ENH: Take in bids root to build reference path, add warnings

Author: mgxd

nibabies/utils/bids.py

@@ -47,7 +47,8 @@ def __getattribute__(self, attr):
         except AttributeError:
             return None
 
-    def __init__(self, spec: dict | Path | str | None = None, **args):
+    def __init__(self, bids_root: Path | str, spec: dict | Path | str | None = None, **args):
+        self.bids_root = Path(bids_root)
         self.spec = _spec
         if spec is not None:
             if not isinstance(spec, dict):
@@ -81,23 +82,24 @@ def populate(
                 **query,
             )
             if not items or len(items) > 1:
+                warnings.warn(f"Could not find {name}")
                 continue
             item = items[0]
 
             # Skip if derivative does not have valid metadata
             metadata = item.get_metadata()
             if not metadata or not (reference := metadata.get('SpatialReference')):
-                # raise warning
+                warnings.warn(f"No metadata found for {item}")
                 continue
             if isinstance(reference, list):
                 if len(reference) > 1:
-                    # raise warning
+                    warnings.warn(f"Multiple reference found: {reference}")
                     continue
                 reference = reference[0]
 
-            reference = (Path(deriv_path) / reference).absolute()
+            reference = self.bids_root / reference
             if not self.validate(item.path, str(reference)):
-                # raise warning
+                warnings.warn(f"Validation failed between: {item.path} and {reference}")
                 continue
 
             setattr(self, name, Path(item.path))

nibabies/workflows/base.py

@@ -39,6 +39,7 @@
 .. autofunction:: init_single_subject_wf
 
 """
+from __future__ import annotations
 
 import os
 import sys
@@ -227,7 +228,7 @@ def init_single_subject_wf(
         subject_data["t2w"] = []
 
     anat_only = config.workflow.anat_only
-    derivatives = Derivatives()
+    derivatives = Derivatives(bids_root=config.execution.layout.root)
     anat_modality = "t1w" if subject_data["t1w"] else "t2w"
     # Make sure we always go through these two checks
     if not anat_only and not subject_data["bold"]:
@@ -241,13 +242,13 @@ def init_single_subject_wf(
 
     if config.execution.derivatives:
         for deriv_path in config.execution.derivatives:
-            config.loggers.workflow.debug("Searching for derivatives in %s", deriv_path)
+            config.loggers.workflow.info("Searching for derivatives in %s", deriv_path)
             derivatives.populate(
                 deriv_path,
                 subject_id,
                 session_id=session_id,
             )
-        config.loggers.workflow.info(f"Found precomputed derivatives: {derivatives}")
+        config.loggers.workflow.info("Found precomputed derivatives %s", derivatives)
 
     workflow = Workflow(name=name)
     workflow.__desc__ = """