Script to fix incorrect namespace attributes in NWB files in dandiset 000114

fix_dandiset_000114.py

import glob
import h5py
import argparse
from typing import Union


def replace_namespace(_: str, h5obj: Union[h5py.Dataset, h5py.Group]):
    # change the attribute "namespace" from value "hdmf-experimental" to "hdmf-common"
    # for all DynamicTableRegion and VectorData neurodata types from ndx-photometry.
    if h5obj.attrs.get("namespace") == "hdmf-experimental":
        assert h5obj.attrs.get("neurodata_type") in (
            "DynamicTableRegion",
            "VectorData",
        )
        h5obj.attrs["namespace"] = "hdmf-common"
        print("Changed namespace for", h5obj.name)

def adjust(filepath):
    print("-------------------------------------------------------------------")
    print("Adjusting NWB file:", filepath)
    with h5py.File(filepath, "a") as f:
        f.visititems(replace_namespace)

def main():
    parser = argparse.ArgumentParser()
    parser.add_argument(
        "path", help="path to the NWB file or directory of NWB files to adjust"
    )
    args = parser.parse_args()
    path = args.path

    if path.endswith(".nwb"):
        filepaths = [path]
    else:
        filepaths = glob.glob(path + "/**/*.nwb", recursive=True)

    print("Adjusting these NWB files:", filepaths, sep="\n")
    for filepath in filepaths:
        adjust(filepath=filepath)


if __name__ == "__main__":
    main()

Expected output for each ophys NWB file is:

Changed namespace for /acquisition/RoiResponseSeries/rois
Changed namespace for /general/fiber_photometry/excitation_sources/commanded_voltage
Changed namespace for /general/fiber_photometry/excitation_sources/peak_wavelength
Changed namespace for /general/fiber_photometry/excitation_sources/source_type
Changed namespace for /general/fiber_photometry/fibers/excitation_source
Changed namespace for /general/fiber_photometry/fibers/fluorophores
Changed namespace for /general/fiber_photometry/fibers/location
Changed namespace for /general/fiber_photometry/fibers/notes
Changed namespace for /general/fiber_photometry/fibers/photodetector
Changed namespace for /general/fiber_photometry/fluorophores/coordinates
Changed namespace for /general/fiber_photometry/fluorophores/label
Changed namespace for /general/fiber_photometry/fluorophores/location
Changed namespace for /general/fiber_photometry/photodetectors/gain
Changed namespace for /general/fiber_photometry/photodetectors/peak_wavelength
Changed namespace for /general/fiber_photometry/photodetectors/type
Changed namespace for /processing/behavior/behavioral_events/behavior
Changed namespace for /processing/behavior/behavioral_events/start_time
Changed namespace for /processing/behavior/behavioral_events/stop_time

Expected output for each ecephys NWB file is:

Changed namespace for /acquisition/ElectricalSeries/electrodes
Changed namespace for /general/extracellular_ephys/electrodes/channel_name
Changed namespace for /general/extracellular_ephys/electrodes/gain_to_uV
Changed namespace for /general/extracellular_ephys/electrodes/group
Changed namespace for /general/extracellular_ephys/electrodes/group_name
Changed namespace for /general/extracellular_ephys/electrodes/location
Changed namespace for /general/extracellular_ephys/electrodes/offset_to_uV