PopulationSpikeTrain.py

import sys
sys.path.append('/Users/nicholasc/Janelia_NWB_Hackathon/pynwb/src')
from pynwb import NWBNamespaceBuilder, NWBGroupSpec, NWBAttributeSpec
import numpy as np
from pynwb import get_class, load_namespaces
from datetime import datetime
from pynwb import NWBFile
from form.backends.hdf5 import HDF5IO
from pynwb import get_build_manager

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

nwb_as = NWBAttributeSpec('data', 'int', 'gid')

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='PopulationSpikeTrain')

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

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

PopulationSpikeTrain = get_class('PopulationSpikeTrain', 'mylab')

fs = PopulationSpikeTrain(data=(10*np.random.random(5)).astype(np.int),
                      name='my_population',
                      source='acquisition',
                      unit='second',
                      timestamps=np.random.rand(5))
f = NWBFile('tmp.nwb', 'my first synthetic recording', 'EXAMPLE_ID', datetime.now(),
            experimenter='Dr. Bilbo Baggins',
            lab='Bag End Labatory',
            institution='University of Middle Earth at the Shire',
            experiment_description='I went on an adventure with thirteen dwarves to reclaim vast treasures.',
            session_id='LONELYMTN')

f.add_raw_timeseries(fs)



manager = get_build_manager()
io = HDF5IO('tmp.nwb', manager, mode='w')
io.write(f)
io.close()

Traceback (most recent call last):
  File "/Users/nicholasc/PycharmProjects/Sandbox/pop_spike_series.py", line 48, in <module>
    io.write(f)
  File "/Users/nicholasc/Janelia_NWB_Hackathon/pynwb/src/form/utils.py", line 260, in func_call
    return func(self, **parsed['args'])
  File "/Users/nicholasc/Janelia_NWB_Hackathon/pynwb/src/form/backends/io.py", line 24, in write
    f_builder = self.__manager.build(container, source=self.__source)
  File "/Users/nicholasc/Janelia_NWB_Hackathon/pynwb/src/form/utils.py", line 260, in func_call
    return func(self, **parsed['args'])
  File "/Users/nicholasc/Janelia_NWB_Hackathon/pynwb/src/form/build/map.py", line 29, in build
    result = self.__type_map.build(container, self, source=getargs('source', kwargs))
  File "/Users/nicholasc/Janelia_NWB_Hackathon/pynwb/src/form/utils.py", line 260, in func_call
    return func(self, **parsed['args'])
  File "/Users/nicholasc/Janelia_NWB_Hackathon/pynwb/src/form/build/map.py", line 818, in build
    builder = attr_map.build(container, manager, source=getargs('source', kwargs))
  File "/Users/nicholasc/Janelia_NWB_Hackathon/pynwb/src/form/utils.py", line 260, in func_call
    return func(self, **parsed['args'])
  File "/Users/nicholasc/Janelia_NWB_Hackathon/pynwb/src/form/build/map.py", line 355, in build
    self.__add_groups(builder, self.__spec.groups, container, manager)
  File "/Users/nicholasc/Janelia_NWB_Hackathon/pynwb/src/form/build/map.py", line 427, in __add_groups
    self.__add_groups(sub_builder, spec.groups, container, build_manager)
  File "/Users/nicholasc/Janelia_NWB_Hackathon/pynwb/src/form/build/map.py", line 427, in __add_groups
    self.__add_groups(sub_builder, spec.groups, container, build_manager)
  File "/Users/nicholasc/Janelia_NWB_Hackathon/pynwb/src/form/build/map.py", line 442, in __add_groups
    self.__add_containers(builder, spec, attr_value, build_manager)
  File "/Users/nicholasc/Janelia_NWB_Hackathon/pynwb/src/form/build/map.py", line 467, in __add_containers
    self.__add_containers(builder, spec, container, build_manager)
  File "/Users/nicholasc/Janelia_NWB_Hackathon/pynwb/src/form/build/map.py", line 446, in __add_containers
    rendered_obj = build_manager.build(value)
  File "/Users/nicholasc/Janelia_NWB_Hackathon/pynwb/src/form/utils.py", line 260, in func_call
    return func(self, **parsed['args'])
  File "/Users/nicholasc/Janelia_NWB_Hackathon/pynwb/src/form/build/map.py", line 29, in build
    result = self.__type_map.build(container, self, source=getargs('source', kwargs))
  File "/Users/nicholasc/Janelia_NWB_Hackathon/pynwb/src/form/utils.py", line 260, in func_call
    return func(self, **parsed['args'])
  File "/Users/nicholasc/Janelia_NWB_Hackathon/pynwb/src/form/build/map.py", line 818, in build
    builder = attr_map.build(container, manager, source=getargs('source', kwargs))
  File "/Users/nicholasc/Janelia_NWB_Hackathon/pynwb/src/form/utils.py", line 260, in func_call
    return func(self, **parsed['args'])
  File "/Users/nicholasc/Janelia_NWB_Hackathon/pynwb/src/form/build/map.py", line 359, in build
    self.__add_attributes(builder, self.__spec.attributes, container)
  File "/Users/nicholasc/Janelia_NWB_Hackathon/pynwb/src/form/build/map.py", line 381, in __add_attributes
    raise Warning("missing required attribute '%s' for '%s'" % (spec.name, builder.name))
Warning: missing required attribute 'data' for 'my_population'

Process finished with exit code 1

Try the following:

nwb_as should be an NWBDatasetSpec. Within the constructor, you need to specify name=data and attributes=[NWBAttributeSpec('unit', value='gid')]