # Load the namespace
 load_namespaces(str(__spec_path))
 
-# TODO: Define your classes here to make them accessible at the package level.
-# Either have PyNWB generate a class from the spec using `get_class` as shown
-# below or write a custom class and register it using the class decorator
-# `@register_class("TetrodeSeries", "ndx-ophys-devices")`
-TetrodeSeries = get_class("TetrodeSeries", "ndx-ophys-devices")
 
-# NOTE: `widgets/tetrode_series_widget.py` adds a "widget"
-# attribute to the TetrodeSeries class. This attribute is used by NWBWidgets.
-# Delete the `widgets` subpackage or the `tetrode_series_widget.py` module
-# if you do not want to define a custom widget for your extension neurodata
-# type.
+Indicator = get_class("Indicator", "ndx-ophys-devices")
+OpticalFiber = get_class("OpticalFiber", "ndx-ophys-devices")
+ExcitationSource = get_class("ExcitationSource", "ndx-ophys-devices")
+Photodetector = get_class("Photodetector", "ndx-ophys-devices")
+DichroicMirror = get_class("DichroicMirror", "ndx-ophys-devices")
+BandOpticalFilter = get_class("BandOpticalFilter", "ndx-ophys-devices")
+EdgeOpticalFilter = get_class("EdgeOpticalFilter", "ndx-ophys-devices")
+ObjectiveLens = get_class("ObjectiveLens", "ndx-ophys-devices")
+Effector = get_class("Effector", "ndx-ophys-devices")
+Microscope = get_class("Microscope", "ndx-ophys-devices")
 
-# Remove these functions from the package
 del load_namespaces, get_class

src/pynwb/ndx_ophys_devices/testing/__init__.py

@@ -0,0 +1,25 @@
+from ._mock import (
+    mock_Indicator,
+    mock_Effector,
+    mock_OpticalFiber,
+    mock_Photodetector,
+    mock_DichroicMirror,
+    mock_BandOpticalFilter,
+    mock_EdgeOpticalFilter,
+    mock_ObjectiveLens,
+    mock_ExcitationSource,
+    mock_Microscope,
+)
+
+__all__ = [
+    "mock_Indicator",
+    "mock_Effector",
+    "mock_OpticalFiber",
+    "mock_Photodetector",
+    "mock_DichroicMirror",
+    "mock_BandOpticalFilter",
+    "mock_EdgeOpticalFilter",
+    "mock_ObjectiveLens",
+    "mock_ExcitationSource",
+    "mock_Microscope",
+]