View job log here
UserWarning: Failed to load /entry/instrument/event_mode_detectors/timepix3 as _StrippedDetector: Could not determine signal field or dimensions. Falling back to loading HDF5 group children as scipp.DataGroup.
In provider ess.reduce.nexus.workflow.load_nexus_component(
location: ess.reduce.nexus.types.NeXusComponentLocationSpec[scippnexus.nxdetector.NXdetector, ess.reduce.nexus.types.SampleRun],
nx_class: ess.reduce.nexus.types.NeXusClass[scippnexus.nxdetector.NXdetector],
) -> ess.reduce.nexus.types.NeXusComponent[scippnexus.nxdetector.NXdetector, ess.reduce.nexus.types.SampleRun]
.tox/nexusfiles-scipp-odin/lib/python3.12/site-packages/scippnexus/base.py:409: UserWarning
Full output
self = <scippnexus.base.Group object at 0x7fd2e1bd8b90>, sel = ()
def __getitem__(self, sel):
"""
Get a child group or child dataset, a selection of child groups, or load and
return the current group.
Three cases are supported:
- String name: The child group or child dataset of that name is returned.
- Class such as ``NXdata`` or ``NXlog``: A dict containing all direct children
with a matching ``NX_class`` attribute are returned. Also accepts a tuple of
classes. ``Field`` selects all child fields, i.e., all datasets but not
groups.
- Scipp-style index: Load the specified slice of the current group, returning
a :class:`scipp.DataArray` or :class:`scipp.DataGroup`.
Parameters
----------
sel:
Child name, class, or index.
Returns
-------
:
Field, group, dict of fields, or loaded data.
"""
if isinstance(sel, str):
# We cannot get the child directly from the HDF5 group, since we need to
# create the parent group, to ensure that fields get the correct properties
# such as sizes and dtype.
if '/' in sel:
sel_path = PurePosixPath(sel)
if sel_path.is_absolute():
return self.file[sel_path.relative_to('/').as_posix()]
# If the path is a single name, we can directly access the child
elif len(sel_path.parts) == 1:
return self[sel_path.as_posix()]
else:
grp = sel_path.parts[0]
return self[grp][sel_path.relative_to(grp).as_posix()]
elif sel == '..':
return self.parent
child = self._children[sel]
if isinstance(child, Field):
self._populate_fields()
return child
def isclass(x):
return inspect.isclass(x) and issubclass(x, Field | NXobject)
if isclass(sel) or (
isinstance(sel, list) and len(sel) and all(isclass(x) for x in sel)
):
return self._get_children_by_nx_class(sel)
dg = self._nexus.read_children(sel)
if not dg:
# Bail out early to avoid fallback warnings. Everything is optional in
# NeXus so we cannot assume that the group is invalid (in contrast to
# likely partially incomplete groups that will fail to assemble below).
return dg
try:
> dg = self._nexus.assemble(dg)
^^^^^^^^^^^^^^^^^^^^^^^^
.tox/nexusfiles-scipp-odin/lib/python3.12/site-packages/scippnexus/base.py:390:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
.tox/nexusfiles-scipp-odin/lib/python3.12/site-packages/scippnexus/nxdetector.py:98: in assemble
out = self._assemble_as_physical_component(
.tox/nexusfiles-scipp-odin/lib/python3.12/site-packages/scippnexus/nxdata.py:417: in _assemble_as_physical_component
assembled_nxdata = self._assemble_as_data(data_items)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <ess.reduce.nexus.workflow._StrippedDetector object at 0x7fd2e1bd97c0>
dg = DataGroup(sizes={'x_pixel_offset': 4096, 'y_pixel_offset': 4096}, keys=[
detector_number: Variable({'x_pixel_offse...el_offset: Variable({'y_pixel_offset': 4096}),
data: Variable({'x_pixel_offset': 4096, 'y_pixel_offset': 4096}),
])
def _assemble_as_data(
self, dg: sc.DataGroup
) -> sc.DataGroup | sc.DataArray | sc.Dataset:
if not self._valid:
> raise NexusStructureError("Could not determine signal field or dimensions.")
E scippnexus.base.NexusStructureError: Could not determine signal field or dimensions.
.tox/nexusfiles-scipp-odin/lib/python3.12/site-packages/scippnexus/nxdata.py:362: NexusStructureError
During handling of the above exception, another exception occurred:
workflow = <sciline.pipeline.Pipeline object at 0x7fd2d93e3d40>
coda_nexus_file_path = PosixPath('/ess/data/coda/999999/raw/coda_odin_999999_00018332.hdf')
check_everything_events = <function _check_everything_events at 0x7fd2e50f54e0>
def test_odin_read_detector_everything__timepix3(
workflow: sciline.Pipeline,
coda_nexus_file_path: Path,
check_everything_events: Callable,
) -> None:
workflow[Filename[SampleRun]] = coda_nexus_file_path
workflow[NeXusDetectorName] = "event_mode_detectors/timepix3"
> result = workflow.compute(RawDetector[SampleRun])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
tests/nexusfiles-scipp/odin/odin_load_nexus_test.py:117:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
.tox/nexusfiles-scipp-odin/lib/python3.12/site-packages/sciline/pipeline.py:191: in compute
return self.get(tp, **kwargs).compute(reporter=reporter)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.tox/nexusfiles-scipp-odin/lib/python3.12/site-packages/sciline/task_graph.py:122: in compute
return self._scheduler.get(self._graph, [targets], reporter=reporter)[0]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.tox/nexusfiles-scipp-odin/lib/python3.12/site-packages/sciline/scheduler.py:140: in get
return self._dask_get(dsk, list(map(_to_dask_key, keys)))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.tox/nexusfiles-scipp-odin/lib/python3.12/site-packages/dask/threaded.py:115: in get
results = get_async(
.tox/nexusfiles-scipp-odin/lib/python3.12/site-packages/dask/local.py:547: in get_async
raise_exception(exc, tb)
.tox/nexusfiles-scipp-odin/lib/python3.12/site-packages/dask/local.py:351: in reraise
raise exc
.tox/nexusfiles-scipp-odin/lib/python3.12/site-packages/dask/local.py:256: in execute_task
result = task(data)
^^^^^^^^^^
.tox/nexusfiles-scipp-odin/lib/python3.12/site-packages/dask/_task_spec.py:768: in __call__
return self.func(*new_argspec)
^^^^^^^^^^^^^^^^^^^^^^^
.tox/nexusfiles-scipp-odin/lib/python3.12/site-packages/dask/utils.py:81: in apply
return func(*args)
^^^^^^^^^^^
.tox/nexusfiles-scipp-odin/lib/python3.12/site-packages/sciline/_provider.py:145: in __call__
return self._func(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
.tox/nexusfiles-scipp-odin/lib/python3.12/site-packages/ess/reduce/nexus/workflow.py:242: in load_nexus_component
nexus.load_component(location, nx_class=nx_class, definitions=definitions)
.tox/nexusfiles-scipp-odin/lib/python3.12/site-packages/ess/reduce/nexus/_nexus_loader.py:105: in load_component
loaded = cast(sc.DataGroup, group[selection])
^^^^^^^^^^^^^^^^
.tox/nexusfiles-scipp-odin/lib/python3.12/site-packages/scippnexus/base.py:392: in __getitem__
self._warn_fallback(e)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <scippnexus.base.Group object at 0x7fd2e1bd8b90>
e = NexusStructureError('Could not determine signal field or dimensions.')
def _warn_fallback(self, e: Exception) -> None:
msg = (
f"Failed to load {self.name} as {type(self._nexus).__name__}: {e} "
"Falling back to loading HDF5 group children as scipp.DataGroup."
)
> warnings.warn(msg, stacklevel=2)
E UserWarning: Failed to load /entry/instrument/event_mode_detectors/timepix3 as _StrippedDetector: Could not determine signal field or dimensions. Falling back to loading HDF5 group children as scipp.DataGroup.
E In provider ess.reduce.nexus.workflow.load_nexus_component(
E location: ess.reduce.nexus.types.NeXusComponentLocationSpec[scippnexus.nxdetector.NXdetector, ess.reduce.nexus.types.SampleRun],
E nx_class: ess.reduce.nexus.types.NeXusClass[scippnexus.nxdetector.NXdetector],
E ) -> ess.reduce.nexus.types.NeXusComponent[scippnexus.nxdetector.NXdetector, ess.reduce.nexus.types.SampleRun]
.tox/nexusfiles-scipp-odin/lib/python3.12/site-packages/scippnexus/base.py:409: UserWarning
