From ce31460ca1a74170492fb0baff217fd0e7a40b80 Mon Sep 17 00:00:00 2001
From: Patrick Sadil <psadil@gmail.com>
Date: Tue, 1 Oct 2024 22:32:48 -0400
Subject: [PATCH] FIX: Repair search for precomputed transforms (#3369)

---
 fmriprep/data/io_spec.json                    |  4 +--
 fmriprep/utils/bids.py                        | 17 ++++++---
 fmriprep/utils/tests/test_derivative_cache.py | 36 +++++++++++++++++++
 3 files changed, 50 insertions(+), 7 deletions(-)
 create mode 100644 fmriprep/utils/tests/test_derivative_cache.py

diff --git a/fmriprep/data/io_spec.json b/fmriprep/data/io_spec.json
index 5d90f184c..364cff7e3 100644
--- a/fmriprep/data/io_spec.json
+++ b/fmriprep/data/io_spec.json
@@ -33,7 +33,7 @@
       },
       "boldref2anat": {
         "datatype": "func",
-        "from": "orig",
+        "from": "boldref",
         "to": "anat",
         "mode": "image",
         "suffix": "xfm",
@@ -41,7 +41,7 @@
       },
       "boldref2fmap": {
         "datatype": "func",
-        "from": "orig",
+        "from": "boldref",
         "mode": "image",
         "suffix": "xfm",
         "extension": ".txt"
diff --git a/fmriprep/utils/bids.py b/fmriprep/utils/bids.py
index 0bdc03ff1..b29275475 100644
--- a/fmriprep/utils/bids.py
+++ b/fmriprep/utils/bids.py
@@ -68,14 +68,21 @@ 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 = {**entities, **q}
+        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
 
 
diff --git a/fmriprep/utils/tests/test_derivative_cache.py b/fmriprep/utils/tests/test_derivative_cache.py
new file mode 100644
index 000000000..1a2c59acc
--- /dev/null
+++ b/fmriprep/utils/tests/test_derivative_cache.py
@@ -0,0 +1,36 @@
+from pathlib import Path
+
+import pytest
+
+from fmriprep.utils import bids
+
+
+@pytest.mark.parametrize('xfm', ['boldref2fmap', 'boldref2anat', 'hmc'])
+def test_transforms_found_as_str(tmp_path: Path, xfm: str):
+    subject = '0'
+    task = 'rest'
+    fromto = {
+        'hmc': 'from-orig_to-boldref',
+        'boldref2fmap': 'from-boldref_to-auto00000',
+        'boldref2anat': 'from-boldref_to-anat',
+    }[xfm]
+
+    to_find = tmp_path.joinpath(
+        f'sub-{subject}', 'func', f'sub-{subject}_task-{task}_{fromto}_mode-image_xfm.txt'
+    )
+    to_find.parent.mkdir(parents=True)
+    to_find.touch()
+
+    entities = {
+        'subject': subject,
+        'task': task,
+        'suffix': 'bold',
+        'extension': '.nii.gz',
+    }
+
+    derivs = bids.collect_derivatives(
+        derivatives_dir=tmp_path,
+        entities=entities,
+        fieldmap_id='auto_00000',
+    )
+    assert derivs == {'transforms': {xfm: str(to_find)}}