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Ignore unselected subjects in BIDSLayoutIndexer #3236

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Merged
effigies merged 6 commits into from
Mar 9, 2024
Merged

Ignore unselected subjects in BIDSLayoutIndexer #3236

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d0f1aa5
Ignore unselected subjects in BIDSLayoutIndexer.
tsalo Feb 23, 2024
22ee716
Merge remote-tracking branch 'upstream/master' into ignore-unselected…
tsalo Mar 5, 2024
4769d1a
Address review.
tsalo Mar 5, 2024
46e05b9
Update fmriprep/config.py
tsalo Mar 8, 2024
e1593dd
Merge remote-tracking branch 'upstream/master' into ignore-unselected…
effigies Mar 8, 2024
acf39af
FIX: Check for word boundary or underscore to identify end-of-entity
effigies Mar 8, 2024
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26 changes: 16 additions & 10 deletions fmriprep/config.py
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Original file line number Diff line number Diff line change
Expand Up @@ -472,18 +472,24 @@ def init(cls):
_db_path.mkdir(exist_ok=True, parents=True)

# Recommended after PyBIDS 12.1
ignore_patterns = [
'code',
'stimuli',
'sourcedata',
'models',
re.compile(r'^\.'),
re.compile(r'sub-[a-zA-Z0-9]+(/ses-[a-zA-Z0-9]+)?/(beh|dwi|eeg|ieeg|meg|perf)'),
]
if cls.participant_label and cls.bids_database_dir is None:
# Ignore any subjects who aren't the requested ones.
# This is only done if the database is written out to a run-specific folder.
ignore_patterns.append(
re.compile(r'sub-(?!(' + '|'.join(cls.participant_label) + r')(\b|_))')
)

_indexer = BIDSLayoutIndexer(
validate=False,
ignore=(
'code',
'stimuli',
'sourcedata',
'models',
re.compile(r'^\.'),
re.compile(
r'sub-[a-zA-Z0-9]+(/ses-[a-zA-Z0-9]+)?/(beh|dwi|eeg|ieeg|meg|perf)'
),
),
ignore=ignore_patterns,
)
cls._layout = BIDSLayout(
str(cls.bids_dir),
Expand Down