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

import os.path

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

NAMESPACE = 'ndx-aibs-stimulus-template'


def main():

    ns_builder = NWBNamespaceBuilder(
        doc="Stimulus images",
        name=f"""{NAMESPACE}""",
        version="""0.1.0""",
        author="""Allen Institute for Brain Science""",
        contact="""waynew@alleninstitute.org"""
    )

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

    stimulus_template_spec = NWBGroupSpec(
        neurodata_type_def='StimulusTemplate',
        neurodata_type_inc='ImageSeries',
        doc='Note: image names in control_description are referenced by '
            'stimulus/presentation table as well as intervals '
            '\n'
            'Each image shown to the animals is warped to account for '
            'distance and eye position relative to the monitor. This  '
            'extension stores the warped images that were shown to the animal '
            'as well as an unwarped version of each image in which a mask has '
            'been applied such that only the pixels visible after warping are '
            'included',
        datasets=[
            NWBDatasetSpec(
                name='unwarped',
                dtype='float',
                doc='Original image with mask applied such that only the '
                    'pixels visible after warping are included',
                shape=(None, None, None)
            )
        ]
    )

    new_data_types = [stimulus_template_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()