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May 2, 2025
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docs: add more example files and change data fetching functions #152

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ab9469a
docs: add more example files and change data fetching functions
jokasimr May 1, 2025
8619348
fix: remove year
jokasimr May 2, 2025
d743be6
fix
jokasimr May 2, 2025
94335f6
fix: use int
jokasimr May 2, 2025
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14 changes: 7 additions & 7 deletions docs/user-guide/amor/amor-reduction.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -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",
Expand Down Expand Up @@ -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."
]
},
{
Expand All @@ -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",
Expand Down
4 changes: 2 additions & 2 deletions docs/user-guide/amor/compare-to-eos.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -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",
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@SimonHeybrock SimonHeybrock May 2, 2025

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Above you passed runs as string, but an int here? Should it all be ints?

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@jokasimr jokasimr May 2, 2025

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Both work but I agree it's better to be consistent.

"\n",
"reference_result = workflow.compute(ReducedReference)\n",
"# Set the result back onto the pipeline to cache it\n",
Expand Down Expand Up @@ -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",
Expand Down
37 changes: 29 additions & 8 deletions src/ess/amor/data.py
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Original file line number Diff line number Diff line change
@@ -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

Expand Down Expand Up @@ -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",
},
)

Expand All @@ -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]:
Expand All @@ -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",
]
22 changes: 11 additions & 11 deletions tests/amor/pipeline_test.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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(
Expand All @@ -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
Expand All @@ -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
Expand All @@ -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"
Expand All @@ -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')

Expand All @@ -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(
Expand All @@ -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(
Expand All @@ -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]
Expand Down
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