diff --git a/reduction_tools/crystfel_split_var.py b/reduction_tools/crystfel_split_var.py index c74f964..94043e5 100644 --- a/reduction_tools/crystfel_split_var.py +++ b/reduction_tools/crystfel_split_var.py @@ -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 ) \ No newline at end of file