FIX: refmask source files and test

Author: mnoergaard

petprep/workflows/pet/fit.py

@@ -492,13 +492,14 @@ def init_pet_fit_wf(
                     ds_refmask_wf,
                     [
                         ('segmentation', 'inputnode.segmentation'),
+                        ('t1w_preproc', 'inputnode.anat_sources'),
                     ],
                 ),
                 (
-                    petref_buffer,
+                    gm_select,
                     ds_refmask_wf,
                     [
-                        ('pet_file', 'inputnode.source_files'),
+                        ('out', 'inputnode.source_files'),
                     ],
                 ),
                 (

petprep/workflows/pet/outputs.py

@@ -493,12 +493,14 @@ def init_ds_refmask_wf(
     workflow = pe.Workflow(name=name)
 
     inputnode = pe.Node(
-        niu.IdentityInterface(fields=['source_files', 'segmentation', 'refmask']),
+        niu.IdentityInterface(
+            fields=['source_files', 'anat_sources', 'segmentation', 'refmask']
+        ),
         name='inputnode',
     )
     outputnode = pe.Node(niu.IdentityInterface(fields=['refmask']), name='outputnode')
 
-    merge_source_files = pe.Node(niu.Merge(2), name='merge_source_files')
+    merge_source_files = pe.Node(niu.Merge(3), name='merge_source_files')
 
     sources = pe.Node(
         BIDSURI(
@@ -526,7 +528,8 @@ def init_ds_refmask_wf(
     workflow.connect([
         (inputnode, merge_source_files, [
             ('source_files', 'in1'),
-            ('segmentation', 'in2'),
+            ('anat_sources', 'in2'),
+            ('segmentation', 'in3'),
         ]),
         (merge_source_files, sources, [('out', 'in1')]),
         (inputnode, ds_refmask, [

petprep/workflows/pet/tests/test_outputs.py

@@ -1,3 +1,4 @@
+import json
 from pathlib import Path
 
 import nibabel as nb
@@ -52,3 +53,41 @@ def test_datasink_datatype(tmp_path: Path):
         assert wf.get_node('ds_pet').inputs.datatype == 'pet'
         assert wf.get_node('ds_ref').inputs.datatype == 'pet'
         assert wf.get_node('ds_mask').inputs.datatype == 'pet'
+
+
+def test_refmask_sources(tmp_path: Path):
+    bids_dir = _prep_bids(tmp_path)
+    out_dir = tmp_path / 'out'
+    gm_file = bids_dir / 'sub-01' / 'anat' / 'sub-01_label-GM_probseg.nii.gz'
+    seg_file = bids_dir / 'sub-01' / 'anat' / 'sub-01_desc-aparcaseg_dseg.nii.gz'
+    refmask_file = tmp_path / 'refmask.nii.gz'
+
+    img = nb.Nifti1Image(np.zeros((2, 2, 2)), np.eye(4))
+    for path in (gm_file, seg_file, refmask_file):
+        path.parent.mkdir(parents=True, exist_ok=True)
+        img.to_filename(path)
+
+    t1_file = bids_dir / 'sub-01' / 'anat' / 'sub-01_T1w.nii.gz'
+
+    with mock_config(bids_dir=bids_dir):
+        wf = init_ds_refmask_wf(output_dir=out_dir, ref_name='test')
+        wf.base_dir = tmp_path / 'work'
+
+        inputnode = wf.get_node('inputnode')
+        inputnode.inputs.source_files = str(gm_file)
+        inputnode.inputs.anat_sources = str(t1_file)
+        inputnode.inputs.segmentation = str(seg_file)
+        inputnode.inputs.refmask = str(refmask_file)
+
+        wf.run()
+
+        out_files = list(out_dir.rglob('*desc-refmask*_mask.nii.gz'))
+        assert out_files, 'Reference mask derivative was not generated'
+        out_file = Path(out_files[0])
+        metadata = json.loads(out_file.with_suffix('').with_suffix('.json').read_text())
+        sources = metadata.get('Sources', [])
+
+        assert any('label-GM_probseg' in src for src in sources)
+        assert any('T1w' in src for src in sources)
+        assert any('dseg' in src for src in sources)
+        assert all('/pet/' not in src for src in sources)