ENH: Find B0FieldIdentifiers when one image contributes to multiple (#…

…298) * fix/hacks for pepolar scheme with B0FieldIdentifier as lists * fix if no B0FieldIdentifier, empty list, (testing) * Update sdcflows/fieldmaps.py Co-authored-by: Chris Markiewicz <[email protected]> * Update sdcflows/fieldmaps.py Co-authored-by: Chris Markiewicz <[email protected]> * Update sdcflows/fieldmaps.py Co-authored-by: Chris Markiewicz <[email protected]> * FIX: Update logic for finding b0 fields * FIX: Break layout.get calls into separate lines, use repr for match instead of custom wrapping * FIX: A more perfect union * FIX: JSON, not repr Co-authored-by: Chris Markiewicz <[email protected]>
nipreps · Dec 6, 2022 · 82e7593 · 82e7593
1 parent 7898fac
commit 82e7593
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Showing 2 changed files with 38 additions and 22 deletions.
diff --git a/sdcflows/fieldmaps.py b/sdcflows/fieldmaps.py
@@ -404,27 +404,31 @@ 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:
-                raise ValueError(
-                    f"Multiple ``B0FieldIdentifier`` set: <{', '.join(bids_ids)}>"
-                )
-            elif bids_ids:
+            b0_ids = [
+                listify(f.metadata.get("B0FieldIdentifier"))
+                for f in self.sources
+                if f.metadata.get("B0FieldIdentifier")
+            ]
+
+            if b0_ids:
+                # Find common IDs
+                bids_ids = set(b0_ids[0]).intersection(*b0_ids[1:])
+                if not bids_ids:
+                    raise ValueError(
+                        f"No common ``B0FieldIdentifier`` found: <{', '.join(map(str, b0_ids))}>"
+                    )
+                elif len(bids_ids) > 1:
+                    raise ValueError(
+                        f"Multiple common ``B0FieldIdentifier``s found: <{', '.join(bids_ids)}>"
+                    )
                 object.__setattr__(self, "bids_id", bids_ids.pop())
-            else:
-                bids_id = _estimators.add(self.paths())
-                object.__setattr__(self, "bids_id", bids_id)
-                for intent_file in intents_meta:
-                    _intents[intent_file].add(bids_id)
-                return
-
-        _estimators[self.bids_id] = self.paths()
+
+        if self.bids_id:
+            _estimators[self.bids_id] = self.paths()
+        else:
+            bids_id = _estimators.add(self.paths())
+            object.__setattr__(self, "bids_id", bids_id)
+
         for intent_file in intents_meta:
             _intents[intent_file].add(self.bids_id)
 

diff --git a/sdcflows/utils/wrangler.py b/sdcflows/utils/wrangler.py
@@ -22,6 +22,7 @@
 #
 """Find fieldmaps on the BIDS inputs for :abbr:`SDC (susceptibility distortion correction)`."""
 import logging
+from functools import reduce
 from itertools import product
 from contextlib import suppress
 from pathlib import Path
@@ -293,7 +294,12 @@ def find_estimators(
     # Step 1. Use B0FieldIdentifier metadata
     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 = reduce(
+            set.union,
+            (listify(ids) for ids in layout.get_B0FieldIdentifiers(**base_entities)),
+            set()
+        )
 
     if b0_ids:
         logger.debug(
@@ -305,9 +311,15 @@ def find_estimators(
             b0_entities = base_entities.copy()
             b0_entities["B0FieldIdentifier"] = b0_id
 
+            bare_ids = layout.get(**base_entities, B0FieldIdentifier=b0_id)
+            listed_ids = layout.get(
+                **base_entities,
+                B0FieldIdentifier=f'"{b0_id}"',  # Double quotes to match JSON, not Python repr
+                regex_search=True,
+            )
             e = fm.FieldmapEstimation([
                 fm.FieldmapFile(fmap.path, metadata=fmap.get_metadata())
-                for fmap in layout.get(**b0_entities)
+                for fmap in bare_ids + listed_ids
             ])
             _log_debug_estimation(logger, e, layout.root)
             estimators.append(e)