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Description
What happened?
HDF5IO is not yet set up to read certain IO settings from Zarr.
Steps to Reproduce
from datetime import datetime
from dateutil.tz import tzlocal
import numpy as np
from pynwb import NWBFile, TimeSeries, NWBHDF5IO
from hdmf_zarr import ZarrDataIO
from hdmf_zarr.nwb import NWBZarrIO
# Create the NWBFile
nwbfile = NWBFile(
session_description="my first synthetic recording",
identifier="EXAMPLE_ID",
session_start_time=datetime.now(tzlocal())
)
data_with_data_io = ZarrDataIO(
data=np.arange(10000),
chunks=(1000, ),
)
ts = TimeSeries(
name="test",
data=data_with_data_io,
rate=1.0,
unit="unit",
)
nwbfile.add_acquisition(ts)
zarr_path = "rechunking.nwb.zarr"
with NWBZarrIO(path=zarr_path, mode="w") as io:
io.write(nwbfile)
hdf5_path = "rechunking.nwb"
with NWBZarrIO(path=zarr_path, mode="r") as read_io:
read_nwbfile = read_io.read()
print(read_nwbfile.acquisition["test"].data.chunks)
with NWBHDF5IO(hdf5_path, mode='w') as export_io:
export_io.export(src_io=read_io, write_args=dict(link_data=False))
with NWBHDF5IO(hdf5_path, mode='r') as hdf5_read_io:
read_nwbfile = hdf5_read_io.read()
print(read_nwbfile.acquisition["test"].data.chunks)
Traceback
Output:
(1000, )
None
Operating System
macOS
Python Version
3.13
Package Versions
No response