def test_few_reflections(dials_data):
u"""
Test that dials.symmetry does something sensible if given few reflections.
Use some example integrated data generated from two ten-image 1° sweeps. These
each contain a few dozen integrated reflections.
Also test the behaviour of dials.merge and dials.report on the output.
By suppressing the output from dials.scale and dials.report, we obviate the need to
run in a temporary directory.
Args:
dials_data: DIALS custom Pytest fixture for access to test data.
"""
# Get the input experiment lists and reflection tables.
data_dir = dials_data("l_cysteine_dials_output")
experiments = ExperimentList.from_file(data_dir / "11_integrated.expt")
experiments.extend(
ExperimentList.from_file(data_dir / "23_integrated.expt"))
refls = "11_integrated.refl", "23_integrated.refl"
reflections = [
flex.reflection_table.from_file(data_dir / refl) for refl in refls
]
# Get and use the default parameters for dials.scale, suppressing HTML output.
scale_params = scale.phil_scope.fetch(
source=phil.parse("output.html=None")).extract()
# Does what it says on the tin. Run scaling.
scaled_expt, scaled_refl = scale.run_scaling(scale_params, experiments,
reflections)
# Get and use the default parameters for dials.merge.
merge_params = merge.phil_scope.fetch(source=phil.parse("")).extract()
# Run dials.merge on the scaling output.
merge.merge_data_to_mtz(merge_params, scaled_expt, [scaled_refl])
# Get and use the default parameters for dials.report, suppressing HTML output.
report_params = report.phil_scope.fetch(
source=phil.parse("output.html=None")).extract()
# Get an Analyser object, which does the dials.report stuff.
analyse = report.Analyser(
report_params,
grid_size=report_params.grid_size,
centroid_diff_max=report_params.centroid_diff_max,
)
# Run dials.report on scaling output.
analyse(scaled_refl, scaled_expt)
def export_merged_mtz(self, filename, d_min=None):
params = merge.phil_scope.extract()
params.d_min = d_min
params.assess_space_group = False
mtz_obj = merge.merge_data_to_mtz(params, self._experiments,
[self._reflections])
mtz_obj.write(filename)
def _export_merged_mtz(params, experiments, joint_table):
"""Export merged data."""
# call dials.merge
from dials.command_line.merge import merge_data_to_mtz
from dials.command_line.merge import phil_scope as merge_phil_scope
merge_params = merge_phil_scope.extract()
merge_params.reporting.wilson_stats = False
merge_params.reporting.merging_stats = False
merge_params.assess_space_group = False
merge_params.partiality_threshold = params.cut_data.partiality_cutoff
mtz_file = merge_data_to_mtz(merge_params, experiments, [joint_table])
logger.info("\nWriting merged data to %s", (params.output.merged_mtz))
out = StringIO()
mtz_file.show_summary(out=out)
logger.info(out.getvalue())
mtz_file.write(params.output.merged_mtz)
def _export_merged_mtz(params, experiments, joint_table):
"""Export merged data."""
# call dials.merge
from dials.command_line.merge import merge_data_to_mtz
from dials.command_line.merge import phil_scope as merge_phil_scope
merge_params = merge_phil_scope.extract()
logger.disabled = True
merge_params.assess_space_group = False
merge_params.partiality_threshold = params.cut_data.partiality_cutoff
merge_params.output.crystal_names = [params.output.crystal_name]
merge_params.output.project_name = params.output.project_name
merge_params.best_unit_cell = params.reflection_selection.best_unit_cell
mtz_file = merge_data_to_mtz(merge_params, experiments, [joint_table])
logger.disabled = False
logger.info("\nWriting merged data to %s", (params.output.merged_mtz))
out = StringIO()
mtz_file.show_summary(out=out)
logger.info(out.getvalue())
mtz_file.write(params.output.merged_mtz)
