Revert "create specs"

This reverts commit eda56cd.

README.md

@@ -13,7 +13,3 @@ 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

@@ -1,220 +1,8 @@
 groups:
-- neurodata_type_def: Indicator
-  neurodata_type_inc: Device
-  doc: Extends Device to hold metadata on the Indicator.
+- neurodata_type_def: TetrodeSeries
+  neurodata_type_inc: ElectricalSeries
+  doc: An extension of ElectricalSeries to include the tetrode ID for each time series.
   attributes:
-  - 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
-    shape:
-    - 2
-    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
-    shape:
-    - 2
-    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: Miscroscope
-  neurodata_type_inc: Device
-  doc: Extends Device to hold a Miscroscope.
-  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 miscroscope.
-    required: false
+  - name: trode_id
+    dtype: int32
+    doc: The tetrode ID.

spec/ndx-ophys-devices.namespace.yaml

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

src/spec/create_extension_spec.py

@@ -0,0 +1,49 @@
+# -*- coding: utf-8 -*-
+import os.path
+
+from pynwb.spec import NWBNamespaceBuilder, export_spec, NWBGroupSpec, NWBAttributeSpec
+
+# TODO: import other spec classes as needed
+# from pynwb.spec import NWBDatasetSpec, NWBLinkSpec, NWBDtypeSpec, NWBRefSpec
+
+
+def main():
+    # these arguments were auto-generated from your cookiecutter inputs
+    ns_builder = NWBNamespaceBuilder(
+        name="""ndx-ophys-devices""",
+        version="""0.1.0""",
+        doc="""This is an NWB extension for storing metadata of devices used in optical experimental setup (microscopy, fiber photometry, optogenetic stimulation etc.)""",
+        author=[
+            "Alessandra Trapani", 
+        ],
+        contact=[
+            "[email protected]", 
+        ],
+    )
+    ns_builder.include_namespace("core")
+
+    # TODO: if your extension builds on another extension, include the namespace
+    # of the other extension below
+    # ns_builder.include_namespace("ndx-other-extension")
+
+    # TODO: define your new data types
+    # see https://pynwb.readthedocs.io/en/stable/tutorials/general/extensions.html
+    # for more information
+    tetrode_series = NWBGroupSpec(
+        neurodata_type_def="TetrodeSeries",
+        neurodata_type_inc="ElectricalSeries",
+        doc="An extension of ElectricalSeries to include the tetrode ID for each time series.",
+        attributes=[NWBAttributeSpec(name="trode_id", doc="The tetrode ID.", dtype="int32")],
+    )
+
+    # TODO: add all of your new data types to this list
+    new_data_types = [tetrode_series]
+
+    # export the spec to yaml files in the spec folder
+    output_dir = os.path.abspath(os.path.join(os.path.dirname(__file__), "..", "..", "spec"))
+    export_spec(ns_builder, new_data_types, output_dir)
+
+
+if __name__ == "__main__":
+    # usage: python create_extension_spec.py
+    main()