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Sessions label bug #48

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Merged
merged 4 commits into from
Nov 26, 2024
Merged

Sessions label bug #48

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ad631f1
sessions existed where 'sessions_label' should have existed
bendhouseart Nov 25, 2024
befbb7b
update version seeking
bendhouseart Nov 25, 2024
53acbc0
remove if conditional
bendhouseart Nov 26, 2024
9a507e5
Update pyproject.toml
bendhouseart Nov 26, 2024
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71 changes: 28 additions & 43 deletions petdeface/petdeface.py
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Original file line number Diff line number Diff line change
Expand Up @@ -24,6 +24,7 @@
from niworkflows.utils.misc import check_valid_fs_license

from petutils.petutils import collect_anat_and_pet
from importlib.metadata import version


try:
Expand All @@ -42,43 +43,27 @@
pathlib.Path(__file__).parent.parent.absolute(),
]

__version__ = "unable to locate version number in pyproject.toml"
__version__ = "unable to locate version number"
# we use the default version at the time of this writing, but the most current version
# can be found in the pyproject.toml file under the [tool.bids] section
__bids_version__ = "1.8.0"


# search for toml file
for place in places_to_look:
for root, folders, files in os.walk(place):
for file in files:
if file.endswith("pyproject.toml") and "petdeface" in os.path.join(
root, file
):
toml_file = os.path.join(root, file)

with open(toml_file, "r") as f:
for line in f.readlines():
if (
"version" in line
and len(line.split("=")) > 1
and "bids_version" not in line
):
if __version__ == "unable to locate version number":
# we try to load the version using import lib
try:
__version__ = version(__package__)
except ValueError:
# if we can't load the version using importlib we try to load it from the pyproject.toml
for place in places_to_look:
try:
with open(place / "pyproject.toml") as f:
for line in f:
if "version" in line and "bid" not in line.lower():
__version__ = line.split("=")[1].strip().replace('"', "")
if "bids_version" in line and len(line.split("=")) > 1:
__bids_version__ = (
line.split("=")[1].strip().replace('"', "")
)
# if the version number is found and is formatted with major.minor.patch formating we can break
# we check the version with a regex expression to see if all of the parts are there
if re.match(r"\d+\.\d+\.\d+", __version__):
break

if __version__ != "unable to locate version number in pyproject.toml":
# we try to load the version using import lib
__version__ = importlib.metadata.version("petdeface")
if re.match(r"\d+\.\d+\.\d+", __version__):
break
break
except FileNotFoundError:
pass


def locate_freesurfer_license():
Expand Down Expand Up @@ -231,9 +216,7 @@ def deface(args: Union[dict, argparse.Namespace]) -> None:
# right side of the sub- string as the subject label
if any("sub-" in subject for subject in subjects):
print("One or more subject contains sub- string")
subjects = [
subject.replace("sub-", "") for subject in subjects if "sub-" in subject
]
subjects = [subject.replace("sub-", "") for subject in subjects]
# raise error if a supplied subject is not contained in the dataset
participants = collect_participants(
args.bids_dir, bids_validate=~args.skip_bids_validator
Expand All @@ -257,7 +240,9 @@ def deface(args: Union[dict, argparse.Namespace]) -> None:
subject.replace("sub-", "") for subject in args.participant_label_exclude
]
subjects = [
subject for subject in subjects if subject not in args.participant_label_exclude
subject
for subject in subjects
if subject not in args.participant_label_exclude
]

print(f"Subjects remaining in the defacing workflow: {subjects}")
Expand All @@ -277,7 +262,7 @@ def deface(args: Union[dict, argparse.Namespace]) -> None:
args.bids_dir,
preview_pics=args.preview_pics,
anat_only=args.anat_only,
session=args.session_label,
session_label=args.session_label,
session_label_exclude=args.session_label_exclude,
)
except FileNotFoundError:
Expand Down Expand Up @@ -305,7 +290,7 @@ def init_single_subject_wf(
output_dir: pathlib.Path = None,
preview_pics=False,
anat_only=False,
session=[],
session_label=[],
session_label_exclude=[],
) -> Workflow:
"""
Expand Down Expand Up @@ -343,10 +328,10 @@ def init_single_subject_wf(

# we combine the sessions to include and exclude into a single set of sessions to exclude from
# the set of all sessions
if session:
if session_label:
sessions_to_exclude = list(
set(bids_data.get_sessions())
- (set(bids_data.get_sessions()) & set(session))
- (set(bids_data.get_sessions()) & set(session_label))
| set(session_label_exclude)
)
else:
Expand Down Expand Up @@ -768,7 +753,7 @@ def __init__(
placement="adjacent",
preview_pics=True,
participant_label_exclude=[],
session=[],
session_label=[],
session_label_exclude=[],
):
self.bids_dir = bids_dir
Expand All @@ -781,7 +766,7 @@ def __init__(
self.skip_bids_validator = skip_bids_validator
self.preview_pics = preview_pics
self.participant_label_exclude = participant_label_exclude
self.session = session
self.session_label = session_label
self.session_label_exclude = session_label_exclude

# check if freesurfer license is valid
Expand Down Expand Up @@ -813,7 +798,7 @@ def run(self):
"remove_existing": self.remove_existing,
"preview_pics": self.preview_pics,
"participant_label_exclude": self.participant_label_exclude,
"session": self.session,
"session_label": self.session_label,
"session_label_exclude": self.session_label_exclude,
}
)
Expand Down Expand Up @@ -1133,7 +1118,7 @@ def main(): # noqa: max-complexity: 12
placement=args.placement,
preview_pics=args.preview_pics,
participant_label_exclude=args.participant_label_exclude,
session=args.session_label,
session_label=args.session_label,
session_label_exclude=args.session_label_exclude,
)
petdeface.run()
Expand Down
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