hackathon

extension_1.py

from pynwb import NWBNamespaceBuilder, NWBGroupSpec, NWBAttributeSpec
import numpy as np

ns_path = "mylab.namespace.yaml"
ext_source = "mylab.extensions.yaml"

nwb_as = NWBAttributeSpec('unit', 'str', 'the population name', value = 'Hz')

ns_builder = NWBNamespaceBuilder('Extension for use in my Lab', "mylab")
ext = NWBGroupSpec('A custom TimeSeries for my lab',
                   attributes=[nwb_as],
                   neurodata_type_inc='TimeSeries',
                   neurodata_type_def='FiringRateSeries')

ns_builder.add_spec(ext_source, ext)
ns_builder.export(ns_path)

from pynwb import get_class, load_namespaces

ns_path = "mylab.namespace.yaml"
load_namespaces(ns_path)

FiringRateSeries = get_class('FiringRateSeries', 'mylab')

fs = FiringRateSeries(data=np.random.rand(5),
                      name='my_population',
                      source='acquisition')

Traceback (most recent call last):
  File "/Users/nicholasc/PycharmProjects/Sandbox/janelia_sandbox.py", line 33, in <module>
    source='acquisition')
  File "/Users/nicholasc/Janelia_NWB_Hackathon/pynwb/src/form/utils.py", line 270, in func_call
    raise TypeError(', '.join(parse_err)) from None
TypeError: missing argument 'unit'

Process finished with exit code 1```

my-lab.extensions.yaml:

groups:

• attributes:
  • doc: the population name
    dtype: str
    name: unit
    value: Hz
    doc: A custom TimeSeries for my lab
    neurodata_type_def: FiringRateSeries
    neurodata_type_inc: TimeSeries