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ENH: Find B0FieldIdentifiers when one image contributes to multiple #298

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merged 11 commits into from
Dec 6, 2022
Merged

ENH: Find B0FieldIdentifiers when one image contributes to multiple #298

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b029cee
fix/hacks for pepolar scheme with B0FieldIdentifier as lists
bpinsard Nov 10, 2022
1273a12
fix if no B0FieldIdentifier, empty list, (testing)
bpinsard Nov 10, 2022
56432af
Update sdcflows/fieldmaps.py
bpinsard Dec 3, 2022
bf922fc
Update sdcflows/fieldmaps.py
bpinsard Dec 3, 2022
69aa60e
Update sdcflows/fieldmaps.py
bpinsard Dec 3, 2022
80d7cc1
FIX: Update logic for finding b0 fields
effigies Dec 4, 2022
2e6151a
FIX: Break layout.get calls into separate lines, use repr for match i…
effigies Dec 4, 2022
68585e3
FIX: A more perfect union
effigies Dec 4, 2022
08d06e5
FIX: JSON, not repr
effigies Dec 6, 2022
dd4f02b
Merge remote-tracking branch 'upstream/master' into fix/pepolar_b0fie…
effigies Dec 6, 2022
df111a6
Merge remote-tracking branch 'upstream/master' into fix/pepolar_b0fie…
effigies Dec 6, 2022
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22 changes: 13 additions & 9 deletions sdcflows/fieldmaps.py
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Original file line number Diff line number Diff line change
Expand Up @@ -404,16 +404,20 @@ def __attrs_post_init__(self):
# Register this estimation method
if not self.bids_id:
# If not manually set, try to get it from BIDS metadata
bids_ids = set(
[
f.metadata.get("B0FieldIdentifier")
for f in self.sources
if f.metadata.get("B0FieldIdentifier")
]
)
if len(bids_ids) > 1:
b0_ids = [
listify(f.metadata.get("B0FieldIdentifier"))
for f in self.sources
if f.metadata.get("B0FieldIdentifier")
]
bids_ids = set.intersection(*b0_ids)
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if not bids_ids:
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raise ValueError(
f"No common ``B0FieldIdentifier`` found: <{', '.join(b0_ids)}>"
)
elif len(bids_ids) > 1:
raise ValueError(
f"Multiple ``B0FieldIdentifier`` set: <{', '.join(bids_ids)}>"
f"Multiple common ``B0FieldIdentifier``s found: <{', '.join(bids_ids)}>"
)
elif bids_ids:
object.__setattr__(self, "bids_id", bids_ids.pop())
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5 changes: 4 additions & 1 deletion sdcflows/utils/wrangler.py
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Original file line number Diff line number Diff line change
Expand Up @@ -283,6 +283,8 @@ def find_estimators(
b0_ids = tuple()
with suppress(BIDSEntityError):
b0_ids = layout.get_B0FieldIdentifiers(**base_entities)
# flatten lists from json (tupled in pybids for hashing), then unique
b0_ids = set(sum([(b0_id if isinstance(b0_id, tuple) else (b0_id,)) for b0_id in b0_ids ],()))

if b0_ids:
logger.debug(
Expand All @@ -296,7 +298,8 @@ def find_estimators(

e = fm.FieldmapEstimation([
fm.FieldmapFile(fmap.path, metadata=fmap.get_metadata())
for fmap in layout.get(**b0_entities)
for fmap in layout.get(**base_entities, B0FieldIdentifier=b0_id) +
layout.get(**base_entities, B0FieldIdentifier=f'"{b0_id}"', regex_search=True)
])
_log_debug_estimation(logger, e, layout.root)
estimators.append(e)
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