def test_SumIntensityReducer():
"""Test the methods of the SumIntensityReducer class"""
reflections = generate_integrated_test_reflections()
reflections = SumIntensityReducer.reduce_on_intensities(reflections)
# reflections = reduce_on_summation_intensities(reflections)
assert list(reflections["intensity.sum.value"]) == [11.0, 12.0, 13.0, 14.0]
assert list(reflections["intensity.sum.variance"]) == [1.1, 1.2, 1.3, 1.4]
reflections = generate_test_reflections_for_scaling()
reflections = SumIntensityReducer.apply_scaling_factors(reflections)
assert list(
reflections["intensity.sum.value"]) == [110.0, 13.0, 14.0, 60.0, 8.0]
assert list(reflections["intensity.sum.variance"]) == pytest.approx(
[110.0, 1.3, 1.4, 24.0, 0.4])
# check it still passes with no partiality correction
reflections = generate_test_reflections_for_scaling()
del reflections["partiality"]
reflections = SumIntensityReducer.apply_scaling_factors(reflections)
assert list(reflections["intensity.sum.value"]) == [
11.0,
12.0,
13.0,
14.0,
60.0,
8.0,
]
# test IsgiI selecting
r = flex.reflection_table()
r["intensity.sum.value"] = flex.double([1.0, 2.0])
r["intensity.sum.variance"] = flex.double([1.0, 1.0])
r = SumIntensityReducer.filter_on_min_isigi(r, 1.5)
assert list(r["intensity.sum.value"]) == [2.0]
# now test a typical case - reflection table with inv scale factor,
# check that we only apply that correction and do any relevant filtering
reflections = generate_integrated_test_reflections()
reflections["lp"] = flex.double(6, 2)
reflections["partiality"] = flex.double([1.0, 1.0, 0.5, 0.1, 1.0, 1.0])
reflections["d"] = flex.double([5.0, 5.0, 0.1, 5.0, 5.0, 5.0])
reflections = SumIntensityReducer.filter_for_export(
reflections, partiality_threshold=0.25, d_min=1.0)
assert list(reflections["intensity.sum.value"]) == pytest.approx(
[22.0, 24.0])
assert list(reflections["intensity.sum.variance"]) == pytest.approx(
[4.4, 4.8])
assert "intensity.prf.value" not in reflections
assert "intensity.scale.value" not in reflections
assert "intensity.prf.variance" not in reflections
assert "intensity.scale.variance" not in reflections
def test_IntensityReducer_instantiations():
"""Test that all classes can be instantiated (have the required implemented
methods) and have an intensities list with at least one str values"""
allowed_intensities = FilterForExportAlgorithm.allowed_intensities
SumIntensityReducer()
assert all(i in allowed_intensities for i in SumIntensityReducer.intensities)
PrfIntensityReducer()
assert all(i in allowed_intensities for i in PrfIntensityReducer.intensities)
SumAndPrfIntensityReducer()
assert all(i in allowed_intensities for i in SumAndPrfIntensityReducer.intensities)
ScaleIntensityReducer()
assert all(i in allowed_intensities for i in ScaleIntensityReducer.intensities)