FIX: Remove segmentation and dseg_tsv from outputnode

Author: mnoergaard

petprep/workflows/pet/base.py

@@ -399,9 +399,7 @@ def init_pet_wf(
                 ('t1w_tpms', 'inputnode.t1w_tpms'),
                 ('subjects_dir', 'inputnode.subjects_dir'),
                 ('subject_id', 'inputnode.subject_id'),
-            ]),
-            (pet_fit_wf, pet_pvc_wf, [
-                ('outputnode.segmentation', 'inputnode.segmentation'),
+                ('segmentation', 'inputnode.segmentation'),
             ]),
             (petref_t1w, pet_pvc_wf, [('output_image', 'inputnode.petref')]),
             (pet_pvc_wf, psf_meta, [
@@ -719,9 +717,9 @@ def init_pet_wf(
 
     workflow.connect([
         (pet_t1w_src, pet_tacs_wf, [(pet_t1w_field, 'inputnode.pet_anat')]),
-        (pet_fit_wf, pet_tacs_wf, [
-            ('outputnode.segmentation', 'inputnode.segmentation'),
-            ('outputnode.dseg_tsv', 'inputnode.dseg_tsv'),
+        (inputnode, pet_tacs_wf, [
+            ('segmentation', 'inputnode.segmentation'),
+            ('dseg_tsv', 'inputnode.dseg_tsv'),
         ]),
         (pet_tacs_wf, ds_pet_tacs, [('outputnode.timeseries', 'in_file')]),
     ])  # fmt:skip

petprep/workflows/pet/fit.py

@@ -119,10 +119,6 @@ def init_pet_fit_wf(
     petref2anat_xfm
         Affine transform mapping from PET reference space to the anatomical
         space.
-    segmentation
-        Segmentation file in T1w space
-    dseg_tsv
-        TSV with segmentation statistics
 
     See Also
     --------
@@ -191,8 +187,6 @@ def init_pet_fit_wf(
                 'pet_mask',
                 'motion_xfm',
                 'petref2anat_xfm',
-                'segmentation',
-                'dseg_tsv',
                 'refmask',
             ],
         ),
@@ -201,11 +195,6 @@ def init_pet_fit_wf(
 
     # If all derivatives exist, inputnode could go unconnected, so add explicitly
     workflow.add_nodes([inputnode])
-    workflow.connect(
-        [
-            (inputnode, outputnode, [('segmentation', 'segmentation'), ('dseg_tsv', 'dseg_tsv')]),
-        ]
-    )
 
     petref_buffer = pe.Node(
         niu.IdentityInterface(fields=['petref', 'pet_file']),

petprep/workflows/pet/tests/test_base.py

@@ -205,8 +205,8 @@ def test_pvc_receives_segmentation(bids_root: Path):
 
         wf = init_pet_wf(pet_series=pet_series, precomputed={})
 
-    edge = wf._graph.get_edge_data(wf.get_node('pet_fit_wf'), wf.get_node('pet_pvc_wf'))
-    assert ('outputnode.segmentation', 'inputnode.segmentation') in edge['connect']
+    edge = wf._graph.get_edge_data(wf.get_node('inputnode'), wf.get_node('pet_pvc_wf'))
+    assert ('segmentation', 'inputnode.segmentation') in edge['connect']
 
 
 def test_pet_tacs_wf_connections(bids_root: Path):
@@ -226,9 +226,9 @@ def test_pet_tacs_wf_connections(bids_root: Path):
     edge_anat = wf._graph.get_edge_data(wf.get_node('pet_anat_wf'), wf.get_node('pet_tacs_wf'))
     assert ('outputnode.pet_file', 'inputnode.pet_anat') in edge_anat['connect']
 
-    edge_fit = wf._graph.get_edge_data(wf.get_node('pet_fit_wf'), wf.get_node('pet_tacs_wf'))
-    assert ('outputnode.segmentation', 'inputnode.segmentation') in edge_fit['connect']
-    assert ('outputnode.dseg_tsv', 'inputnode.dseg_tsv') in edge_fit['connect']
+    edge_input = wf._graph.get_edge_data(wf.get_node('inputnode'), wf.get_node('pet_tacs_wf'))
+    assert ('segmentation', 'inputnode.segmentation') in edge_input['connect']
+    assert ('dseg_tsv', 'inputnode.dseg_tsv') in edge_input['connect']
 
     edge_ds = wf._graph.get_edge_data(wf.get_node('pet_tacs_wf'), wf.get_node('ds_pet_tacs'))
     assert ('outputnode.timeseries', 'in_file') in edge_ds['connect']