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ENH: Resolve BIDS-URIs #349

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merged 3 commits into from
Jan 18, 2024
Merged

ENH: Resolve BIDS-URIs #349

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064b556
ENH: Resolve BIDS-URIs
effigies Apr 17, 2023
6380a1c
Merge branch 'master' into enh/bids-uris
oesteban Nov 28, 2023
cea2cee
fix: import future annotations
oesteban Nov 28, 2023
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23 changes: 17 additions & 6 deletions sdcflows/utils/tests/test_wrangler.py
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Original file line number Diff line number Diff line change
Expand Up @@ -47,13 +47,13 @@
"EchoTime": 1.2,
"PhaseEncodingDirection": "j-",
"TotalReadoutTime": 0.8,
"IntendedFor": "ses-02/func/sub-01_ses-02_task-rest_bold.nii.gz"
"IntendedFor": "bids::sub-01/ses-02/func/sub-01_ses-02_task-rest_bold.nii.gz"
}},
{"suffix": "epi", "dir": "PA", "metadata": {
"EchoTime": 1.2,
"PhaseEncodingDirection": "j",
"TotalReadoutTime": 0.8,
"IntendedFor": "ses-02/func/sub-01_ses-02_task-rest_bold.nii.gz"
"IntendedFor": "bids::sub-01/ses-02/func/sub-01_ses-02_task-rest_bold.nii.gz"
}}
],
"func": [
Expand All @@ -76,13 +76,13 @@
"EchoTime": 1.2,
"PhaseEncodingDirection": "j-",
"TotalReadoutTime": 0.8,
"IntendedFor": "ses-03/func/sub-01_ses-03_task-rest_bold.nii.gz"
"IntendedFor": "bids::sub-01/ses-03/func/sub-01_ses-03_task-rest_bold.nii.gz"
}},
{"suffix": "epi", "dir": "PA", "metadata": {
"EchoTime": 1.2,
"PhaseEncodingDirection": "j",
"TotalReadoutTime": 0.8,
"IntendedFor": "ses-03/func/sub-01_ses-03_task-rest_bold.nii.gz"
"IntendedFor": "bids::sub-01/ses-03/func/sub-01_ses-03_task-rest_bold.nii.gz"
}}
],
"func": [
Expand Down Expand Up @@ -176,7 +176,7 @@
"metadata": {
"EchoTime1": 1.2,
"EchoTime2": 1.4,
"IntendedFor": "ses-02/func/sub-01_ses-02_task-rest_bold.nii.gz"
"IntendedFor": "bids::sub-01/ses-02/func/sub-01_ses-02_task-rest_bold.nii.gz"
}
},
{"suffix": "magnitude1", "metadata": {"EchoTime": 1.2}},
Expand All @@ -203,7 +203,7 @@
"metadata": {
"EchoTime1": 1.2,
"EchoTime2": 1.4,
"IntendedFor": "ses-03/func/sub-01_ses-03_task-rest_bold.nii.gz"
"IntendedFor": "bids::sub-01/ses-03/func/sub-01_ses-03_task-rest_bold.nii.gz"
}
},
{"suffix": "magnitude1", "metadata": {"EchoTime": 1.2}},
Expand Down Expand Up @@ -255,6 +255,17 @@ def test_wrangler_filter(tmpdir, name, skeleton, estimations):
assert len(est) == estimations
clear_registry()

@pytest.mark.parametrize('name,skeleton,estimations', [
('pepolar', pepolar, 3),
('phasediff', phasediff, 3),
])
def test_wrangler_URIs(tmpdir, name, skeleton, estimations):
bids_dir = str(tmpdir / name)
generate_bids_skeleton(bids_dir, skeleton)
layout = gen_layout(bids_dir)
est = find_estimators(layout=layout, subject='01')
assert len(est) == estimations
clear_registry()

def test_single_reverse_pedir(tmp_path):
bids_dir = tmp_path / "bids"
Expand Down
15 changes: 14 additions & 1 deletion sdcflows/utils/wrangler.py
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Original file line number Diff line number Diff line change
Expand Up @@ -33,6 +33,19 @@
from .. import fieldmaps as fm


def _resolve_intent(
intent: str,
layout: BIDSLayout,
subject: str
) -> str | None:
root = Path(layout.root)
if intent.startswith("bids::"):
return str(root / intent[6:])
if not intent.startswith("bids:"):
return str(root / f"sub-{subject}" / intent)
return intent


def find_estimators(
*,
layout: BIDSLayout,
Expand Down Expand Up @@ -426,7 +439,7 @@ def find_estimators(
# Find existing IntendedFor targets and warn if missing
all_targets = []
for intent in listify(epi_base_md["IntendedFor"]):
target = layout.get_file(str(subject_root / intent))
target = layout.get_file(_resolve_intent(intent, layout, subject))
if target is None:
logger.debug("Single PE target %s not found", intent)
continue
Expand Down
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