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Fix for namespaces issue #2714

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merged 1 commit into from
Sep 8, 2023
Merged

Fix for namespaces issue #2714

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3 changes: 0 additions & 3 deletions allensdk/brain_observatory/ecephys/ecephys_session_api/ecephys_nwb_session_api.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,9 +9,6 @@

from .ecephys_session_api import EcephysSessionApi
from allensdk.brain_observatory.nwb.nwb_api import NwbApi
import \
allensdk.brain_observatory.ecephys.nwb # noqa Necessary to import pyNWB
# namespaces
from allensdk.brain_observatory.ecephys import get_unit_filter_value
from allensdk.brain_observatory.nwb import check_nwbfile_version
from .._channels import Channels
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6 changes: 1 addition & 5 deletions allensdk/brain_observatory/nwb/nwb_api.py
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Original file line number Diff line number Diff line change
Expand Up @@ -10,10 +10,6 @@
from allensdk.brain_observatory.running_speed import RunningSpeed
from allensdk.brain_observatory.behavior.image_api import ImageApi

namespace_path = Path(__file__).parent / \
'ndx-aibs-behavior-ophys.namespace.yaml'
pynwb.load_namespaces(str(namespace_path))


class NwbApi:

Expand All @@ -24,7 +20,7 @@ def nwbfile(self):
if hasattr(self, '_nwbfile'):
return self._nwbfile

io = pynwb.NWBHDF5IO(self.path, 'r')
io = pynwb.NWBHDF5IO(self.path, 'r', load_namespaces=True)
return io.read()

def __init__(self, path, **kwargs):
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