sf-mx/crystfel_tools
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added bug fix for progress bar crash

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Beale John Henry
2024-02-01 09:10:10 +01:00
parent 88ce19d2d0
commit 0488b99515
1 changed files with 9 additions and 9 deletions
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18
reduction_tools/partialator.py
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@@ -268,6 +268,7 @@ def main( cwd, name, stream, pointgroup, model, iterations, cell, shells, part_h
print( "DONE" ) print( "DONE" )
# use progress bar to track job completion # use progress bar to track job completion
time.sleep(30)
wait_for_jobs(submitted_job_ids, 1 ) wait_for_jobs(submitted_job_ids, 1 )
print("slurm processing done") 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", print_df = stats_df[ [ "1_d", "d", "min",
"max", "nref", "poss", "max", "nref", "poss",
"comp", "obs", "mult", "comp", "obs", "mult",
"snr", "I", "cc", "ccstar"] ] "snr", "I", "rsplit", "cc", "ccstar"] ]
print_df.to_csv( "summary_table.csv", sep="\t", index=False ) print_df.to_csv( "summary_table.csv", sep="\t", index=False )
# calculate cc metrics # calculate cc metrics
@@ -324,44 +325,43 @@ if __name__ == "__main__":
parser.add_argument( parser.add_argument(
"-m", "-m",
"--model", "--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, type=str,
default="unity" default="unity"
) )
parser.add_argument( parser.add_argument(
"-i", "-i",
"--iterations", "--iterations",
help="number of iterations used for partialator run. Default = 1", help="number of iterations used for partialator run. Default = 1.",
type=int, type=int,
default=1 default=1
) )
parser.add_argument( parser.add_argument(
"-c", "-c",
"--cell_file", "--cell_file",
help="path to CrystFEL cell file for partialator", help="path to CrystFEL cell file for partialator.",
type=os.path.abspath, type=os.path.abspath,
required=True required=True
) )
parser.add_argument( parser.add_argument(
"-b", "-b",
"--bins", "--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, type=int,
default=20 default=20
) )
parser.add_argument( parser.add_argument(
"-r", "-r",
"--resolution", "--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, type=float,
default=1.3 default=1.3
) )
parser.add_argument( parser.add_argument(
"-a", "-a",
"--max_adu", "--max_adu",
help="maximum detector counts to allow. Default is 12000", help="maximum detector counts to allow. Default is 12000.",
type=int, type=int
default=12000
) )
args = parser.parse_args() args = parser.parse_args()
# run main # run main