Repair search for precomputed transforms

Author: psadil

fmriprep/utils/bids.py

@@ -68,14 +68,28 @@ 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}
+        # 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':
-            query['to'] = fieldmap_id
-        item = layout.get(return_type='filename', **q)
+            # 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 +1,44 @@
+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'
+    else:
+        to_find = f'sub-{entities['subject']}_task-{entities['task']} \
+            _from-{spec['from']}_to-{spec['to']}_mode-image_xfm.txt'
+
+    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))
+