def test_stills_indexer_multi_lattice_bug_MosaicSauter2014(
dials_regression, tmpdir):
"""Problem: In stills_indexer, before calling the refine function, the
experiment list contains a list of dxtbx crystal models (that are not
MosaicSauter2014 models). The conversion to MosaicSauter2014 is made
during the refine step when functions from nave_parameters is called.
If the experiment list contains more than 1 experiment, for eg.
multiple lattices, only the first crystal gets assigned mosaicity. In
actuality, all crystal models should be assigned mosaicity. This test
only compares whether or not all crystal models have been assigned a
MosaicSauter2014 model."""
import dxtbx.model
from dxtbx.model import Crystal
from dxtbx.model.experiment_list import (
Experiment,
ExperimentList,
ExperimentListFactory,
)
from dials.algorithms.indexing.stills_indexer import StillsIndexer
from dials.array_family import flex
from dials.command_line.stills_process import (
phil_scope as stills_process_phil_scope, )
experiment_data = os.path.join(
dials_regression,
"refinement_test_data",
"cspad_refinement",
"cspad_refined_experiments_step6_level2_300.json",
)
reflection_data = os.path.join(
dials_regression,
"refinement_test_data",
"cspad_refinement",
"cspad_reflections_step7_300.pickle",
)
refl = flex.reflection_table.from_file(reflection_data)
explist = ExperimentListFactory.from_json_file(experiment_data,
check_format=False)[0:2]
reflist = refl.select(
refl["id"] < 2) # Only use the first 2 for convenience
# Construct crystal models that don't have mosaicity. These A,B,C values are the same
# as read in from the dials_regression folder
# Crystal-0
cs0 = Crystal(explist[0].crystal)
exp0 = Experiment(
imageset=explist[0].imageset,
beam=explist[0].beam,
detector=explist[0].detector,
goniometer=None,
scan=None,
crystal=cs0,
)
# Crystal-1
cs1 = Crystal(explist[1].crystal)
exp1 = Experiment(
imageset=explist[1].imageset,
beam=explist[1].beam,
detector=explist[1].detector,
goniometer=None,
scan=None,
crystal=cs1,
)
# Construct a new experiment_list that will be passed on for refinement
unrefined_explist = ExperimentList([exp0, exp1])
# Get default params from stills_process and construct StillsIndexer, then run refinement
params = stills_process_phil_scope.extract()
SI = StillsIndexer(reflist, unrefined_explist, params=params)
refined_explist, new_reflist = SI.refine(unrefined_explist, reflist)
# Now check whether the models have mosaicity after stills_indexer refinement
# Also check that mosaicity values are within expected limits
for ii, crys in enumerate(refined_explist.crystals()):
assert isinstance(crys, dxtbx.model.MosaicCrystalSauter2014)
if ii == 0:
assert crys.get_domain_size_ang() == pytest.approx(2242.0, rel=0.1)
if ii == 1:
assert crys.get_domain_size_ang() == pytest.approx(2689.0, rel=0.1)
def test_stills_indexer_multi_lattice_bug_MosaicSauter2014(
dials_regression, tmpdir):
""" Problem: In stills_indexer, before calling the refine function, the experiment list contains a list of
dxtbx crystal models (that are not MosaicSauter2014 models). The conversion to MosaicSauter2014 is made
during the refine step when functions from nave_parameters is called. If the experiment list contains
more than 1 experiment, for eg. multiple lattices, only the first crystal gets assigned mosaicity. In
actuality, all crystal models should be assigned mosaicity. This test only compares whether or not all crystal models
have been assigned a MosaicSauter2014 model. """
import libtbx
from dxtbx.model.experiment_list import ExperimentListFactory
from dxtbx.model.experiment_list import Experiment, ExperimentList
from dials.array_family import flex
from dxtbx.model import Crystal
from scitbx.matrix import col
from dials.algorithms.indexing.stills_indexer import StillsIndexer
from dials.command_line.stills_process import (
phil_scope as stills_process_phil_scope, )
import dxtbx_model_ext # needed for comparison of types
xfel_regression = libtbx.env.find_in_repositories(
relative_path="xfel_regression", test=os.path.isdir)
if not xfel_regression:
pytest.skip("test requires xfel_regression")
experiment_data = os.path.join(xfel_regression, "cspad_cbf_metrology",
"input_combined_experiments_300.json")
reflection_data = os.path.join(xfel_regression, "cspad_cbf_metrology",
"input_combined_reflections_300.pickle")
refl = flex.reflection_table.from_file(reflection_data)
explist = ExperimentListFactory.from_json_file(experiment_data,
check_format=False)[0:2]
reflist = refl.select(
refl["id"] < 2) # Only use the first 2 for convenience
# Construct crystal models that don't have mosaicity. These A,B,C values are the same
# as read in from the xfel_regression folder
# Crystal-0
sg = "P6122"
c = col((-6.273802315592485, 130.0982158871206, -5.79093135302508))
b = col((12.889379382910931, -3.488465493571038, -92.33550227410447))
a = col((73.48274403946694, 6.087949131831335, 57.16094537694445))
cs0 = Crystal(a, b, c, sg)
exp0 = Experiment(
imageset=explist[0].imageset,
beam=explist[0].beam,
detector=explist[0].detector,
goniometer=None,
scan=None,
crystal=cs0,
)
# Crystal-1
a1 = col((-9.848734136977392, -91.47863873838793, 15.37304224517648))
b1 = col((-61.88040624461757, 60.16978337475523, 35.38476831968059))
c1 = col((-72.13672676543942, -10.447921098609202, -108.38564134527415))
cs1 = Crystal(a1, b1, c1, sg)
exp1 = Experiment(
imageset=explist[1].imageset,
beam=explist[1].beam,
detector=explist[1].detector,
goniometer=None,
scan=None,
crystal=cs1,
)
# Construct a new experiment_list that will be passed on for refinement
unrefined_explist = ExperimentList([exp0, exp1])
# Get default params from stills_process and construct StillsIndexer, then run refinement
params = stills_process_phil_scope.extract()
SI = StillsIndexer(reflist, unrefined_explist, params=params)
refined_explist, new_reflist = SI.refine(unrefined_explist, reflist)
# Now check whether the models have mosaicity after stills_indexer refinement
for crys in refined_explist.crystals():
assert isinstance(crys, dxtbx_model_ext.MosaicCrystalSauter2014)