diff --git a/reduction_tools/partialator.py b/reduction_tools/partialator.py index 321d759..e4259bb 100644 --- a/reduction_tools/partialator.py +++ b/reduction_tools/partialator.py @@ -268,6 +268,7 @@ def main( cwd, name, stream, pointgroup, model, iterations, cell, shells, part_h print( "DONE" ) # use progress bar to track job completion + time.sleep(30) wait_for_jobs(submitted_job_ids, 1 ) print("slurm processing done") @@ -283,7 +284,7 @@ def main( cwd, name, stream, pointgroup, model, iterations, cell, shells, part_h print_df = stats_df[ [ "1_d", "d", "min", "max", "nref", "poss", "comp", "obs", "mult", - "snr", "I", "cc", "ccstar"] ] + "snr", "I", "rsplit", "cc", "ccstar"] ] print_df.to_csv( "summary_table.csv", sep="\t", index=False ) # calculate cc metrics @@ -324,44 +325,43 @@ if __name__ == "__main__": parser.add_argument( "-m", "--model", - help="model used partialator, e.g., unity or xsphere, unity = default", + help="model used partialator, e.g., unity or xsphere. Default = unity.", type=str, default="unity" ) parser.add_argument( "-i", "--iterations", - help="number of iterations used for partialator run. Default = 1", + help="number of iterations used for partialator run. Default = 1.", type=int, default=1 ) parser.add_argument( "-c", "--cell_file", - help="path to CrystFEL cell file for partialator", + help="path to CrystFEL cell file for partialator.", type=os.path.abspath, required=True ) parser.add_argument( "-b", "--bins", - help="number of resolution bins to use. Should be more than 20. Default = 20", + help="number of resolution bins to use. Should be more than 20. Default = 20.", type=int, default=20 ) parser.add_argument( "-r", "--resolution", - help="high res limit - need something here. Default set to 1.3", + help="high res limit - need something here. Default set to 1.3.", type=float, default=1.3 ) parser.add_argument( "-a", "--max_adu", - help="maximum detector counts to allow. Default is 12000", - type=int, - default=12000 + help="maximum detector counts to allow. Default is 12000.", + type=int ) args = parser.parse_args() # run main