refactor: rename ioq to reflectivity and add resolution as coord

Author: jokasimr

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

@@ -18,6 +18,16 @@
     "## Setup"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import warnings\n",
+    "warnings.filterwarnings('ignore')"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -85,7 +95,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "workflow.visualize(NormalizedIofQ, graph_attr={'rankdir': 'LR'})"
+    "workflow.visualize(ReflectivityOverQ, graph_attr={'rankdir': 'LR'})"
    ]
   },
   {
@@ -128,7 +138,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "workflow.visualize(NormalizedIofQ, graph_attr={'rankdir': 'LR'})"
+    "workflow.visualize(ReflectivityOverQ, graph_attr={'rankdir': 'LR'})"
    ]
   },
   {
@@ -158,7 +168,7 @@
     "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 +195,8 @@
    "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/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

@@ -1,10 +1,10 @@
 # SPDX-License-Identifier: BSD-3-Clause
 # Copyright (c) 2023 Scipp contributors (https://github.com/scipp)
 
-from .types import NormalizedIofQ, NormalizedIofQ1D
+from .types import ReflectivityOverQ, ReflectivityOverQ1D
 
 
-def average_over_detectors(iofq: NormalizedIofQ) -> NormalizedIofQ1D:
+def average_over_detectors(iofq: ReflectivityOverQ) -> ReflectivityOverQ1D:
     """Average over all detector pixels."""
     return iofq.mean(dim='detector_number')
 

src/ess/reflectometry/types.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."""
 

tests/amor/pipeline_test.py

@@ -13,9 +13,9 @@
 from ess.reflectometry import orso
 from ess.reflectometry.types import (
     Filename,
-    NormalizedIofQ,
     QBins,
     ReferenceRun,
+    ReflectivityOverQ,
     SampleRotation,
     SampleRun,
     SampleSize,
@@ -57,7 +57,7 @@ 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