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Fix #908 #998

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Fix #908 #998

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21aa4b6
add condition on ndx-events version
alessandratrapani Aug 12, 2024
edcf28d
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Aug 12, 2024
d24b262
update CHANGELOG.md
alessandratrapani Aug 12, 2024
30bb1d0
Merging configure_beckend_with_ndx-events_0.3.0
alessandratrapani Aug 12, 2024
19ebd9f
Update CHANGELOG.md
alessandratrapani Aug 12, 2024
9682a12
combine checks on ndx-events
alessandratrapani Aug 12, 2024
f3f0ef7
Update src/neuroconv/tools/nwb_helpers/_configure_backend.py
alessandratrapani Aug 13, 2024
b303182
Merge branch 'main' into configure_backend_with_ndx-events_0.3.0
weiglszonja Aug 14, 2024
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -14,6 +14,7 @@
### Bug fixes
* Fixed the default naming of multiple electrical series in the `SpikeGLXConverterPipe`. [PR #957](https://github.com/catalystneuro/neuroconv/pull/957)
* Write new properties to the electrode table use the global identifier channel_name, group [PR #984](https://github.com/catalystneuro/neuroconv/pull/984)
* Fixed a check in `_configure_backend` on neurodata_object ndx_events.Events to work only when ndx-events==0.2.0 is used. [PR #998](https://github.com/catalystneuro/neuroconv/pull/998)

### Improvements
* The `OpenEphysBinaryRecordingInterface` now uses `lxml` for extracting the session start time from the settings.xml file and does not depend on `pyopenephys` anymore. [PR #971](https://github.com/catalystneuro/neuroconv/pull/971)
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18 changes: 10 additions & 8 deletions src/neuroconv/tools/nwb_helpers/_configure_backend.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,11 +4,12 @@
from typing import Union

from hdmf.common import Data
from packaging import version
from pynwb import NWBFile, TimeSeries

from ._configuration_models._hdf5_backend import HDF5BackendConfiguration
from ._configuration_models._zarr_backend import ZarrBackendConfiguration
from ..importing import is_package_installed
from ..importing import get_package_version, is_package_installed


def configure_backend(
Expand Down Expand Up @@ -53,13 +54,14 @@ def configure_backend(
dataset_name=dataset_name, data_io_class=data_io_class, data_io_kwargs=data_io_kwargs
)
# Special ndx-events v0.2.0 types
elif is_ndx_events_installed and isinstance(neurodata_object, ndx_events.Events):
neurodata_object.set_data_io(
dataset_name=dataset_name, data_io_class=data_io_class, data_io_kwargs=data_io_kwargs
)
# But temporarily skipping LabeledEvents
elif is_ndx_events_installed and isinstance(neurodata_object, ndx_events.LabeledEvents):
continue
elif is_ndx_events_installed and (get_package_version("ndx-events") == version.parse("0.2.0")):
# Temporarily skipping LabeledEvents
if isinstance(neurodata_object, ndx_events.LabeledEvents):
continue
elif isinstance(neurodata_object, ndx_events.Events):
neurodata_object.set_data_io(
dataset_name=dataset_name, data_io_class=data_io_class, data_io_kwargs=data_io_kwargs
)
# Skip the setting of a DataIO when target dataset is a link (assume it will be found in parent)
elif isinstance(neurodata_object, TimeSeries) and is_dataset_linked:
continue
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