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Merge pull request #97 from scipp/cleanup-nexus
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Cleanup nexus module
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@SimonHeybrock
SimonHeybrock authored Sep 5, 2024
2 parents a0358da + 593cb89 commit aef4a3c
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Showing 4 changed files with 98 additions and 366 deletions.
18 changes: 6 additions & 12 deletions src/ess/reduce/nexus/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -12,24 +12,18 @@

from . import types
from ._nexus_loader import (
extract_detector_data,
extract_monitor_data,
load_detector,
load_event_data,
group_event_data,
load_monitor,
load_sample,
load_source,
load_component,
compute_component_position,
extract_events_or_histogram,
)

__all__ = [
'types',
'extract_detector_data',
'extract_monitor_data',
'group_event_data',
'load_detector',
'load_event_data',
'load_monitor',
'load_sample',
'load_source',
'load_component',
'compute_component_position',
'extract_events_or_histogram',
]
310 changes: 20 additions & 290 deletions src/ess/reduce/nexus/_nexus_loader.py
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Original file line number Diff line number Diff line change
Expand Up @@ -13,21 +13,7 @@
import scippnexus as snx

from ..logging import get_logger
from .types import (
AnyNeXusMonitorName,
AnyRunAnyNeXusMonitor,
AnyRunFilename,
AnyRunNeXusDetector,
AnyRunNeXusSample,
AnyRunNeXusSource,
NeXusDetectorName,
NeXusEntryName,
NeXusGroup,
NeXusLocationSpec,
NeXusSourceName,
RawDetectorData,
RawMonitorData,
)
from .types import AnyRunFilename, NeXusEntryName, NeXusGroup, NeXusLocationSpec


class NoNewDefinitionsType: ...
Expand All @@ -36,206 +22,6 @@ class NoNewDefinitionsType: ...
NoNewDefinitions = NoNewDefinitionsType()


def load_detector(
file_path: AnyRunFilename,
selection=(),
*,
detector_name: NeXusDetectorName,
entry_name: NeXusEntryName | None = None,
definitions: Mapping | None | NoNewDefinitionsType = NoNewDefinitions,
) -> AnyRunNeXusDetector:
"""Load a single detector (bank) from a NeXus file.
The detector positions are computed automatically from NeXus transformations,
and the combined transformation is stored under the name 'transform'.
Parameters
----------
file_path:
Indicates where to load data from.
One of:
- Path to a NeXus file on disk.
- File handle or buffer for reading binary data.
- A ScippNexus group of the root of a NeXus file.
detector_name:
Name of the detector (bank) to load.
Must be a group in an instrument group in the entry (see below).
entry_name:
Name of the entry that contains the detector.
If ``None``, the entry will be located based
on its NeXus class, but there cannot be more than 1.
definitions:
Definitions used by scippnexus loader, see :py:`scippnexus.File`
for documentation.
Returns
-------
:
A data group containing the detector events or histogram
and any auxiliary data stored in the same NeXus group.
"""
return AnyRunNeXusDetector(
load_component(
NeXusLocationSpec(
filename=file_path,
component_name=detector_name,
entry_name=entry_name,
selection=selection,
),
nx_class=snx.NXdetector,
definitions=definitions,
)
)


def load_monitor(
file_path: AnyRunFilename,
selection=(),
*,
monitor_name: AnyNeXusMonitorName,
entry_name: NeXusEntryName | None = None,
definitions: Mapping | None | NoNewDefinitionsType = NoNewDefinitions,
) -> AnyRunAnyNeXusMonitor:
"""Load a single monitor from a NeXus file.
The monitor position is computed automatically from NeXus transformations,
and the combined transformation is stored under the name 'transform'.
Parameters
----------
file_path:
Indicates where to load data from.
One of:
- Path to a NeXus file on disk.
- File handle or buffer for reading binary data.
- A ScippNexus group of the root of a NeXus file.
monitor_name:
Name of the monitor to load.
Must be a group in an instrument group in the entry (see below).
entry_name:
Name of the entry that contains the monitor.
If ``None``, the entry will be located based
on its NeXus class, but there cannot be more than 1.
definitions:
Definitions used by scippnexus loader, see :py:`scippnexus.File`
for documentation.
Returns
-------
:
A data group containing the monitor events or histogram
and any auxiliary data stored in the same NeXus group.
"""
return AnyRunAnyNeXusMonitor(
load_component(
NeXusLocationSpec(
filename=file_path,
component_name=monitor_name,
entry_name=entry_name,
selection=selection,
),
nx_class=snx.NXmonitor,
definitions=definitions,
)
)


def load_source(
file_path: AnyRunFilename,
*,
source_name: NeXusSourceName | None = None,
entry_name: NeXusEntryName | None = None,
definitions: Mapping | None | NoNewDefinitionsType = NoNewDefinitions,
) -> AnyRunNeXusSource:
"""Load a source from a NeXus file.
The source position is computed automatically from NeXus transformations,
and the combined transformation is stored under the name 'transform'.
Parameters
----------
file_path:
Indicates where to load data from.
One of:
- Path to a NeXus file on disk.
- File handle or buffer for reading binary data.
- A ScippNexus group of the root of a NeXus file.
source_name:
Name of the source to load.
Must be a group in an instrument group in the entry (see below).
If ``None``, the source will be located based
on its NeXus class.
entry_name:
Name of the instrument that contains the source.
If ``None``, the entry will be located based
on its NeXus class, but there cannot be more than 1.
definitions:
Definitions used by scippnexus loader, see :py:`scippnexus.File`
for documentation.
Returns
-------
:
A data group containing all data stored in
the source NeXus group.
"""
return AnyRunNeXusSource(
load_component(
NeXusLocationSpec(
filename=file_path, component_name=source_name, entry_name=entry_name
),
nx_class=snx.NXsource,
definitions=definitions,
)
)


def load_sample(
file_path: AnyRunFilename,
entry_name: NeXusEntryName | None = None,
definitions: Mapping | None | NoNewDefinitionsType = NoNewDefinitions,
) -> AnyRunNeXusSample:
"""Load a sample from a NeXus file.
The sample is located based on its NeXus class.
There can be only one sample in a NeXus file or
in the entry indicated by ``entry_name``.
Parameters
----------
file_path:
Indicates where to load data from.
One of:
- Path to a NeXus file on disk.
- File handle or buffer for reading binary data.
- A ScippNexus group of the root of a NeXus file.
entry_name:
Name of the instrument that contains the source.
If ``None``, the entry will be located based
on its NeXus class, but there cannot be more than 1.
definitions:
Definitions used by scippnexus loader, see :py:`scippnexus.File`
for documentation.
Returns
-------
:
A data group containing all data stored in
the sample NeXus group.
"""
return AnyRunNeXusSample(
load_component(
NeXusLocationSpec(filename=file_path, entry_name=entry_name),
nx_class=snx.NXsample,
definitions=definitions,
)
)


def load_component(
location: NeXusLocationSpec,
*,
Expand All @@ -254,24 +40,26 @@ def load_component(
instrument = _unique_child_group(entry, snx.NXinstrument, None)
component = _unique_child_group(instrument, nx_class, group_name)
loaded = cast(sc.DataGroup, component[selection])
loaded['nexus_component_name'] = component.name.split('/')[-1]
return compute_component_position(loaded)

transform_out_name = 'transform'
if transform_out_name in loaded:
raise RuntimeError(
f"Loaded data contains an item '{transform_out_name}' but we want to "
"store the combined NeXus transformations under that name."
)
position_out_name = 'position'
if position_out_name in loaded:
raise RuntimeError(
f"Loaded data contains an item '{position_out_name}' but we want to "
"store the computed positions under that name."
)
loaded = snx.compute_positions(
loaded, store_position=position_out_name, store_transform=transform_out_name

def compute_component_position(dg: sc.DataGroup) -> sc.DataGroup:
transform_out_name = 'transform'
if transform_out_name in dg:
raise RuntimeError(
f"Loaded data contains an item '{transform_out_name}' but we want to "
"store the combined NeXus transformations under that name."
)
loaded['nexus_component_name'] = component.name.split('/')[-1]
return loaded
position_out_name = 'position'
if position_out_name in dg:
raise RuntimeError(
f"Loaded data contains an item '{position_out_name}' but we want to "
"store the computed positions under that name."
)
return snx.compute_positions(
dg, store_position=position_out_name, store_transform=transform_out_name
)


def _open_nexus_file(
Expand Down Expand Up @@ -311,65 +99,7 @@ def _unique_child_group(
return next(iter(children.values())) # type: ignore[return-value]


def extract_detector_data(detector: AnyRunNeXusDetector) -> RawDetectorData:
"""Get and return the events or histogram from a detector loaded from NeXus.
This function looks for a data array in the detector group and returns that.
Parameters
----------
detector:
A detector loaded from NeXus.
Returns
-------
:
A data array containing the events or histogram.
Raises
------
ValueError
If there is more than one data array.
See also
--------
load_detector:
Load a detector from a NeXus file in a format compatible with
``extract_detector_data``.
"""
return RawDetectorData(_extract_events_or_histogram(detector))


def extract_monitor_data(monitor: AnyRunAnyNeXusMonitor) -> RawMonitorData:
"""Get and return the events or histogram from a monitor loaded from NeXus.
This function looks for a data array in the monitor group and returns that.
Parameters
----------
monitor:
A monitor loaded from NeXus.
Returns
-------
:
A data array containing the events or histogram.
Raises
------
ValueError
If there is more than one data array.
See also
--------
load_monitor:
Load a monitor from a NeXus file in a format compatible with
``extract_monitor_data``.
"""
return RawMonitorData(_extract_events_or_histogram(monitor))


def _extract_events_or_histogram(dg: sc.DataGroup) -> sc.DataArray:
def extract_events_or_histogram(dg: sc.DataGroup) -> sc.DataArray:
event_data_arrays = {
key: value
for key, value in dg.items()
Expand Down
4 changes: 2 additions & 2 deletions src/ess/reduce/nexus/workflow.py
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Original file line number Diff line number Diff line change
Expand Up @@ -358,7 +358,7 @@ def get_calibrated_detector(
bank_sizes:
Dictionary of detector bank sizes.
"""
da = nexus.extract_detector_data(detector)
da = nexus.extract_events_or_histogram(detector)
if (
sizes := (bank_sizes or {}).get(detector.get('nexus_component_name'))
) is not None:
Expand Down Expand Up @@ -421,7 +421,7 @@ def get_calibrated_monitor(
Position of the neutron source.
"""
return AnyRunAnyCalibratedMonitor(
nexus.extract_monitor_data(monitor).assign_coords(
nexus.extract_events_or_histogram(monitor).assign_coords(
position=monitor['position'] + offset.to(unit=monitor['position'].unit),
source_position=source_position,
)
Expand Down
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