sf-mx/crystfel_tools
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more bug fixes

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This commit is contained in:
Beale John Henry
2025-01-22 12:38:25 +01:00
parent 6f16f39015
commit 6d64d9248e
1 changed files with 9 additions and 9 deletions
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18
reduction_tools/crystfel_split_var.py
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@@ -287,7 +287,7 @@ def main( cwd, name, lst, chunk_size, geom_file, cell_file,
print( "reading SwissFEL lst file" )
print( "creating {0} image chunks of lst".format( chunk_size ) )
list_df = h5_split( lst, chunk_size )
print( "DONE" )
print( "done" )
# run crystfel runs on individual splits
print( "submitting jobs to cluster" )
@@ -334,7 +334,7 @@ def main( cwd, name, lst, chunk_size, geom_file, cell_file,
mean_beta, std_beta = round(df.beta.mean(), 2 ), round( df.beta.std(), 2 )
mean_gamma, std_gamma = round( df.gamma.mean(), 2 ), round( df.gamma.std(), 2 )
logger.info( "images = {0}".format( chunks ) )
logger.info( "image = {0}".format( chunks ) )
logger.info( "crystals = {0}".format( xtals ) )
logger.info( "indexing rate = {0} %".format( index_rate ) )
logger.info( "mean resolution = {0} +/- {1} A".format( mean_res, std_res ) )
@@ -343,12 +343,12 @@ def main( cwd, name, lst, chunk_size, geom_file, cell_file,
logger.info( "mean a = {0} +/- {1} A".format( mean_a, std_a ) )
logger.info( "mean b = {0} +/- {1} A".format( mean_b, std_b ) )
logger.info( "mean c = {0} +/- {1} A".format( mean_c, std_c ) )
logger.info( "mean alpha = {0} +/- {1} deg".format( mean_alpha, std_alpha ) )
logger.info( "mean beta = {0} +/- {1} deg".format( mean_beta, std_beta ) )
logger.info( "mean gamma = {0} +/- {1} deg".format( mean_gamma, std_gamma ) )
logger.info( "mean alpha = {0} +/- {1} A".format( mean_alpha, std_alpha ) )
logger.info( "mean beta = {0} +/- {1} A".format( mean_beta, std_beta ) )
logger.info( "mean gamma = {0} +/- {1} A".format( mean_gamma, std_gamma ) )
print( "printing stats" )
print( "images = {0}".format( chunks ) )
print( "image = {0}".format( chunks ) )
print( "crystals = {0}".format( xtals ) )
print( "indexing rate = {0} %".format( index_rate ) )
print( "mean resolution = {0} +/- {1} A".format( mean_res, std_res ) )
@@ -458,7 +458,7 @@ if __name__ == "__main__":
"--multi",
help="do you wnat to look for multiple lattices. Default = True",
type=bool,
default=True
default=False
)
parser.add_argument(
"-r",
@@ -483,7 +483,7 @@ if __name__ == "__main__":
)
parser.add_argument(
"-q",
"--min-res",
"--min_res",
help="min-res for spot-finding in pixels. Default = 85.",
type=int,
default=85
@@ -525,4 +525,4 @@ if __name__ == "__main__":
args.geom_file, args.cell_file, args.indexer, args.peakfinder,
args.integrator, args.tolerance, args.threshold,
args.min_snr, args.int_radius, multi, retry, args.min_pix, args.bg_rad,
args.min_res, args.reservation )
args.min_res, args.reservation )