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[FIX] Fixes conditions of overlapping B0FieldIdentifier, resulting in no estimators #497

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Merged
merged 2 commits into from
Jul 28, 2025
Merged

[FIX] Fixes conditions of overlapping B0FieldIdentifier, resulting in no estimators #497

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c825243
fix overlapping B0FieldIdentifier, resulting in no estimators
bpinsard Jul 17, 2025
a42eef3
add tests for B0Field cases
bpinsard Jul 18, 2025
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162 changes: 152 additions & 10 deletions sdcflows/utils/tests/test_wrangler.py
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Original file line number Diff line number Diff line change
Expand Up @@ -202,6 +202,146 @@ def gen_layout(bids_dir, database_dir=None):
}


pepolar_b0ids = {
'01': [
{
'session': '01',
'anat': [{'suffix': 'T1w', 'metadata': {'EchoTime': 1}}],
'func': [
{
'task': 'rest',
'run': 1,
'suffix': 'bold',
'metadata': {
'RepetitionTime': 0.8,
'TotalReadoutTime': 0.5,
'PhaseEncodingDirection': 'j',
'B0FieldIdentifier': 'b0_pepolar',
'B0FieldSource': 'b0_pepolar',
},
},
{
'task': 'rest',
'run': 2,
'suffix': 'bold',
'metadata': {
'RepetitionTime': 0.8,
'TotalReadoutTime': 0.5,
'PhaseEncodingDirection': 'j-',
'B0FieldIdentifier': 'b0_pepolar',
'B0FieldSource': 'b0_pepolar',
},
},
],
},
{
'session': '02',
'anat': [{'suffix': 'T1w', 'metadata': {'EchoTime': 1}}],
'func': [
{
'task': 'rest',
'run': 1,
'suffix': 'bold',
'metadata': {
'RepetitionTime': 0.8,
'TotalReadoutTime': 0.5,
'PhaseEncodingDirection': 'j',
'B0FieldSource': 'b0_pepolar',
},
},
{
'task': 'rest',
'run': 2,
'suffix': 'bold',
'metadata': {
'RepetitionTime': 0.8,
'TotalReadoutTime': 0.5,
'PhaseEncodingDirection': 'j-',
'B0FieldSource': 'b0_pepolar',
},
},
{
'task': 'rest',
'run': 1,
'suffix': 'sbref',
'metadata': {
'RepetitionTime': 0.8,
'TotalReadoutTime': 0.5,
'PhaseEncodingDirection': 'j',
'B0FieldIdentifier': 'b0_pepolar',
'B0FieldSource': 'b0_pepolar',
},
},
{
'task': 'rest',
'run': 2,
'suffix': 'sbref',
'metadata': {
'RepetitionTime': 0.8,
'TotalReadoutTime': 0.5,
'PhaseEncodingDirection': 'j-',
'B0FieldIdentifier': 'b0_pepolar',
'B0FieldSource': 'b0_pepolar',
},
},
],
},
{
'session': '03',
'anat': [{'suffix': 'T1w', 'metadata': {'EchoTime': 1}}],
'func': [
{
'task': 'rest',
'run': 1,
'suffix': 'bold',
'metadata': {
'RepetitionTime': 0.8,
'TotalReadoutTime': 0.5,
'PhaseEncodingDirection': 'j',
'B0FieldSource': 'b0_pepolar',
},
},
{
'task': 'rest',
'run': 2,
'suffix': 'bold',
'metadata': {
'RepetitionTime': 0.8,
'TotalReadoutTime': 0.5,
'PhaseEncodingDirection': 'j-',
'B0FieldSource': 'b0_pepolar',
},
},
{
'task': 'rest',
'run': 1,
'suffix': 'sbref',
'metadata': {
'RepetitionTime': 0.8,
'TotalReadoutTime': 0.5,
'PhaseEncodingDirection': 'j',
'B0FieldIdentifier': ['b0_pepolar', 'b0_pepolar_dup'],
'B0FieldSource': 'b0_pepolar',
},
},
{
'task': 'rest',
'run': 2,
'suffix': 'sbref',
'metadata': {
'RepetitionTime': 0.8,
'TotalReadoutTime': 0.5,
'PhaseEncodingDirection': 'j-',
'B0FieldIdentifier': ['b0_pepolar', 'b0_pepolar_dup'],
'B0FieldSource': 'b0_pepolar',
},
},
],
},
]
}


phasediff = {
'01': [
{
Expand Down Expand Up @@ -304,26 +444,28 @@ def gen_layout(bids_dir, database_dir=None):


@pytest.mark.parametrize(
'name,skeleton,estimations',
'name,skeleton,estimations,bids_filters',
[
('pepolar', pepolar, 1),
('phasediff', phasediff, 1),
('pepolar', pepolar, 1, 'fmap'),
('pepolar_b0ids', pepolar_b0ids, 1, 'bold'),
('phasediff', phasediff, 1, 'fmap'),
],
)
def test_wrangler_filter(tmpdir, name, skeleton, estimations):
def test_wrangler_filter(tmpdir, name, skeleton, estimations, bids_filters):
bids_dir = str(tmpdir / name)
generate_bids_skeleton(bids_dir, skeleton)
layout = gen_layout(bids_dir)
est = find_estimators(layout=layout, subject='01', bids_filters=filters['fmap'])
est = find_estimators(layout=layout, subject='01', bids_filters=filters[bids_filters])
assert len(est) == estimations
clear_registry()


@pytest.mark.parametrize(
'name,skeleton,total_estimations',
'name,skeleton,total_estimations,test_auto',
[
('pepolar', pepolar, 5),
('phasediff', phasediff, 3),
('pepolar', pepolar, 5, True),
('pepolar_b0ids', pepolar_b0ids, 2, False),
('phasediff', phasediff, 3, True),
],
)
@pytest.mark.parametrize(
Expand All @@ -335,7 +477,7 @@ def test_wrangler_filter(tmpdir, name, skeleton, estimations):
(None, None),
],
)
def test_wrangler_URIs(tmpdir, name, skeleton, session, estimations, total_estimations):
def test_wrangler_URIs(tmpdir, name, skeleton, session, estimations, total_estimations, test_auto):
bids_dir = str(tmpdir / name)
generate_bids_skeleton(bids_dir, skeleton)
layout = gen_layout(bids_dir)
Expand All @@ -345,7 +487,7 @@ def test_wrangler_URIs(tmpdir, name, skeleton, session, estimations, total_estim
sessions=[session] if session else None,
)
assert len(est) == estimations or total_estimations
if session:
if session and test_auto:
bold = layout.get(session=session, suffix='bold', extension='.nii.gz')[0]
intended_rel = re.sub(r'^sub-[a-zA-Z0-9]*/', '', str(Path(bold).relative_to(layout.root)))
b0_id = get_identifier(intended_rel)
Expand Down
3 changes: 2 additions & 1 deletion sdcflows/utils/wrangler.py
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Original file line number Diff line number Diff line change
Expand Up @@ -377,7 +377,8 @@ def find_estimators(
[
fm.FieldmapFile(fmap.path, metadata=fmap.get_metadata())
for fmap in bare_ids + listed_ids
]
],
bids_id=b0_id,
)
except (ValueError, TypeError) as err:
_log_debug_estimator_fail(
Expand Down
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