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Mask

mask

cctbx_start

Attributes

logger module-attribute 

logger = getLogger(__name__)

Functions

main 

main(args)

Main entry point allowing external calls Entry point for console_scripts Args: args ([str]): command line parameter list

Source code in scripts/cctbx/mask.py 
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def main(args):
    """
    Main entry point allowing external calls
    Entry point for console_scripts
    Args:
      args ([str]): command line parameter list
    """
    args = parse_args(args)
    exp = args.experiment
    facility = args.facility
    run = args.run
    group = args.group

    mask(exp, run, facility, group)

mask 

mask(exp, run, facility, group)
Source code in scripts/cctbx/mask.py 
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def mask(exp, run, facility, group):
    logging.info("Making New Mask")

    if facility == "NERSC":
        mfx_dir=f"/pscratch/sd/c/cctbx/{exp}"
        out_path=f"{mfx_dir}/common/results/averages/{run}/{group}/out"
        mask_path=f"{mfx_dir}/common/masks"
    elif facility == "S3DF":
        exp=f'{exp}'  #fix this
        mfx_dir=f"/sdf/data/lcls/ds/mfx/{exp}/results"
        out_path=f"{mfx_dir}/common/results/averages/{run}/{group}/out"
        mask_path=f"{mfx_dir}/common/results/masks"
    else:
        logging.warning(f"Facility not found: {facility}")

    img = dxtbx.load(f'{out_path}/std.cbf')
    logging.info(f'load: {out_path}/std.cbf')
    mask = [m > 0 for m in img.get_raw_data()]
    easy_pickle.dump(f'{out_path}/{run}_stddev.mask', tuple(mask))
    logging.info(f'dump: {out_path}/{run}_stddev.mask')

parse_args 

parse_args(args)

Parse command line parameters

Args: args ([str]): command line parameters as list of strings

Returns: :obj:argparse.Namespace: command line parameters namespace

Source code in scripts/cctbx/mask.py 
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def parse_args(args):
    """Parse command line parameters

    Args:
      args ([str]): command line parameters as list of strings

    Returns:
      :obj:`argparse.Namespace`: command line parameters namespace
    """
    parser = argparse.ArgumentParser(
        description="startup script for cctbx on iana."
    )
    parser.add_argument(
        "--experiment",
        "-e",
        dest="experiment",
        default=None,
        help="Enter -e to specify experiment number",
    )
    parser.add_argument(
        "--facility",
        "-f",
        dest="facility",
        default=None,
        help="Enter -f to specify facility",
    )
    parser.add_argument(
        "--run",
        "-r",
        dest="run",
        default=None,
        help="Enter -r for the run number",
    )
    parser.add_argument(
        "--group",
        "-g",
        dest="group",
        default=None,
        help="Enter -g for the trial "+
        "and rungroup number in the format 000_rg005."+
        "Default is newest folder"
    )

    return parser.parse_args(args)

run 

run()

Entry point for console_scripts

Source code in scripts/cctbx/mask.py 
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def run():
    """Entry point for console_scripts"""
    main(sys.argv[1:])