Merge pull request #342 from effigies/rf/split_pepolar_by_intent

RF: Split PEPolar fieldmaps by intent, if available

Author: effigies

sdcflows/utils/wrangler.py

@@ -129,7 +129,9 @@ def find_estimators(
     [FieldmapEstimation(sources=<2 files>, method=<EstimatorType.PHASEDIFF: 3>,
                         bids_id='auto_00006'),
      FieldmapEstimation(sources=<2 files>, method=<EstimatorType.PEPOLAR: 2>,
-                        bids_id='auto_00007')]
+                        bids_id='auto_00007'),
+     FieldmapEstimation(sources=<2 files>, method=<EstimatorType.PEPOLAR: 2>,
+                        bids_id='auto_00008')]
 
     Finally, *SDCFlows*' "*dataset A*" and "*dataset B*" contain BIDS structures
     with zero-byte NIfTI files and some corresponding metadata:
@@ -363,21 +365,22 @@ def find_estimators(
             )
             dirs = layout.get_directions(**entities)
             if len(dirs) > 1:
-                fieldmaps = layout.get(**{**entities, **{"direction": dirs}})
-                try:
-                    e = fm.FieldmapEstimation(
-                        [
-                            fm.FieldmapFile(fmap.path, metadata=fmap.get_metadata())
-                            for fmap in fieldmaps
-                        ]
-                    )
-                except ValueError as err:
-                    _log_debug_estimator_fail(
-                        logger, "unnamed PEPOLAR", fieldmaps, layout.root, str(err)
-                    )
-                else:
-                    _log_debug_estimation(logger, e, layout.root)
-                    estimators.append(e)
+                by_intent = {}
+                for fmap in layout.get(**{**entities, **{'direction': dirs}}):
+                    fmapfile = fm.FieldmapFile(fmap.path, metadata=fmap.get_metadata())
+                    by_intent.setdefault(
+                        tuple(fmapfile.metadata.get('IntendedFor', ())), []
+                    ).append(fmapfile)
+                for collection in by_intent.values():
+                    try:
+                        e = fm.FieldmapEstimation(collection)
+                    except (ValueError, TypeError) as err:
+                        _log_debug_estimator_fail(
+                            logger, "unnamed PEPOLAR", collection, layout.root, str(err)
+                        )
+                    else:
+                        _log_debug_estimation(logger, e, layout.root)
+                        estimators.append(e)
 
         # At this point, only single-PE _epi files WITH ``IntendedFor`` can
         # be automatically processed.
@@ -398,23 +401,43 @@ def find_estimators(
             logger.debug("Found single PE fieldmap %s", epi_fmap.relpath)
             epi_base_md = epi_fmap.get_metadata()
 
-            # There are two possible interpretations of an IntendedFor list:
-            # 1) The fieldmap and each intended target are combined separately
-            # 2) The fieldmap and all intended targets are combined at once
-            #
-            # (1) has been the historical interpretation of NiPreps,
-            # so construct a separate estimator for each target.
+            # 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))
                 if target is None:
                     logger.debug("Single PE target %s not found", intent)
                     continue
+                all_targets.append(target)
+
+            # If sbrefs are targets, then the goal is generally to estimate with epi+sbref
+            # and correct bold/dwi
+            sbrefs = [
+                target for target in all_targets if target.entities["suffix"] == "sbref"
+            ]
+            if sbrefs:
+                targets = sbrefs
+                intent_map = []
+                for sbref in sbrefs:
+                    ents = sbref.entities.copy()
+                    ents["suffix"] = ["bold", "dwi"]
+                    intent_map.append(
+                        [
+                            target
+                            for target in layout.get(**ents)
+                            if target in all_targets
+                        ]
+                    )
+            else:
+                targets = all_targets
+                intent_map = [[target] for target in all_targets]
 
+            for target, intent in zip(targets, intent_map):
                 logger.debug("Found single PE target %s", target.relpath)
                 # The new estimator is IntendedFor the individual targets,
                 # even if the EPI file is IntendedFor multiple
                 estimator_md = epi_base_md.copy()
-                estimator_md["IntendedFor"] = [intent]
+                estimator_md["IntendedFor"] = intent
                 try:
                     e = fm.FieldmapEstimation(
                         [