Standard DIALS command_line program boilerplate

new_dials_command.py

"""
dials.new_dials_command

Put a description of your program in the top docstring. This will be
used in the OptionParser to display program help.
"""

from __future__ import absolute_import, division, print_function

import pickle
import logging
import sys

import libtbx.phil

import dials.util
import dials.util.log
from dials.util.options import OptionParser, flatten_experiments, flatten_reflections

# Define a logger. __name__ cannot be used as this script is called directly.
logger = logging.getLogger("dials.command_line.new_dials_command")

# Define the master PHIL scope for this program
phil_scope = libtbx.phil.parse(
    """
output {
    reflections = stronger.refl
        .type = path

    log = 'dials.new_dials_command.log'
        .type = str
        .help = "The log filename"
}
bool_parameter = False
    .type = bool
integer_parameter = 0
    .type = int
"""
)


def new_dials_command(experiments, reflections, params):
    """Write the behaviour of the program outside run()"""
    logger.info("Hello world!")

    # Include file output here - any API interface should go elsewhere
    logger.info("Writing reflection table to {}".format(params.output.reflections))
    with open(params.output.reflections, "w") as f:
        pickle.dump(reflections, f)


def run(args=None, phil=phil_scope):
    """
    Validate and load the arguments, then run new_dials_command

    Try to keep this function minimal, defining only what is necessary to run
    the program from the command line.

    Arguments:
        args (List[str]): If specified, use these instead of sys.argv[1:]
        phil (libtbx.phil.scope): Overrides the master phil_scope for this
    """

    usage = "dials.new_dials_command [options] model.expt strong.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)

    # Configure the logging
    dials.util.log.config(verbosity=options.verbose, logfile=params.output.log)

    # Log the PHIL diff. Done _after_ log config so written to log
    diff_phil = parser.diff_phil.as_str()
    if diff_phil:
        logger.info("The following parameters have been modified:\n%s", diff_phil)

    experiments = flatten_experiments(params.input.experiments)
    reflections = flatten_reflections(params.input.reflections)

    # Do any simple loading validation here
    if len(reflections) != 1:
        sys.exit("Error: Exactly one reflection file needed")
    if len(experiments) != 1:
        sys.exit("Error: Exactly one experiment list required")

    new_dials_command(experiments, reflections, params)


if __name__ == "__main__":
    with dials.util.show_mail_on_error():
        run()