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[ENH] Age float change + handling of sessions.tsv ages #394

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[ENH] Age float change + handling of sessions.tsv ages #394

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9e14a8e
Add support for non-integer age values
erikglee Sep 12, 2024
36ffb2a
adjust _get_age_from_tsv to grab age from first anat file if scans.ts…
erikglee Sep 12, 2024
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24 changes: 18 additions & 6 deletions nibabies/utils/bids.py
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Original file line number Diff line number Diff line change
Expand Up @@ -244,7 +244,7 @@ def parse_bids_for_age_months(

scans_tsv = session_level / f'{prefix}_scans.tsv'
if scans_tsv.exists():
age = _get_age_from_tsv(scans_tsv)
age = _get_age_from_tsv(scans_tsv, is_scans_tsv = True)

if age is not None:
return age
Expand All @@ -264,8 +264,8 @@ def parse_bids_for_age_months(


def _get_age_from_tsv(
bids_tsv: Path, index_column: str | None = None, index_val: str | None = None
) -> int | None:
bids_tsv: Path, index_column: str | None = None, index_val: str | None = None,
is_scans_tsv: bool = False) -> float | None:
import pandas as pd

df = pd.read_csv(str(bids_tsv), sep='\t')
Expand All @@ -277,6 +277,14 @@ def _get_age_from_tsv(
break
if age_col is None:
return

if is_scans_tsv: #If it is a scans.tsv, grab try to grab age from first anat file
try:
index_column = 'filename'
index_val = df.loc[df['filename'].str.startswith('anat'), 'filename'].iloc[0]
except:
index_column = None
index_val = None

if not index_column or not index_val: # Just grab first value
idx = df.index[0]
Expand All @@ -285,7 +293,7 @@ def _get_age_from_tsv(

try:
# extract age value from row
age = int(df.loc[idx, age_col].item())
age = float(df.loc[idx, age_col].item())
except Exception: # noqa: BLE001
return

Expand Down Expand Up @@ -318,12 +326,14 @@ def _get_age_units(bids_json: Path) -> ty.Literal['weeks', 'months', 'years', Fa
return False


def age_to_months(age: int, units: ty.Literal['weeks', 'months', 'years']) -> int:
def age_to_months(age: float, units: ty.Literal['weeks', 'months', 'years']) -> int:
"""
Convert a given age, in either "weeks", "months", or "years", into months.

>>> age_to_months(1, 'years')
12
>>> age_to_months(0.5, 'years')
6
>>> age_to_months(2, 'weeks')
0
>>> age_to_months(3, 'weeks')
Expand All @@ -337,5 +347,7 @@ def age_to_months(age: int, units: ty.Literal['weeks', 'months', 'years']) -> in
if units == 'weeks':
age = round(age * WEEKS_TO_MONTH)
elif units == 'years':
age *= YEARS_TO_MONTH
age = round(age * YEARS_TO_MONTH)
elif units == 'months':
age = round(age)
return age