Merge pull request #458 from effigies/fix/bids-uris-nonepi

FIX: Normalize BIDS-URIs to subject-relative

Author: effigies

sdcflows/utils/tests/test_wrangler.py

@@ -1,10 +1,13 @@
-import pytest
+import re
+from pathlib import Path
 from shutil import rmtree
 
+import pytest
+
 from niworkflows.utils.testing import generate_bids_skeleton
 
 from sdcflows.utils.wrangler import find_estimators
-from sdcflows.fieldmaps import clear_registry
+from sdcflows.fieldmaps import clear_registry, get_identifier
 
 
 def gen_layout(bids_dir, database_dir=None):
@@ -339,6 +342,12 @@ 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:
+        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)
+        assert b0_id == ('auto_00000',)
+
     clear_registry()
 
 

sdcflows/utils/wrangler.py

@@ -34,6 +34,22 @@
 from .. import fieldmaps as fm
 
 
+def _normalize_intent(
+    intent: str,
+    subject: str
+) -> str | None:
+    """Convert BIDS-URI intent to subject-relative intent
+
+    SDCFlows currently makes strong assumptions about old-style intents,
+    and a change to that needs to be carefully considered and tested.
+    """
+    if intent.startswith("bids::"):
+        # bids::sub-<subject>/
+        #          ^- 10     ^- 11
+        return intent[11 + len(subject):]
+    return intent
+
+
 def _resolve_intent(
     intent: str,
     layout: BIDSLayout,
@@ -47,6 +63,17 @@ def _resolve_intent(
     return intent
 
 
+def _filter_metadata(
+    metadata: Dict[str, Any],
+    subject: str
+) -> Dict[str, Any]:
+    intents = metadata.get("IntendedFor")
+    if intents:
+        updated = [_normalize_intent(intent, subject) for intent in listify(intents)]
+        return {**metadata, "IntendedFor": updated}
+    return metadata
+
+
 def find_estimators(
     *,
     layout: BIDSLayout,
@@ -377,7 +404,10 @@ def find_estimators(
         ):
             try:
                 e = fm.FieldmapEstimation(
-                    fm.FieldmapFile(fmap.path, metadata=fmap.get_metadata())
+                    fm.FieldmapFile(
+                        fmap.path,
+                        metadata=_filter_metadata(fmap.get_metadata(), subject),
+                    )
                 )
             except (ValueError, TypeError) as err:
                 _log_debug_estimator_fail(
@@ -405,7 +435,10 @@ def find_estimators(
             if len(dirs) > 1:
                 by_intent = {}
                 for fmap in layout.get(**{**entities, **{'direction': dirs}}):
-                    fmapfile = fm.FieldmapFile(fmap.path, metadata=fmap.get_metadata())
+                    fmapfile = fm.FieldmapFile(
+                        fmap.path,
+                        metadata=_filter_metadata(fmap.get_metadata(), subject),
+                    )
                     by_intent.setdefault(
                         tuple(fmapfile.metadata.get('IntendedFor', ())), []
                     ).append(fmapfile)