Merge pull request #152 from scipp/update-example-files

docs: add more example files and change data fetching functions

Author: jokasimr

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

@@ -98,7 +98,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "workflow[Filename[ReferenceRun]] = amor.data.amor_reference_run()\n",
+    "workflow[Filename[ReferenceRun]] = amor.data.amor_run(614)\n",
     "# The sample rotation value in the file is slightly off, so we set it manually\n",
     "workflow[SampleRotation[ReferenceRun]] = sc.scalar(0.65, unit='deg')\n",
     "\n",
@@ -147,14 +147,14 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "amor.data.amor_sample_run('608')"
+    "amor.data.amor_run(608)"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "When you encounter `amor.data.amor_sample_run` you should imagining replacing that with a path to your own dataset."
+    "When you encounter `amor.data.amor_run` you should imagining replacing that with a path to your own dataset."
    ]
   },
   {
@@ -168,19 +168,19 @@
     "        # The sample rotation values in the files are slightly off, so we replace\n",
     "        # them with corrected values.\n",
     "        SampleRotation[SampleRun]: sc.scalar(0.85, unit='deg'),\n",
-    "        Filename[SampleRun]: amor.data.amor_sample_run('608'),\n",
+    "        Filename[SampleRun]: amor.data.amor_run(608),\n",
     "    },\n",
     "    '609': {\n",
     "        SampleRotation[SampleRun]: sc.scalar(2.25, unit='deg'),\n",
-    "        Filename[SampleRun]: amor.data.amor_sample_run('609'),\n",
+    "        Filename[SampleRun]: amor.data.amor_run(609),\n",
     "    },\n",
     "    '610': {\n",
     "        SampleRotation[SampleRun]: sc.scalar(3.65, unit='deg'),\n",
-    "        Filename[SampleRun]: amor.data.amor_sample_run('610'),\n",
+    "        Filename[SampleRun]: amor.data.amor_run(610),\n",
     "    },\n",
     "    '611': {\n",
     "        SampleRotation[SampleRun]: sc.scalar(5.05, unit='deg'),\n",
-    "        Filename[SampleRun]: amor.data.amor_sample_run('611'),\n",
+    "        Filename[SampleRun]: amor.data.amor_run(611),\n",
     "    },\n",
     "}\n",
     "\n",

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

@@ -97,7 +97,7 @@
     "workflow[ChopperPhase[ReferenceRun]] = sc.scalar(-7.5, unit='deg')\n",
     "# The sample rotation value in the file is slightly off, so we set it manually\n",
     "workflow[SampleRotation[ReferenceRun]] = sc.scalar(0.65, unit='deg')\n",
-    "workflow[Filename[ReferenceRun]] = amor.data.amor_reference_run()\n",
+    "workflow[Filename[ReferenceRun]] = amor.data.amor_run(614)\n",
     "\n",
     "reference_result = workflow.compute(ReducedReference)\n",
     "# Set the result back onto the pipeline to cache it\n",
@@ -126,7 +126,7 @@
     "for key, angle in mu.items():\n",
     "    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",
+    "    workflow[Filename[SampleRun]] = amor.data.amor_run(key)\n",
     "    da = workflow.compute(ReflectivityOverQ).hist()\n",
     "    da.coords['Q'] = sc.midpoints(da.coords['Q'], dim='Q')\n",
     "    results['ess'][key] = da\n",

src/ess/amor/data.py

@@ -1,5 +1,6 @@
 # SPDX-License-Identifier: BSD-3-Clause
 # Copyright (c) 2025 Scipp contributors (https://github.com/scipp)
+import re
 
 from ..reflectometry.types import Filename, ReferenceRun, SampleRun
 
@@ -50,6 +51,24 @@ def _make_pooch():
             "611.Rqz.ort": "md5:0c51e8ac5c00041434417673be186151",
             "612.Rqz.ort": "md5:d785d27151e7f1edc05e86d35bef6a63",
             "613.Rqz.ort": "md5:e999c85f7a47665c4ddd1538b19d402d",
+            "amor2024n001632.hdf": "md5:2253f0ec6d2e96a986a6aa35d43a7480",
+            "amor2024n001634.hdf": "md5:7cdd87bbd96fb3fb1e046800a9b1d77e",
+            "amor2024n001635.hdf": "md5:fb9eb0e7b803c13f1804d085b3b0058f",
+            "amor2024n001636.hdf": "md5:f7deb51d22652d1f5d0e4b51927af5a3",
+            "amor2024n001637.hdf": "md5:06e5957d34d82035cfece40cbbf47d7a",
+            "amor2024n001638.hdf": "md5:1193fe808af2afeb0f48d3b0022fe40b",
+            "amor2024n001639.hdf": "md5:ff24e31a07c4020927aaa6df9f2ee05f",
+            "amor2024n001640.hdf": "md5:051335fea1c369322a2328d530dedb77",
+            "amor2024n001641.hdf": "md5:d543b5890b63707cf8d7f6666e8830a4",
+            "amor2024n001642.hdf": "md5:b1474e32cc64371e1005f44f2c5b6ae7",
+            "amor2024n004079.hdf": "md5:5bf1dabc2ff902a57ed7593903c8e1a5",
+            "amor2024n004080.hdf": "md5:7dcaa5da00b7eedc178b9e55209bfbce",
+            "amor2024n004081.hdf": "md5:2f4f46f0e56ab75aad0c2933060df504",
+            "amor2024n004083.hdf": "md5:ffd13420e44cbf966b94bd532e293c1c",
+            "amor2024n004084.hdf": "md5:5041a9486b3cd6407a9b9f44104c9b54",
+            "amor2024n004085.hdf": "md5:152ac63bad6f3b2b5cf1c4e4c7df5e30",
+            "amor2024n004152.hdf": "md5:244459be7a3caeac523c289815c5b7dc",
+            "amor2024n004154.hdf": "md5:6184553f795fd2b230baab9a421da9e4",
         },
     )
 
@@ -65,12 +84,15 @@ def amor_old_reference_run() -> Filename[ReferenceRun]:
     return Filename[ReferenceRun](_pooch.fetch("reference.nxs"))
 
 
-def amor_reference_run() -> Filename[ReferenceRun]:
-    return Filename[ReferenceRun](_pooch.fetch("amor2023n000614.hdf"))
-
-
-def amor_sample_run(number: int | str) -> Filename[SampleRun]:
-    return Filename[SampleRun](_pooch.fetch(f"amor2023n{int(number):06d}.hdf"))
+def amor_run(number: int | str) -> Filename[SampleRun]:
+    fnames = [
+        name
+        for name in _pooch.registry.keys()
+        if re.match(f'amor\\d{{4}}n{int(number):06d}.hdf', name)
+    ]
+    if len(fnames) != 1:
+        raise ValueError(f'Expected exactly one matching file, found {len(fnames)}')
+    return Filename[SampleRun](_pooch.fetch(fnames[0]))
 
 
 def amor_psi_software_result(number: int | str) -> Filename[SampleRun]:
@@ -79,6 +101,5 @@ def amor_psi_software_result(number: int | str) -> Filename[SampleRun]:
 
 __all__ = [
     "amor_psi_software_result",
-    "amor_reference_run",
-    "amor_sample_run",
+    "amor_run",
 ]

tests/amor/pipeline_test.py

@@ -48,7 +48,7 @@ def amor_pipeline() -> sciline.Pipeline:
     )
     # The sample rotation value in the file is slightly off, so we set it manually
     pl[SampleRotation[ReferenceRun]] = sc.scalar(0.65, unit="deg")
-    pl[Filename[ReferenceRun]] = amor.data.amor_reference_run()
+    pl[Filename[ReferenceRun]] = amor.data.amor_run(614)
 
     pl[orso.OrsoCreator] = orso.OrsoCreator(
         fileio.base.Person(
@@ -65,7 +65,7 @@ def amor_pipeline() -> sciline.Pipeline:
 def test_has_expected_coordinates(amor_pipeline: sciline.Pipeline):
     # The sample rotation value in the file is slightly off, so we set it manually
     amor_pipeline[SampleRotation[SampleRun]] = sc.scalar(0.85, unit="deg")
-    amor_pipeline[Filename[SampleRun]] = amor.data.amor_sample_run(608)
+    amor_pipeline[Filename[SampleRun]] = amor.data.amor_run(608)
     reflectivity_over_q = amor_pipeline.compute(ReflectivityOverQ)
     assert "Q" in reflectivity_over_q.coords
     assert "Q_resolution" in reflectivity_over_q.coords
@@ -76,7 +76,7 @@ def test_has_expected_coordinates(amor_pipeline: sciline.Pipeline):
 def test_pipeline_no_gravity_correction(amor_pipeline: sciline.Pipeline):
     # The sample rotation value in the file is slightly off, so we set it manually
     amor_pipeline[SampleRotation[SampleRun]] = sc.scalar(0.85, unit="deg")
-    amor_pipeline[Filename[SampleRun]] = amor.data.amor_sample_run(608)
+    amor_pipeline[Filename[SampleRun]] = amor.data.amor_run(608)
     amor_pipeline[amor.types.GravityToggle] = False
     reflectivity_over_q = amor_pipeline.compute(ReflectivityOverQ)
     assert "Q" in reflectivity_over_q.coords
@@ -88,7 +88,7 @@ def test_pipeline_no_gravity_correction(amor_pipeline: sciline.Pipeline):
 def test_orso_pipeline(amor_pipeline: sciline.Pipeline):
     # The sample rotation value in the file is slightly off, so we set it manually
     amor_pipeline[SampleRotation[SampleRun]] = sc.scalar(0.85, unit="deg")
-    amor_pipeline[Filename[SampleRun]] = amor.data.amor_sample_run(608)
+    amor_pipeline[Filename[SampleRun]] = amor.data.amor_run(608)
     res = amor_pipeline.compute(orso.OrsoIofQDataset)
     assert res.info.data_source.experiment.instrument == "Amor"
     assert res.info.reduction.software.name == "ess.reflectometry"
@@ -109,7 +109,7 @@ def test_save_reduced_orso_file(amor_pipeline: sciline.Pipeline, output_folder:
     from orsopy import fileio
 
     amor_pipeline[SampleRotation[SampleRun]] = sc.scalar(0.85, unit="deg")
-    amor_pipeline[Filename[SampleRun]] = amor.data.amor_sample_run(608)
+    amor_pipeline[Filename[SampleRun]] = amor.data.amor_run(608)
     res = amor_pipeline.compute(orso.OrsoIofQDataset)
     fileio.orso.save_orso(datasets=[res], fname=output_folder / 'amor_reduced_iofq.ort')
 
@@ -120,8 +120,8 @@ def test_pipeline_can_compute_reflectivity_merging_events_from_multiple_runs(
     amor_pipeline: sciline.Pipeline,
 ):
     sample_runs = [
-        amor.data.amor_sample_run(608),
-        amor.data.amor_sample_run(609),
+        amor.data.amor_run(608),
+        amor.data.amor_run(609),
     ]
     pipeline = with_filenames(amor_pipeline, SampleRun, sample_runs)
     pipeline[SampleRotation[SampleRun]] = pipeline.compute(
@@ -135,16 +135,16 @@ def test_pipeline_can_compute_reflectivity_merging_events_from_multiple_runs(
 @pytest.mark.filterwarnings("ignore:Invalid transformation, missing attribute")
 def test_pipeline_merging_events_result_unchanged(amor_pipeline: sciline.Pipeline):
     sample_runs = [
-        amor.data.amor_sample_run(608),
+        amor.data.amor_run(608),
     ]
     pipeline = with_filenames(amor_pipeline, SampleRun, sample_runs)
     pipeline[SampleRotation[SampleRun]] = pipeline.compute(
         SampleRotation[SampleRun]
     ) + sc.scalar(0.05, unit="deg")
     result = pipeline.compute(ReflectivityOverQ).hist()
     sample_runs = [
-        amor.data.amor_sample_run(608),
-        amor.data.amor_sample_run(608),
+        amor.data.amor_run(608),
+        amor.data.amor_run(608),
     ]
     pipeline = with_filenames(amor_pipeline, SampleRun, sample_runs)
     pipeline[SampleRotation[SampleRun]] = pipeline.compute(
@@ -162,7 +162,7 @@ def test_pipeline_merging_events_result_unchanged(amor_pipeline: sciline.Pipelin
 @pytest.mark.filterwarnings("ignore:Failed to convert .* into a transformation")
 @pytest.mark.filterwarnings("ignore:Invalid transformation, missing attribute")
 def test_proton_current(amor_pipeline: sciline.Pipeline):
-    amor_pipeline[Filename[SampleRun]] = amor.data.amor_sample_run(611)
+    amor_pipeline[Filename[SampleRun]] = amor.data.amor_run(611)
     da_without_proton_current = amor_pipeline.compute(ReducibleData[SampleRun])
 
     proton_current = [1, 2, 0.1]