Open
Description
What happened?
See comment in #276 (review) for reference.
This had come up recently in hdmf, but there seems to also be an error with hdmf-zarr writing scalar datasets with a compound dtype.
Steps to Reproduce
from pynwb import NWBFile
from uuid import uuid4
from datetime import datetime
from hdmf_zarr import NWBZarrIO
nwbfile = NWBFile(
session_description="no description.",
session_start_time=datetime.now(),
identifier=str(uuid4()),
)
device = nwbfile.create_device(name="Device", description="no description.")
electrode_group = nwbfile.create_electrode_group(
name="ElectrodeGroup",
description="no description.",
device=device,
location="unknown",
position=(1.0, 2.0, 3.0),
)
with NWBZarrIO('test.nwb', 'w') as io:
io.write(nwbfile) # errors here
with NWBZarrIO('test.nwb', 'r') as io:
read_nwbfile = io.read()
print(read_nwbfile.electrode_groups['ElectrodeGroup'].position.shape)Traceback
File "/Users/smprince/.vscode/extensions/ms-python.debugpy-2025.8.0-darwin-arm64/bundled/libs/debugpy/_vendored/pydevd/_pydevd_bundle/pydevd_runpy.py", line 127, in _run_module_code
_run_code(code, mod_globals, init_globals, mod_name, mod_spec, pkg_name, script_name)
File "/Users/smprince/.vscode/extensions/ms-python.debugpy-2025.8.0-darwin-arm64/bundled/libs/debugpy/_vendored/pydevd/_pydevd_bundle/pydevd_runpy.py", line 118, in _run_code
exec(code, run_globals)
File "/Users/smprince/Documents/code/hdmf-zarr/docs/issue_testing.py", line 24, in <module>
io.write(nwbfile)
File "/Users/smprince/Documents/code/hdmf/src/hdmf/utils.py", line 578, in func_call
return func(args[0], **pargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/Users/smprince/Documents/code/hdmf-zarr/src/hdmf_zarr/backend.py", line 347, in write
super(ZarrIO, self).write(**kwargs)
File "/Users/smprince/Documents/code/hdmf/src/hdmf/utils.py", line 578, in func_call
return func(args[0], **pargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/Users/smprince/Documents/code/hdmf/src/hdmf/backends/io.py", line 99, in write
self.write_builder(f_builder, **kwargs)
File "/Users/smprince/Documents/code/hdmf/src/hdmf/utils.py", line 578, in func_call
return func(args[0], **pargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/Users/smprince/Documents/code/hdmf-zarr/src/hdmf_zarr/backend.py", line 522, in write_builder
self.write_group(
File "/Users/smprince/Documents/code/hdmf/src/hdmf/utils.py", line 578, in func_call
return func(args[0], **pargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/Users/smprince/Documents/code/hdmf-zarr/src/hdmf_zarr/backend.py", line 621, in write_group
self.write_group(
File "/Users/smprince/Documents/code/hdmf/src/hdmf/utils.py", line 578, in func_call
return func(args[0], **pargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/Users/smprince/Documents/code/hdmf-zarr/src/hdmf_zarr/backend.py", line 621, in write_group
self.write_group(
File "/Users/smprince/Documents/code/hdmf/src/hdmf/utils.py", line 578, in func_call
return func(args[0], **pargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/Users/smprince/Documents/code/hdmf-zarr/src/hdmf_zarr/backend.py", line 632, in write_group
self.write_dataset(
File "/Users/smprince/Documents/code/hdmf/src/hdmf/utils.py", line 578, in func_call
return func(args[0], **pargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/Users/smprince/Documents/code/hdmf-zarr/src/hdmf_zarr/backend.py", line 1186, in write_dataset
dset = self.__list_fill__(parent, name, data, options)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/smprince/Documents/code/hdmf-zarr/src/hdmf_zarr/backend.py", line 1355, in __list_fill__
data = data[:] # load the data in case we come from HDF5 or another on-disk data source we don't know
~~~~^^^
IndexError: too many indices for array: array is 0-dimensional, but 1 were indexedOperating System
Windows
Python Version
3.12
Package Versions
No response