Use ess.reduce.nexus NeXus workflows as basis for all workflows

docs/user-guide/common/beam-center-finder.ipynb

@@ -77,7 +77,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "raw = workflow.compute(RawDetector[SampleRun])['spectrum', :61440]\n",
+    "workflow[BeamCenter] = sc.vector([0, 0, 0], unit='m')\n",
+    "raw = workflow.compute(DetectorData[SampleRun])['spectrum', :61440]\n",
     "\n",
     "p = isis.plot_flat_detector_xy(raw.hist(), norm='log')\n",
     "p.ax.plot(0, 0, '+', color='k', ms=10)\n",
@@ -305,10 +306,10 @@
    "outputs": [],
    "source": [
     "workflow[Filename[SampleRun]] = isis.data.sans2d_tutorial_sample_run()\n",
-    "detector = workflow.compute(RawDetector[SampleRun])['spectrum', :61440].assign_masks(\n",
-    "    masked.masks\n",
-    ")\n",
-    "workflow[RawDetector[SampleRun]] = detector"
+    "workflow[BeamCenter] = sc.vector([0, 0, 0], unit='m')\n",
+    "detector = workflow.compute(NeXusDetector[SampleRun]).copy()\n",
+    "detector['data'] = detector['data']['spectrum', :61440].assign_masks(masked.masks)\n",
+    "workflow[NeXusDetector[SampleRun]] = detector"
    ]
   },
   {
@@ -449,7 +450,7 @@
     "workflow[WavelengthBands] = None\n",
     "kwargs = dict(  # noqa: C408\n",
     "    workflow=workflow,\n",
-    "    detector=detector,\n",
+    "    detector=detector['data'],\n",
     "    norm=workflow.compute(NormWavelengthTerm[SampleRun]),\n",
     ")"
    ]

pyproject.toml

@@ -32,7 +32,7 @@ requires-python = ">=3.10"
 dependencies = [
   "dask",
   "graphviz",
-  "essreduce>=24.08.0",
+  "essreduce>=24.08.1",
   "numpy",
   "pandas",
   "plopp",

requirements/base.in

@@ -4,7 +4,7 @@
 # The following was generated by 'tox -e deps', DO NOT EDIT MANUALLY!
 dask
 graphviz
-essreduce>=24.08.0
+essreduce>=24.08.1
 numpy
 pandas
 plopp

requirements/base.txt

@@ -1,4 +1,4 @@
-# SHA1:df4cf8a4a39fd2d213b55c8c11559ef6e4fe6fe1
+# SHA1:4cb11db62c9d3136130eb212e7bcf639441c13e6
 #
 # This file is autogenerated by pip-compile-multi
 # To update, run:
@@ -23,7 +23,7 @@ dask==2024.8.1
     # via -r base.in
 decorator==5.1.1
     # via ipython
-essreduce==24.8.0
+essreduce==24.8.1
     # via -r base.in
 exceptiongroup==1.2.2
     # via ipython
@@ -120,7 +120,9 @@ pytz==2024.1
 pyyaml==6.0.2
     # via dask
 sciline==24.6.2
-    # via -r base.in
+    # via
+    #   -r base.in
+    #   essreduce
 scipp==24.8.0
     # via
     #   -r base.in

src/ess/isissans/__init__.py

@@ -3,9 +3,8 @@
 
 import importlib.metadata
 
-from . import components, general, io, sans2d, zoom
-from .components import DetectorBankOffset, MonitorOffset, SampleOffset
-from .general import default_parameters
+from . import general, io, sans2d, zoom
+from .general import default_parameters, SampleOffset, MonitorOffset, DetectorBankOffset
 from .io import CalibrationFilename
 from .visualization import plot_flat_detector_xy
 
@@ -14,17 +13,17 @@
 except importlib.metadata.PackageNotFoundError:
     __version__ = "0.0.0"
 
-providers = components.providers + general.providers + io.providers
+providers = general.providers
 
 del importlib
 
 __all__ = [
     'CalibrationFilename',
     'DetectorBankOffset',
-    'io',
     'MonitorOffset',
-    'providers',
     'SampleOffset',
+    'io',
+    'providers',
     'plot_flat_detector_xy',
     'sans2d',
     'default_parameters',

src/ess/isissans/data.py

@@ -94,7 +94,9 @@ def zoom_tutorial_calibration() -> Filename[CalibrationFilename]:
 
 
 def zoom_tutorial_sample_run() -> Filename[SampleRun]:
-    return _zoom_registry.get_path('ZOOM00034786.nxs.h5.zip', unzip=True)[0]
+    return Filename[SampleRun](
+        _zoom_registry.get_path('ZOOM00034786.nxs.h5.zip', unzip=True)[0]
+    )
 
 
 def zoom_tutorial_empty_beam_run() -> Filename[EmptyBeamRun]:

src/ess/isissans/general.py

@@ -4,45 +4,68 @@
 Providers for the ISIS instruments.
 """
 
+from typing import NewType
+
+import sciline
 import scipp as sc
 
-from ..sans.types import (
+from ess.sans.types import (
+    BeamCenter,
     CalibratedDetector,
+    CalibratedMonitor,
     CorrectForGravity,
     DetectorData,
     DetectorIDs,
     DetectorPixelShape,
+    DetectorPositionOffset,
     DimsToKeep,
     Incident,
     LabFrameTransform,
+    MonitorData,
+    MonitorPositionOffset,
     MonitorType,
+    NeXusDetector,
+    NeXusMonitor,
     NeXusMonitorName,
     NonBackgroundWavelengthRange,
-    RawDetector,
-    RawMonitor,
-    RawMonitorData,
     RunNumber,
     RunTitle,
     RunType,
+    SamplePosition,
     SampleRun,
     ScatteringRunType,
+    SourcePosition,
     TofData,
     TofMonitor,
     Transmission,
     WavelengthBands,
     WavelengthMask,
 )
-from .components import DetectorBankOffset, MonitorOffset, SampleOffset
+
 from .io import LoadedFileContents
 from .mantidio import Period
 
 
+class MonitorOffset(sciline.Scope[MonitorType, sc.Variable], sc.Variable):
+    """
+    Offset for monitor position for all runs.
+    """
+
+
+DetectorBankOffset = NewType('DetectorBankOffset', sc.Variable)
+SampleOffset = NewType('SampleOffset', sc.Variable)
+
+
 def default_parameters() -> dict:
     return {
         CorrectForGravity: False,
         DimsToKeep: (),
-        MonitorOffset[Incident]: MonitorOffset(sc.vector([0, 0, 0], unit='m')),
-        MonitorOffset[Transmission]: MonitorOffset(sc.vector([0, 0, 0], unit='m')),
+        MonitorOffset[Incident]: MonitorOffset[Incident](
+            sc.vector([0, 0, 0], unit='m')
+        ),
+        MonitorOffset[Transmission]: MonitorOffset[Transmission](
+            sc.vector([0, 0, 0], unit='m')
+        ),
         DetectorBankOffset: DetectorBankOffset(sc.vector([0, 0, 0], unit='m')),
         SampleOffset: SampleOffset(sc.vector([0, 0, 0], unit='m')),
         NonBackgroundWavelengthRange: None,
@@ -52,45 +75,70 @@ def default_parameters() -> dict:
     }
 
 
-def get_detector_data(
-    dg: LoadedFileContents[RunType],
-    sample_offset: SampleOffset,
-    detector_bank_offset: DetectorBankOffset,
-) -> RawDetector[RunType]:
+def to_detector_position_offset(
+    global_offset: DetectorBankOffset, beam_center: BeamCenter
+) -> DetectorPositionOffset[RunType]:
+    return DetectorPositionOffset[RunType](global_offset - beam_center)
+
+
+def to_monitor_position_offset(
+    global_offset: MonitorOffset[MonitorType],
+) -> MonitorPositionOffset[RunType, MonitorType]:
+    return MonitorPositionOffset[RunType, MonitorType](global_offset)
+
+
+def get_source_position(dg: LoadedFileContents[RunType]) -> SourcePosition[RunType]:
+    """Get source position from raw data."""
+    return SourcePosition[RunType](dg['data'].coords['source_position'])
+
+
+def get_sample_position(
+    dg: LoadedFileContents[RunType], offset: SampleOffset
+) -> SamplePosition[RunType]:
+    """Get sample position from raw data and apply user offset."""
+    return SamplePosition[RunType](
+        dg['data'].coords['sample_position'] + offset.to(unit='m')
+    )
+
+
+def get_detector_data(dg: LoadedFileContents[RunType]) -> NeXusDetector[RunType]:
     """Get detector data and apply user offsets to raw data.
 
     Parameters
     ----------
     dg:
         Data loaded with Mantid and converted to Scipp.
-    sample_offset:
-        Sample offset.
-    detector_bank_offset:
-        Detector bank offset.
     """
-    data = dg['data']
-    sample_pos = data.coords['sample_position']
-    sample_pos = sample_pos + sample_offset.to(unit=sample_pos.unit, copy=False)
-    pos = data.coords['position']
-    pos = pos + detector_bank_offset.to(unit=pos.unit, copy=False)
-    return RawDetector[RunType](
-        dg['data'].assign_coords(position=pos, sample_position=sample_pos)
+    # The generic NeXus workflow will try to extract 'data' from this, which is exactly
+    # what we also have in the Mantid data. We use the generic workflow since it also
+    # applies offsets, etc.
+    return NeXusDetector[RunType](dg)
+
+
+def get_monitor_data(
+    dg: LoadedFileContents[RunType], nexus_name: NeXusMonitorName[MonitorType]
+) -> NeXusMonitor[RunType, MonitorType]:
+    # The generic NeXus workflow will try to extract 'data' from this, which is exactly
+    # what we also have in the Mantid data. We use the generic workflow since it also
+    # applies offsets, etc.
+    monitor = dg['monitors'][nexus_name]['data']
+    return NeXusMonitor[RunType, MonitorType](
+        sc.DataGroup(data=monitor, position=monitor.coords['position'])
     )
 
 
-def assemble_detector_data(
+def dummy_assemble_detector_data(
     detector: CalibratedDetector[RunType],
 ) -> DetectorData[RunType]:
     """Dummy assembly of detector data, detector already contains neutron data."""
     return DetectorData[RunType](detector)
 
 
-def get_monitor_data(
-    dg: LoadedFileContents[RunType], nexus_name: NeXusMonitorName[MonitorType]
-) -> RawMonitor[RunType, MonitorType]:
-    # See https://github.com/scipp/sciline/issues/52 why copy needed
-    mon = dg['monitors'][nexus_name]['data'].copy()
-    return RawMonitor[RunType, MonitorType](mon)
+def dummy_assemble_monitor_data(
+    monitor: CalibratedMonitor[RunType, MonitorType],
+) -> MonitorData[RunType, MonitorType]:
+    """Dummy assembly of monitor data, monitor already contains neutron data."""
+    return MonitorData[RunType, MonitorType](monitor)
 
 
 def data_to_tof(
@@ -102,7 +150,7 @@ def data_to_tof(
 
 
 def monitor_to_tof(
-    da: RawMonitorData[RunType, MonitorType],
+    da: MonitorData[RunType, MonitorType],
 ) -> TofMonitor[RunType, MonitorType]:
     """Dummy conversion of monitor data to time-of-flight data.
     The monitor data already has a time-of-flight coordinate."""
@@ -166,7 +214,12 @@ def get_detector_ids_from_sample_run(data: TofData[SampleRun]) -> DetectorIDs:
 
 
 providers = (
-    assemble_detector_data,
+    dummy_assemble_detector_data,
+    dummy_assemble_monitor_data,
+    to_detector_position_offset,
+    to_monitor_position_offset,
+    get_source_position,
+    get_sample_position,
     get_detector_data,
     get_detector_ids_from_sample_run,
     get_monitor_data,