From 213eead2b06d0c5dfda0125d02e8efaddc1f813b Mon Sep 17 00:00:00 2001 From: Stefano Moia <s.moia.research@gmail.com> Date: Thu, 16 Jan 2025 16:29:47 +0100 Subject: [PATCH] Add option to overwrite file (and write out extra files with "verbose") in T2smap workflow (#1166) --- tedana/workflows/t2smap.py | 24 ++++++++++++++++++++++++ tedana/workflows/tedana.py | 2 +- 2 files changed, 25 insertions(+), 1 deletion(-) diff --git a/tedana/workflows/t2smap.py b/tedana/workflows/t2smap.py index cd8390cb0..fdeb119c2 100644 --- a/tedana/workflows/t2smap.py +++ b/tedana/workflows/t2smap.py @@ -152,6 +152,21 @@ def _get_parser(): optional.add_argument( "--quiet", dest="quiet", help=argparse.SUPPRESS, action="store_true", default=False ) + optional.add_argument( + "--verbose", + dest="verbose", + action="store_true", + help="Generate intermediate and additional files.", + default=False, + ) + optional.add_argument( + "--overwrite", + "-f", + dest="overwrite", + action="store_true", + help="Force overwriting of files.", + default=False, + ) parser._action_groups.append(optional) return parser @@ -168,7 +183,9 @@ def t2smap_workflow( fitmode="all", combmode="t2s", debug=False, + verbose=False, quiet=False, + overwrite=False, t2smap_command=None, ): """ @@ -205,6 +222,11 @@ def t2smap_workflow( Combination scheme for TEs: 't2s' (Posse 1999, default), 'paid' (Poser). t2smap_command : :obj:`str`, optional The command used to run t2smap. Default is None. + verbose : :obj:`bool`, optional + Generate intermediate and additional files. Default is False. + overwrite : :obj:`bool`, optional + If True, force overwriting of files. Default is False. + Other Parameters ---------------- @@ -284,6 +306,8 @@ def t2smap_workflow( prefix=prefix, config="auto", make_figures=False, + overwrite=overwrite, + verbose=verbose, ) n_echos = data_cat.shape[1] LGR.debug(f"Resulting data shape: {data_cat.shape}") diff --git a/tedana/workflows/tedana.py b/tedana/workflows/tedana.py index 739a03210..1f54361e6 100644 --- a/tedana/workflows/tedana.py +++ b/tedana/workflows/tedana.py @@ -361,7 +361,7 @@ def _get_parser(): optional.add_argument( "--quiet", dest="quiet", help=argparse.SUPPRESS, action="store_true", default=False ) - parser.add_argument( + optional.add_argument( "--overwrite", "-f", dest="overwrite",