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FIX: Ensure age from sessions file is not overriden #291

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Jun 5, 2023
Merged

FIX: Ensure age from sessions file is not overriden #291

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9 changes: 5 additions & 4 deletions nibabies/utils/bids.py
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Original file line number Diff line number Diff line change
Expand Up @@ -288,13 +288,15 @@ def parse_bids_for_age_months(
age = _get_age_from_tsv(sessions_tsv, level='session', key=f'ses-{session_id}')

participants_tsv = Path(bids_root) / 'participants.tsv'
if participants_tsv.exists():
if participants_tsv.exists() and age is None:
age = _get_age_from_tsv(participants_tsv, level='participant', key=f'sub-{subject_id}')

return age


def _get_age_from_tsv(bids_tsv: Path, level: Literal['session', 'participant'], key: str):
def _get_age_from_tsv(
bids_tsv: Path, level: Literal['session', 'participant'], key: str
) -> Optional[int]:
import pandas as pd

df = pd.read_csv(str(bids_tsv), sep='\t')
Expand Down Expand Up @@ -328,7 +330,6 @@ def _get_age_from_tsv(bids_tsv: Path, level: Literal['session', 'participant'],
def _verify_age_json(bids_json: Path) -> bool:
try:
data = json.loads(bids_json.read_text())
assert data['age']['Units'] == 'months'
return data['age']['Units'].lower() == 'months'
except Exception:
return False
return True