Update extension with optional columns

README.md

@@ -2,6 +2,8 @@
 [![Build Status](https://travis-ci.com/akshay-jaggi/ndx-photometry.svg?branch=master)](https://travis-ci.com/akshay-jaggi/ndx-photometry)
 [![Documentation Status](https://readthedocs.org/projects/ndx-photometry/badge/?version=latest)](https://ndx-photometry.readthedocs.io/en/latest/?badge=latest)
 
+![NWB - Photometry](https://user-images.githubusercontent.com/844306/144680873-3e2d957f-97ff-45cb-b625-517f5e7dfb9f.png)
+
 ## Introduction
 This is an NWB extension for storing photometry recordings and associated metadata. This extension stores photometry information across three folders in the NWB file: acquisition, processing, and general. The acquisiton folder contains an ROIResponseSeries (inherited from `pynwb.ophys`), which references rows of a FibersTable rather than 2 Photon ROIs. The new types for this extension are in metadata and processing
 
@@ -67,6 +69,7 @@ commandedvoltage_series = (
         frequency=30.0,
         power=500.0,
         rate=30.0,
+        unit="volts",
     )
 )
 

setup.py

@@ -22,7 +22,7 @@
 
 setup_args = {
     'name': 'ndx-photometry',
-    'version': '0.1.0',
+    'version': '0.1.1',
     'description': 'extension for fiber photometry data',
     'long_description': readme,
     'long_description_content_type': readme_type,
@@ -33,7 +33,7 @@
     'install_requires': [
         'pynwb>=1.3.0',
         'numpy<1.19.4',
-        'h5py<3'
+        'h5py',
     ],
     'packages': find_packages('src/pynwb'),
     'package_dir': {'': 'src/pynwb'},

spec/ndx-photometry.extensions.yaml

@@ -58,6 +58,7 @@ groups:
     shape:
     - null
     doc: peak wavelength of photodetector
+    quantity: '?'
     attributes:
     - name: unit
       dtype: text
@@ -75,6 +76,7 @@ groups:
     shape:
     - null
     doc: gain on the photodetector
+    quantity: '?'
   - name: model_number
     neurodata_type_inc: VectorData
     dtype: text
@@ -112,6 +114,7 @@ groups:
     shape:
     - null
     doc: references CommandedVoltageSeries
+    quantity: '?'
   - name: output
     neurodata_type_inc: VectorData
     dtype: float
@@ -143,6 +146,7 @@ groups:
   - name: frequency
     dtype: float
     doc: voltage frequency in unit hertz
+    quantity: '?'
     attributes:
     - name: unit
       dtype: text
@@ -202,6 +206,7 @@ groups:
   - name: commanded_voltages
     neurodata_type_inc: MultiCommandedVoltage
     doc: multiple commanded voltage container
+    quantity: '?'
 - neurodata_type_def: FluorophoresTable
   neurodata_type_inc: DynamicTable
   name: fluorophores

src/pynwb/tests/integration/test_photometry.py

@@ -63,10 +63,10 @@ def test_roundtrip(self):
         commandedvoltage_series2 = (
             multi_commanded_voltage.create_commanded_voltage_series(
                 name="commanded_voltage2",
-                data=[1.0, 2.0, 3.0],
-                frequency=30.0,
-                power=500.0,
+                data=[4.0, 5.0, 6.0],
+                power=400.0,
                 rate=30.0,
+                unit="volts",
             )
         )
 
@@ -102,7 +102,7 @@ def test_roundtrip(self):
             name="roi_response_series",
             description="my roi response series",
             data=np.random.randn(100, 1),
-            unit = 'F',
+            unit='F',
             rate=30.0,
             rois=fibers_ref,
         )

src/spec/create_extension_spec.py

@@ -127,6 +127,7 @@ def main():
                 dtype="float",
                 shape=(None,),
                 neurodata_type_inc="VectorData",
+                quantity="?",
                 attributes=[
                     NWBAttributeSpec(
                         name="unit", doc="wavelength unit", value="nanometers", dtype="text"
@@ -146,6 +147,7 @@ def main():
                 dtype="float",
                 shape=(None,),
                 neurodata_type_inc="VectorData",
+                quantity="?",
             ),
             NWBDatasetSpec(
                 name="model_number",
@@ -191,6 +193,7 @@ def main():
                 ),
                 shape=(None,),
                 neurodata_type_inc="VectorData",
+                quantity="?",
             ),
             NWBDatasetSpec(
                 name="output",
@@ -236,6 +239,7 @@ def main():
                         name="unit", doc="frequency unit", value="hertz", dtype="text"
                     )
                 ],
+                quantity="?",
             ),
             NWBDatasetSpec(
                 name="power",
@@ -354,7 +358,8 @@ def main():
             NWBGroupSpec(
                 name='commanded_voltages',
                 neurodata_type_inc='MultiCommandedVoltage',
-                doc='multiple commanded voltage container'
+                doc='multiple commanded voltage container',
+                quantity="?",
             )
         ]
     )