From 8bbf93e526c3eec6b824adc97987d69503c86b9b Mon Sep 17 00:00:00 2001 From: Sander Roet Date: Fri, 23 Aug 2024 14:48:52 +0200 Subject: [PATCH] add options to the entry point --- src/pytom_tm/entry_points.py | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) diff --git a/src/pytom_tm/entry_points.py b/src/pytom_tm/entry_points.py index 1b49e893..cfada298 100644 --- a/src/pytom_tm/entry_points.py +++ b/src/pytom_tm/entry_points.py @@ -533,6 +533,23 @@ def extract_candidates(argv=None): action=ParseLogging, help="Can be set to `info` or `debug`", ) + parser.add_argument( + "--tophat-bins", + type=int, + required=False, + default=50, + action=LargerThanZero, + help="Number of bins to use in the histogram of occurences in the " + "tophat transform code (for both the estimation and the plotting).", + ) + parser.add_argument( + "--plot-bins", + type=int, + required=False, + default=20, + action=LargerThanZero, + help="Number of bins to use for the occurences vs LCC_max plot.", + ) # ---8<--- [end:extract_candidates_usage] @@ -552,6 +569,8 @@ def extract_candidates(argv=None): tophat_connectivity=args.tophat_connectivity, relion5_compat=args.relion5_compat, ignore_tomogram_mask=args.ignore_tomogram_mask, + tophat_bins=args.tophat_bins, + plot_bins=args.plot_bins, ) # write out as a RELION type starfile