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[FIX] Fix type mismatch in clinica.iotools.bids_utils #1376

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merged 2 commits into from
Nov 22, 2024
Merged

[FIX] Fix type mismatch in clinica.iotools.bids_utils #1376

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c56a964
look for 'flutemeta' in file name
NicolasGensollen Nov 14, 2024
449f680
fix
NicolasGensollen Nov 21, 2024
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9 changes: 3 additions & 6 deletions clinica/iotools/bids_utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -576,12 +576,9 @@ def create_scans_dict(
# Some flutemeta lines contain a non-coded string value at the second-to-last position. This value
# contains a comma which adds an extra column and shifts the remaining values to the right. In this
# case, we just remove the erroneous content and replace it with -4 which AIBL uses as n/a value.
on_bad_lines = ( # noqa: E731
lambda bad_line: bad_line[:-3] + [-4, bad_line[-1]]
if "flutemeta" in file_path and study_name == StudyName.AIBL
else "error"
)

on_bad_lines = lambda x: "error" # noqa
if "flutemeta" in file_path.name and study_name == StudyName.AIBL:
on_bad_lines = lambda bad_line: bad_line[:-3] + [-4, bad_line[-1]] # noqa
file_to_read = pd.read_csv(
file_path,
sep=",",
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