Merge pull request #89 from scipp/resolution-refactor

refactor: rename ioq to reflectivity and add resolution as coord

Author: jokasimr

docs/user-guide/amor/amor-reduction.ipynb

@@ -85,7 +85,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "workflow.visualize(NormalizedIofQ, graph_attr={'rankdir': 'LR'})"
+    "workflow.visualize(ReflectivityOverQ, graph_attr={'rankdir': 'LR'})"
    ]
   },
   {
@@ -128,7 +128,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "workflow.visualize(NormalizedIofQ, graph_attr={'rankdir': 'LR'})"
+    "workflow.visualize(ReflectivityOverQ, graph_attr={'rankdir': 'LR'})"
    ]
   },
   {
@@ -158,7 +158,7 @@
     "for file, angle in runs.items():\n",
     "    workflow[Filename[SampleRun]] = amor.data.amor_sample_run(file)\n",
     "    workflow[SampleRotation[SampleRun]] = angle\n",
-    "    results[file] = workflow.compute(NormalizedIofQ).hist()\n",
+    "    results[file] = workflow.compute(ReflectivityOverQ).hist()\n",
     "\n",
     "sc.plot(results, norm='log', vmin=1e-4)"
    ]
@@ -185,7 +185,8 @@
    "outputs": [],
    "source": [
     "from ess.reflectometry.tools import combine_curves\n",
-    "combine_curves(results_scaled.values(), workflow.compute(QBins)).plot(norm='log')"
+    "c = combine_curves(results_scaled.values(), workflow.compute(QBins))\n",
+    "c.plot(norm='log')"
    ]
   },
   {

docs/user-guide/amor/compare-to-eos.ipynb

@@ -123,7 +123,7 @@
     "    print(key, '... ', end='')\n",
     "    workflow[SampleRotation[SampleRun]] = sc.scalar(angle + 0.05, unit='deg')\n",
     "    workflow[Filename[SampleRun]] = amor.data.amor_sample_run(key)\n",
-    "    da = workflow.compute(NormalizedIofQ).hist()\n",
+    "    da = workflow.compute(ReflectivityOverQ).hist()\n",
     "    da.coords['Q'] = sc.midpoints(da.coords['Q'], dim='Q')\n",
     "    results['ess'][key] = da\n",
     "    print('Done!')"

src/ess/amor/load.py

@@ -1,5 +1,8 @@
 # SPDX-License-Identifier: BSD-3-Clause
 # Copyright (c) 2023 Scipp contributors (https://github.com/scipp)
+import warnings
+from functools import wraps
+
 import scipp as sc
 
 from ess.reduce import nexus
@@ -25,12 +28,33 @@
 )
 
 
+def ignore_amor_warnings(func):
+    @wraps(func)
+    def wrapped(*args, **kwargs):
+        with warnings.catch_warnings():
+            warnings.filterwarnings(
+                'ignore',
+                category=UserWarning,
+                message=r'Failed to convert .* into a transformation',
+            )
+            warnings.filterwarnings(
+                'ignore',
+                category=UserWarning,
+                message='Invalid transformation, missing attribute',
+            )
+            return func(*args, **kwargs)
+
+    return wrapped
+
+
+@ignore_amor_warnings
 def load_detector(
     file_path: Filename[RunType], detector_name: NeXusDetectorName[RunType]
 ) -> LoadedNeXusDetector[RunType]:
     return nexus.load_detector(file_path=file_path, detector_name=detector_name)
 
 
+@ignore_amor_warnings
 def load_events(
     detector: LoadedNeXusDetector[RunType], detector_rotation: DetectorRotation[RunType]
 ) -> RawDetectorData[RunType]:
@@ -108,6 +132,7 @@ def compute_tof(
     return ReducibleDetectorData[RunType](data)
 
 
+@ignore_amor_warnings
 def amor_chopper(f: Filename[RunType]) -> RawChopper[RunType]:
     return next(load_nx(f, "NXentry/NXinstrument/NXdisk_chopper"))
 
@@ -140,6 +165,7 @@ def load_amor_ch_frequency(ch: RawChopper[RunType]) -> ChopperFrequency[RunType]
     raise ValueError("No unit was found for the chopper frequency")
 
 
+@ignore_amor_warnings
 def load_amor_sample_rotation(fp: Filename[RunType]) -> SampleRotation[RunType]:
     (mu,) = load_nx(fp, "NXentry/NXinstrument/master_parameters/mu")
     # Jochens Amor code reads the first value of this log
@@ -148,6 +174,7 @@ def load_amor_sample_rotation(fp: Filename[RunType]) -> SampleRotation[RunType]:
     return sc.scalar(mu['value'].data['dim_1', 0]['time', 0].value, unit='deg')
 
 
+@ignore_amor_warnings
 def load_amor_detector_rotation(fp: Filename[RunType]) -> DetectorRotation[RunType]:
     (nu,) = load_nx(fp, "NXentry/NXinstrument/master_parameters/nu")
     # Jochens Amor code reads the first value of this log

src/ess/amor/orso.py

@@ -14,10 +14,10 @@
     OrsoIofQDataset,
     OrsoReduction,
 )
-from ..reflectometry.types import NormalizedIofQ, QResolution
+from ..reflectometry.types import QResolution, ReflectivityOverQ
 
 
-def build_orso_instrument(events: NormalizedIofQ) -> OrsoInstrument:
+def build_orso_instrument(events: ReflectivityOverQ) -> OrsoInstrument:
     """Build ORSO instrument metadata from intermediate reduction results for Amor.
 
     This assumes specular reflection and sets the incident angle equal to the computed
@@ -33,7 +33,7 @@ def build_orso_instrument(events: NormalizedIofQ) -> OrsoInstrument:
 
 
 def build_orso_iofq_dataset(
-    iofq: NormalizedIofQ,
+    iofq: ReflectivityOverQ,
     sigma_q: QResolution,
     data_source: OrsoDataSource,
     reduction: OrsoReduction,

src/ess/amor/utils.py

@@ -2,9 +2,9 @@
 
 from ess.reflectometry.types import (
     DetectorRotation,
-    NormalizedIofQ,
     QBins,
     ReflectivityData,
+    ReflectivityOverQ,
     RunType,
     SampleRotation,
     SampleRun,
@@ -112,7 +112,7 @@ def diagnostic_view(
     lath: WavelengthThetaFigure,
     laz: WavelengthZIndexFigure,
     qth: QThetaFigure,
-    ioq: NormalizedIofQ,
+    ioq: ReflectivityOverQ,
 ) -> ReflectivityDiagnosticsView:
     ioq = ioq.hist().plot(norm="log")
     return (ioq + laz) / (lath + qth)

src/ess/reflectometry/normalize.py

@@ -9,9 +9,10 @@
     FootprintCorrectedData,
     IdealReferenceIntensity,
     NormalizationFactor,
-    NormalizedIofQ,
     QBins,
+    QResolution,
     ReflectivityData,
+    ReflectivityOverQ,
     SampleRun,
     WavelengthBins,
 )
@@ -94,7 +95,8 @@ def reflectivity_over_q(
     da: FootprintCorrectedData[SampleRun],
     n: NormalizationFactor,
     qbins: QBins,
-) -> NormalizedIofQ:
+    qres: QResolution,
+) -> ReflectivityOverQ:
     """
     Normalize the sample measurement by the (ideally calibrated) supermirror.
 
@@ -110,9 +112,9 @@ def reflectivity_over_q(
     :
         Reflectivity as a function of Q
     """
-    return NormalizedIofQ(
-        da.bin(Q=qbins, dim=da.dims) / sc.values(n.hist(Q=qbins, dim=n.dims))
-    )
+    reflectivity = da.bin(Q=qbins, dim=da.dims) / sc.values(n.hist(Q=qbins, dim=n.dims))
+    reflectivity.coords['Q_resolution'] = qres.data
+    return ReflectivityOverQ(reflectivity)
 
 
 def reflectivity_per_event(

src/ess/reflectometry/reductions.py

@@ -64,7 +64,7 @@ class FootprintCorrectedData(sciline.Scope[RunType, sc.DataArray], sc.DataArray)
 NormalizationFactor = NewType("NormalizationFactor", sc.DataArray)
 """:code`IdealReferenceIntensity` with added coordinate "sample"-Q"""
 
-NormalizedIofQ = NewType("NormalizedIofQ", sc.DataArray)
+ReflectivityOverQ = NewType("ReflectivityOverQ", sc.DataArray)
 """Intensity histogram over momentum transfer
 normalized by the calibrated reference measurement."""
 

src/ess/reflectometry/types.py

@@ -13,9 +13,9 @@
 from ess.reflectometry import orso
 from ess.reflectometry.types import (
     Filename,
-    NormalizedIofQ,
     QBins,
     ReferenceRun,
+    ReflectivityOverQ,
     SampleRotation,
     SampleRun,
     SampleSize,
@@ -57,8 +57,9 @@ def amor_pipeline() -> sciline.Pipeline:
 
 
 def test_run_data_pipeline(amor_pipeline: sciline.Pipeline):
-    res = amor_pipeline.compute(NormalizedIofQ)
+    res = amor_pipeline.compute(ReflectivityOverQ)
     assert "Q" in res.coords
+    assert "Q_resolution" in res.coords
 
 
 def test_run_full_pipeline(amor_pipeline: sciline.Pipeline):