Merge pull request #101 from scipp/filter-nan

fix: remove non-finite values

Author: jokasimr

src/ess/amor/orso.py

@@ -61,11 +61,10 @@ def build_orso_iofq_dataset(
     r = sc.values(iofq.data)
     sr = sc.stddevs(iofq.data)
     sqz = sigma_q.to(unit="1/angstrom", copy=False)
-    data = (qz, r, sr, sqz)
 
-    return OrsoIofQDataset(
-        OrsoDataset(header, np.column_stack([_extract_values_array(d) for d in data]))
-    )
+    data = np.column_stack(tuple(map(_extract_values_array, (qz, r, sr, sqz))))
+    data = data[np.isfinite(data).all(axis=-1)]
+    return OrsoIofQDataset(OrsoDataset(header, data))
 
 
 def _extract_values_array(var: sc.Variable) -> np.ndarray:

tests/amor/pipeline_test.py

@@ -69,13 +69,19 @@ def test_run_data_pipeline(amor_pipeline: sciline.Pipeline):
 @pytest.mark.filterwarnings("ignore:Invalid transformation, missing attribute")
 def test_run_full_pipeline(amor_pipeline: sciline.Pipeline):
     amor_pipeline[SampleRotation[SampleRun]] = sc.scalar(0.85, unit="deg")
+    # Make the Q range cover a larger interval than the experiment is sensitive to.
+    # This let's us test the non-covered regions are filtered from the ORSO data.
+    amor_pipeline[QBins] = sc.geomspace(
+        dim="Q", start=0.005, stop=0.15, num=391, unit="1/angstrom"
+    )
     amor_pipeline[Filename[SampleRun]] = amor.data.amor_sample_run(608)
     res = amor_pipeline.compute(orso.OrsoIofQDataset)
     assert res.info.data_source.experiment.instrument == "Amor"
     assert res.info.reduction.software.name == "ess.reflectometry"
     assert res.data.ndim == 2
     assert res.data.shape[1] == 4
     assert np.all(res.data[:, 1] >= 0)
+    assert np.isfinite(res.data).all()
 
 
 @pytest.mark.filterwarnings("ignore:Failed to convert .* into a transformation")