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Add option to overwrite file (and write out extra files with "verbose") in T2smap workflow #1166

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merged 2 commits into from
Jan 16, 2025
Merged

Add option to overwrite file (and write out extra files with "verbose") in T2smap workflow #1166

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b656084
Add arguments "overwrite" and "verbose" to t2smap workflow
smoia Jan 15, 2025
6a37c60
add argument to optional parser group rather than parser itself
smoia Jan 15, 2025
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24 changes: 24 additions & 0 deletions tedana/workflows/t2smap.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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

Expand All @@ -168,7 +183,9 @@ def t2smap_workflow(
fitmode="all",
combmode="t2s",
debug=False,
verbose=False,
quiet=False,
overwrite=False,
t2smap_command=None,
):
"""
Expand Down Expand Up @@ -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
----------------
Expand Down Expand Up @@ -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}")
Expand Down
2 changes: 1 addition & 1 deletion tedana/workflows/tedana.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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",
Expand Down