def test_stills_indexer_methods_i04_weak_data(i04_weak_data, indexing_method,
space_group, unit_cell):
reflections = slice_reflections(i04_weak_data["reflections"], [(1, 2)])
experiments = slice_experiments(i04_weak_data["experiments"], [(1, 2)])
for experiment in experiments:
experiment.imageset = ImageSet(experiment.imageset.data(),
experiment.imageset.indices())
experiment.imageset.set_scan(None)
experiment.imageset.set_goniometer(None)
experiment.scan = None
experiment.goniometer = None
params = phil_scope.fetch().extract()
params.indexing.method = indexing_method
params.indexing.basis_vector_combinations.max_refine = 5
if unit_cell is not None:
params.indexing.known_symmetry.unit_cell = uctbx.unit_cell(unit_cell)
if space_group is not None:
params.indexing.known_symmetry.space_group = sgtbx.space_group_info(
space_group)
try:
idxr = stills_indexer.StillsIndexerBasisVectorSearch(
reflections, experiments, params)
except RuntimeError:
idxr = stills_indexer.StillsIndexerLatticeSearch(
reflections, experiments, params)
idxr.index()
indexed_experiments = idxr.refined_experiments
assert len(indexed_experiments) == 1
assert indexed_experiments[0].crystal.get_unit_cell().parameters(
) == pytest.approx((57.752, 57.776, 150.013, 90.0101, 89.976, 90.008),
rel=1e-2)
def test_BasisVectorSearch_i04_weak_data(i04_weak_data, indexing_method,
space_group, unit_cell):
reflections = i04_weak_data["reflections"]
experiments = i04_weak_data["experiments"]
params = phil_scope.fetch().extract()
params.indexing.refinement_protocol.n_macro_cycles = 2
params.indexing.basis_vector_combinations.max_refine = 5
params.indexing.method = indexing_method
if unit_cell is not None:
params.indexing.known_symmetry.unit_cell = uctbx.unit_cell(unit_cell)
if space_group is not None:
params.indexing.known_symmetry.space_group = sgtbx.space_group_info(
space_group)
idxr = lattice_search.BasisVectorSearch(reflections, experiments, params)
idxr.index()
indexed_experiments = idxr.refined_experiments
assert len(indexed_experiments) == 1
assert indexed_experiments[0].crystal.get_unit_cell().parameters(
) == pytest.approx((57.752, 57.776, 150.013, 90.0101, 89.976, 90.008),
rel=1e-3)
experiments_filename = None
indexed_filename = None
refined_experiments_filename = None
integrated_experiments_filename = None
integrated_filename = None
profile_filename = None
integration_pickle = None
}
indexing {
refinement_protocol {
d_min_start = 2.0
}
}
"""
idx_work_phil = ip.parse(custom_idx_string)
idx_phil = idx_scope.fetch(source=idx_work_phil)
custom_brv_sting = """
crystal_id = 0
output {
directory = "."
log = None
prefix = None
}
"""
brv_work_phil = ip.parse(custom_brv_sting)
brv_phil = brv_scope.fetch(source=brv_work_phil)
custom_int_string = """
output {