Source code for allensdk.brain_observatory.behavior.write_nwb.extensions.event_detection.extension_builder

import os.path

from pynwb.spec import NWBNamespaceBuilder, export_spec, NWBGroupSpec, \
    NWBDatasetSpec

NAMESPACE = 'ndx-aibs-ophys-event-detection'



[docs]def main():

    ns_builder = NWBNamespaceBuilder(
        doc="Detected events from optical physiology ROI fluorescence traces",
        name=f"""{NAMESPACE}""",
        version="""0.1.0""",
        author="""Allen Institute for Brain Science""",
        contact="""waynew@alleninstitute.org"""
    )

    ns_builder.include_type('RoiResponseSeries', namespace='core')
    ns_builder.include_type('DynamicTableRegion', namespace='core')
    ns_builder.include_type('TimeSeries', namespace='core')
    ns_builder.include_type('NWBDataInterface', namespace='core')

    ophys_events_spec = NWBGroupSpec(
        neurodata_type_def='OphysEventDetection',
        neurodata_type_inc='RoiResponseSeries',
        name='event_detection',
        doc='Stores event detection output',
        datasets=[
            NWBDatasetSpec(
                name='lambdas',
                dtype='float',
                doc='calculated regularization weights',
                shape=(None,)
            ),
            NWBDatasetSpec(
                name='noise_stds',
                dtype='float',
                doc='calculated noise std deviations',
                shape=(None,)
            )
        ]
    )

    new_data_types = [ophys_events_spec]

    # export the spec to yaml files in the spec folder
    output_dir = os.path.abspath(os.path.join(os.path.dirname(__file__)))
    export_spec(ns_builder, new_data_types, output_dir)



if __name__ == "__main__":
    # usage: python create_extension_spec.py
    main()