Merge branch 'main' into invert-yaxis

Author: jokasimr

.github/workflows/nightly_at_main.yml

@@ -31,4 +31,5 @@ jobs:
       os-variant: ${{ matrix.os }}
       python-version: ${{ matrix.python.version }}
       tox-env: ${{ matrix.python.tox-env }}
+      test-artifacts-name: 'essreflectometry-test-artifacts-latest'
     secrets: inherit

.github/workflows/nightly_at_release.yml

@@ -38,4 +38,5 @@ jobs:
       python-version: ${{ matrix.python.version }}
       tox-env: ${{ matrix.python.tox-env }}
       checkout_ref: ${{ needs.setup.outputs.release_tag }}
+      test-artifacts-name: 'essreflectometry-test-artifacts-stable'
     secrets: inherit

.github/workflows/test.yml

@@ -20,6 +20,9 @@ on:
       checkout_ref:
         default: ''
         type: string
+      test-artifacts-name:
+        default: ''
+        type: string
   workflow_call:
     inputs:
       os-variant:
@@ -39,6 +42,9 @@ on:
       checkout_ref:
         default: ''
         type: string
+      test-artifacts-name:
+        default: ''
+        type: string
 
 jobs:
   package-test:
@@ -71,9 +77,14 @@ jobs:
           python-version: ${{ inputs.python-version }}
       - run: python -m pip install --upgrade pip
       - run: python -m pip install -r ${{ inputs.pip-recipe }}
-      - run: tox -e ${{ inputs.tox-env }}
+      - run: tox -e ${{ inputs.tox-env }} -- --file-output="tests_outputs"
       - uses: actions/upload-artifact@v4
         if: ${{ inputs.coverage-report }}
         with:
           name: CoverageReport
           path: coverage_html/
+      - uses: actions/upload-artifact@v4
+        if: ${{ inputs.test-artifacts-name != '' }}
+        with:
+          name: ${{ inputs.test-artifacts-name }}
+          path: tests_outputs/

src/ess/amor/__init__.py

@@ -30,6 +30,7 @@
     AngularResolution,
     ChopperFrequency,
     ChopperPhase,
+    GravityToggle,
     QThetaFigure,
     ReflectivityDiagnosticsView,
     SampleSizeResolution,
@@ -76,6 +77,7 @@ def default_parameters() -> dict:
             sc.scalar(-0.75, unit='deg'),
             sc.scalar(0.75, unit='deg'),
         ),
+        GravityToggle: True,
     }
 
 

src/ess/amor/conversions.py

@@ -11,7 +11,7 @@
     ZIndexLimits,
 )
 from .geometry import Detector
-from .types import CoordTransformationGraph
+from .types import CoordTransformationGraph, GravityToggle
 
 
 def theta(wavelength, divergence_angle, L2, sample_rotation, detector_rotation):
@@ -68,6 +68,24 @@ def theta(wavelength, divergence_angle, L2, sample_rotation, detector_rotation):
     return out
 
 
+def theta_no_gravity(wavelength, divergence_angle, sample_rotation, detector_rotation):
+    '''
+    Angle of reflection.
+
+    Computes the angle between the scattering direction of
+    the neutron and the sample surface while disregarding the
+    effect of gravity.
+    '''
+    theta = (
+        divergence_angle.to(unit='rad', copy=False)
+        + detector_rotation.to(unit='rad')
+        - sample_rotation.to(unit='rad')
+    )
+    if wavelength.bins:
+        return sc.bins_like(wavelength, theta)
+    return theta
+
+
 def angle_of_divergence(theta, sample_rotation, angle_to_center_of_beam):
     """
     Difference between the incident angle and the center of the incident beam.
@@ -113,11 +131,11 @@ def wavelength(
     return out.to(unit='angstrom', copy=False)
 
 
-def coordinate_transformation_graph() -> CoordTransformationGraph:
+def coordinate_transformation_graph(gravity: GravityToggle) -> CoordTransformationGraph:
     return {
         "divergence_angle": "pixel_divergence_angle",
         "wavelength": wavelength,
-        "theta": theta,
+        "theta": theta if gravity else theta_no_gravity,
         "angle_of_divergence": angle_of_divergence,
         "Q": reflectometry_q,
         "L1": lambda chopper_distance: sc.abs(chopper_distance),

src/ess/amor/data.py

@@ -12,7 +12,7 @@ def _make_pooch():
     return pooch.create(
         path=pooch.os_cache("ess/amor"),
         env="ESS_AMOR_DATA_DIR",
-        base_url="https://fileserver-cache.johanneskasimir.workers.dev/groups/scipp/ess/amor/{version}/",
+        base_url="https://public.esss.dk/groups/scipp/ess/amor/{version}/",
         version=_version,
         registry={
             "reference.nxs": "md5:56d493c8051e1c5c86fb7a95f8ec643b",

src/ess/amor/types.py

@@ -47,3 +47,5 @@ class AngleCenterOfIncomingToHorizon(
 WavelengthZIndexFigure = NewType("WavelengthZIndexFigure", Any)
 QThetaFigure = NewType("QThetaFigure", Any)
 ReflectivityDiagnosticsView = NewType("ReflectivityDiagnosticsView", Any)
+
+GravityToggle = NewType("GravityToggle", bool)

tests/amor/pipeline_test.py

@@ -1,6 +1,6 @@
 # SPDX-License-Identifier: BSD-3-Clause
 # Copyright (c) 2024 Scipp contributors (https://github.com/scipp)
-# flake8: noqa: F403, F405
+from pathlib import Path
 
 import numpy as np
 import pytest
@@ -71,6 +71,18 @@ def test_has_expected_coordinates(amor_pipeline: sciline.Pipeline):
     assert "Q_resolution" in reflectivity_over_q.coords
 
 
+@pytest.mark.filterwarnings("ignore:Failed to convert .* into a transformation")
+@pytest.mark.filterwarnings("ignore:Invalid transformation, missing attribute")
+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[amor.types.GravityToggle] = False
+    reflectivity_over_q = amor_pipeline.compute(ReflectivityOverQ)
+    assert "Q" in reflectivity_over_q.coords
+    assert "Q_resolution" in reflectivity_over_q.coords
+
+
 @pytest.mark.filterwarnings("ignore:Failed to convert .* into a transformation")
 @pytest.mark.filterwarnings("ignore:Invalid transformation, missing attribute")
 def test_orso_pipeline(amor_pipeline: sciline.Pipeline):
@@ -91,6 +103,17 @@ def test_orso_pipeline(amor_pipeline: sciline.Pipeline):
     assert np.isfinite(res.data).all()
 
 
+@pytest.mark.filterwarnings("ignore:Failed to convert .* into a transformation")
+@pytest.mark.filterwarnings("ignore:Invalid transformation, missing attribute")
+def test_save_reduced_orso_file(amor_pipeline: sciline.Pipeline, output_folder: Path):
+    from orsopy import fileio
+
+    amor_pipeline[SampleRotation[SampleRun]] = sc.scalar(0.85, unit="deg")
+    amor_pipeline[Filename[SampleRun]] = amor.data.amor_sample_run(608)
+    res = amor_pipeline.compute(orso.OrsoIofQDataset)
+    fileio.orso.save_orso(datasets=[res], fname=output_folder / 'amor_reduced_iofq.ort')
+
+
 @pytest.mark.filterwarnings("ignore:Failed to convert .* into a transformation")
 @pytest.mark.filterwarnings("ignore:Invalid transformation, missing attribute")
 def test_pipeline_can_compute_reflectivity_merging_events_from_multiple_runs(

tests/conftest.py

@@ -0,0 +1,19 @@
+# SPDX-License-Identifier: BSD-3-Clause
+# Copyright (c) 2025 Scipp contributors (https://github.com/scipp)
+
+from pathlib import Path
+
+import pytest
+
+
+def pytest_addoption(parser: pytest.Parser) -> None:
+    parser.addoption("--file-output", help='Output folder for reduced data')
+
+
+@pytest.fixture
+def output_folder(request: pytest.FixtureRequest) -> Path:
+    if (path := request.config.getoption("--file-output")) is not None:
+        out = Path(path)
+        out.mkdir(parents=True, exist_ok=True)
+        return out
+    return request.getfixturevalue("tmp_path")