FIX: Repair search for precomputed transforms

fmriprep/data/io_spec.json

@@ -41,7 +41,7 @@
       },
       "boldref2fmap": {
         "datatype": "func",
-        "from": "orig",
+        "from": "boldref",
         "mode": "image",
         "suffix": "xfm",
         "extension": ".txt"

fmriprep/utils/bids.py

@@ -68,14 +68,24 @@ def collect_derivatives(
             continue
         derivs_cache[f'{k}_boldref'] = item[0] if len(item) == 1 else item
 
+    transforms_cache = {}
     for xfm, q in spec['transforms'].items():
-        query = {**q, **entities}
-        if xfm == 'boldref2fmap':
-            query['to'] = fieldmap_id
-        item = layout.get(return_type='filename', **q)
+        # Transform extension will often not match provided entities
+        #   (e.g., ".nii.gz" vs ".txt").
+        # And transform suffixes will be "xfm",
+        #   whereas relevant src file will be "bold".
+        query = {
+            **q,
+            **{k: v for k, v in entities.items() if k not in ['suffix', 'extension']},
+        }
+        if xfm == 'boldref2fmap' and fieldmap_id:
+            # fieldmaps have ids like auto_00000
+            query['to'] = fieldmap_id.replace('_', '')
+        item = layout.get(return_type='filename', **query)
         if not item:
             continue
-        derivs_cache[xfm] = item[0] if len(item) == 1 else item
+        transforms_cache[xfm] = item[0] if len(item) == 1 else item
+    derivs_cache['transforms'] = transforms_cache
     return derivs_cache
 
 

fmriprep/utils/tests/test_derivative_cache.py

@@ -0,0 +1,41 @@
+import json
+from pathlib import Path
+
+import pytest
+
+from fmriprep.data import load as load_data
+from fmriprep.utils import bids
+
+
+@pytest.mark.parametrize('xfm', ['boldref2fmap', 'boldref2anat', 'hmc'])
+def test_transforms_found_as_str(tmp_path: Path, xfm: str):
+    spec = (
+        json.loads(load_data.readable('io_spec.json').read_text())
+        .get('queries')
+        .get('transforms')
+        .get(xfm)
+    )
+    entities = {
+        'subject': '0',
+        'task': 'rest',
+        'suffix': 'bold',
+        'extension': '.nii.gz',
+    }
+    if xfm == 'boldref2fmap':
+        to_find = f'sub-{entities["subject"]}_task-{entities["task"]}_from-{spec["from"]}_to-auto00000_mode-image_xfm.txt'  # noqa: E501
+    else:
+        to_find = f'sub-{entities["subject"]}_task-{entities["task"]}_from-{spec["from"]}_to-{spec["to"]}_mode-image_xfm.txt'  # noqa: E501
+
+    funcd = tmp_path / f'sub-{entities["subject"]}' / 'func'
+    funcd.mkdir(parents=True)
+    (funcd / to_find).touch()
+
+    derivs = bids.collect_derivatives(
+        derivatives_dir=tmp_path,
+        entities=entities,
+        fieldmap_id='auto_00000',
+    )
+    transforms_in_derivs = 'transforms' in derivs
+    xfm_in_transforms = xfm in derivs.get('transforms')
+    transform_is_str = isinstance(derivs.get('transforms').get(xfm), str)
+    assert all((transforms_in_derivs, xfm_in_transforms, transform_is_str))