def run(args: List[str] = None, phil: libtbx.phil.scope = phil_scope) -> None:
"""
Run dials.anvil_correction as from the command line.
Take integrated experiment lists and reflection tables and correct the all the
integrated intensities for the estimated attenuation by the diamond anvils.
Args:
args: The arguments supplied by the user (default: sys.argv[1:]).
phil: The PHIL scope definition (default: phil_scope, the master PHIL scope
for this program).
"""
usage = "dials.anvil_correction [options] integrated.expt integrated.refl"
parser = OptionParser(
usage=usage,
phil=phil,
read_reflections=True,
read_experiments=True,
check_format=False,
epilog=__doc__,
)
params, options = parser.parse_args(args=args, show_diff_phil=False)
# Log the difference between the PHIL scope definition and the active PHIL scope,
# which will include the parsed user inputs.
diff_phil = parser.diff_phil.as_str()
if diff_phil:
logger.info("The following parameters have been modified:\n%s",
diff_phil)
# Check that at least one reflection table and experiment list have been provided.
input_errors = []
if not params.input.experiments:
input_errors.append(
"Please provide at least one valid experiment list (.expt) file.")
if not params.input.reflections:
input_errors.append(
"Please provide at least one valid reflection table (.refl) file.")
if input_errors:
sys.exit("\n".join([parser.format_help()] + input_errors))
if not np.linalg.norm(params.anvil.normal):
sys.exit(
"It seems you have provided a surface normal vector with zero length."
)
# Check that the anvil surface normal really is normalised.
dac_norm = params.anvil.normal / np.linalg.norm(params.anvil.normal)
# Configure the logging.
dials.util.log.config(options.verbose, logfile=params.output.log)
# These functions are commonly used to collate the input.
experiments = flatten_experiments(params.input.experiments)
reflections_list = flatten_reflections(params.input.reflections)
# Work around parse_multiple_datasets dropping unindexed reflections.
unindexed = flex.reflection_table()
for r_table in reflections_list:
unindexed.extend(r_table.select(r_table["id"] == -1))
# Get a single reflection table per experiment object.
reflections_list = parse_multiple_datasets(reflections_list)
reflections_list = sort_tables_to_experiments_order(
reflections_list, experiments)
# Record the density of diamond in g·cm⁻³ (for consistency with NIST tables,
# https://doi.org/10.18434/T4D01F).
density = params.anvil.density / 1000 # g·cm⁻³
# Correct for the attenuation of the incident and diffracted beams by the diamond
# anvil cell.
logger.info(
"Correcting integrated reflection intensities for attenuation by the diamond "
"anvil cell.")
for experiment, reflections in zip(experiments, reflections_list):
correct_intensities_for_dac_attenuation(experiment, reflections,
dac_norm,
params.anvil.thickness,
density)
logger.info("Done.")
# Do optional experiment list file output here.
if params.output.experiments:
logger.info("Writing the experiment list to %s",
params.output.experiments)
experiments.as_file(params.output.experiments)
logger.info("Writing the reflection table to %s",
params.output.reflections)
# Collate reflections into a single reflection table and save it to file.
reflections = unindexed
for r_table in reflections_list:
reflections.extend(r_table)
del reflections_list
reflections.as_file(params.output.reflections)
