Merge pull request #349 from effigies/enh/bids-uris

ENH: Resolve BIDS-URIs

sdcflows/utils/tests/test_wrangler.py

@@ -74,13 +74,13 @@ def gen_layout(bids_dir, database_dir=None):
                     "EchoTime": 1.2,
                     "PhaseEncodingDirection": "j-",
                     "TotalReadoutTime": 0.8,
-                    "IntendedFor": "ses-02/func/sub-01_ses-02_task-rest_bold.nii.gz"
+                    "IntendedFor": "bids::sub-01/ses-02/func/sub-01_ses-02_task-rest_bold.nii.gz"
                 }},
                 {"suffix": "epi", "dir": "PA", "metadata": {
                     "EchoTime": 1.2,
                     "PhaseEncodingDirection": "j",
                     "TotalReadoutTime": 0.8,
-                    "IntendedFor": "ses-02/func/sub-01_ses-02_task-rest_bold.nii.gz"
+                    "IntendedFor": "bids::sub-01/ses-02/func/sub-01_ses-02_task-rest_bold.nii.gz"
                 }}
             ],
             "func": [
@@ -103,13 +103,13 @@ def gen_layout(bids_dir, database_dir=None):
                     "EchoTime": 1.2,
                     "PhaseEncodingDirection": "j-",
                     "TotalReadoutTime": 0.8,
-                    "IntendedFor": "ses-03/func/sub-01_ses-03_task-rest_bold.nii.gz"
+                    "IntendedFor": "bids::sub-01/ses-03/func/sub-01_ses-03_task-rest_bold.nii.gz"
                 }},
                 {"suffix": "epi", "dir": "PA", "metadata": {
                     "EchoTime": 1.2,
                     "PhaseEncodingDirection": "j",
                     "TotalReadoutTime": 0.8,
-                    "IntendedFor": "ses-03/func/sub-01_ses-03_task-rest_bold.nii.gz"
+                    "IntendedFor": "bids::sub-01/ses-03/func/sub-01_ses-03_task-rest_bold.nii.gz"
                 }}
             ],
             "func": [
@@ -203,7 +203,7 @@ def gen_layout(bids_dir, database_dir=None):
                     "metadata": {
                         "EchoTime1": 1.2,
                         "EchoTime2": 1.4,
-                        "IntendedFor": "ses-02/func/sub-01_ses-02_task-rest_bold.nii.gz"
+                        "IntendedFor": "bids::sub-01/ses-02/func/sub-01_ses-02_task-rest_bold.nii.gz"
                     }
                 },
                 {"suffix": "magnitude1", "metadata": {"EchoTime": 1.2}},
@@ -230,7 +230,7 @@ def gen_layout(bids_dir, database_dir=None):
                     "metadata": {
                         "EchoTime1": 1.2,
                         "EchoTime2": 1.4,
-                        "IntendedFor": "ses-03/func/sub-01_ses-03_task-rest_bold.nii.gz"
+                        "IntendedFor": "bids::sub-01/ses-03/func/sub-01_ses-03_task-rest_bold.nii.gz"
                     }
                 },
                 {"suffix": "magnitude1", "metadata": {"EchoTime": 1.2}},
@@ -282,6 +282,17 @@ def test_wrangler_filter(tmpdir, name, skeleton, estimations):
     assert len(est) == estimations
     clear_registry()
 
+@pytest.mark.parametrize('name,skeleton,estimations', [
+    ('pepolar', pepolar, 3),
+    ('phasediff', phasediff, 3),
+])
+def test_wrangler_URIs(tmpdir, name, skeleton, estimations):
+    bids_dir = str(tmpdir / name)
+    generate_bids_skeleton(bids_dir, skeleton)
+    layout = gen_layout(bids_dir)
+    est = find_estimators(layout=layout, subject='01')
+    assert len(est) == estimations
+    clear_registry()
 
 def test_single_reverse_pedir(tmp_path):
     bids_dir = tmp_path / "bids"

sdcflows/utils/wrangler.py

@@ -21,6 +21,7 @@
 #     https://www.nipreps.org/community/licensing/
 #
 """Find fieldmaps on the BIDS inputs for :abbr:`SDC (susceptibility distortion correction)`."""
+from __future__ import annotations
 import logging
 from functools import reduce
 from itertools import product
@@ -33,6 +34,19 @@
 from .. import fieldmaps as fm
 
 
+def _resolve_intent(
+    intent: str,
+    layout: BIDSLayout,
+    subject: str
+) -> str | None:
+    root = Path(layout.root)
+    if intent.startswith("bids::"):
+        return str(root / intent[6:])
+    if not intent.startswith("bids:"):
+        return str(root / f"sub-{subject}" / intent)
+    return intent
+
+
 def find_estimators(
     *,
     layout: BIDSLayout,
@@ -427,7 +441,7 @@ def find_estimators(
             # 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))
+                target = layout.get_file(_resolve_intent(intent, layout, subject))
                 if target is None:
                     logger.debug("Single PE target %s not found", intent)
                     continue