ENH: Tag structural workflows

Author: mgxd

pyproject.toml

@@ -26,7 +26,7 @@ dependencies = [
     "matplotlib >= 3.5",
     "nibabel >= 4.0.1",
     "nipype >= 1.8.5",
-    "niworkflows >= 1.12.1",
+    "niworkflows @ git+https://github.com/nipreps/niworkflows.git@master",
     "numpy >= 1.24",
     "packaging >= 24",
     "pybids >= 0.16",

src/smriprep/workflows/anatomical.py

@@ -39,7 +39,7 @@
 from nipype.interfaces.ants.base import Info as ANTsInfo
 from nipype.pipeline import engine as pe
 from niworkflows.anat.ants import init_brain_extraction_wf, init_n4_only_wf
-from niworkflows.engine.workflows import LiterateWorkflow as Workflow
+from niworkflows.engine import Workflow, tag
 from niworkflows.interfaces.fixes import FixHeaderApplyTransforms as ApplyTransforms
 from niworkflows.interfaces.freesurfer import (
     PatchedLTAConvert as LTAConvert,
@@ -463,6 +463,7 @@ def init_anat_preproc_wf(
     return workflow
 
 
+@tag('anat.fit')
 def init_anat_fit_wf(
     *,
     bids_root: str,

src/smriprep/workflows/outputs.py

@@ -26,7 +26,7 @@
 
 from nipype.interfaces import utility as niu
 from nipype.pipeline import engine as pe
-from niworkflows.engine.workflows import LiterateWorkflow as Workflow
+from niworkflows.engine import Workflow, tag
 from niworkflows.interfaces.fixes import FixHeaderApplyTransforms as ApplyTransforms
 from niworkflows.interfaces.nibabel import ApplyMask, GenerateSamplingReference
 from niworkflows.interfaces.space import SpaceDataSource
@@ -41,6 +41,7 @@
 BIDS_TISSUE_ORDER = ('GM', 'WM', 'CSF')
 
 
+@tag('anat.reports')
 def init_anat_reports_wf(*, spaces, freesurfer, output_dir, sloppy=False, name='anat_reports_wf'):
     """
     Set up a battery of datasinks to store reports in the right location.

src/smriprep/workflows/surfaces.py

@@ -35,7 +35,7 @@
 from nipype.interfaces import utility as niu
 from nipype.interfaces.base import Undefined
 from nipype.pipeline import engine as pe
-from niworkflows.engine.workflows import LiterateWorkflow as Workflow
+from niworkflows.engine import Workflow, tag
 from niworkflows.interfaces.freesurfer import (
     FSDetectInputs,
     FSInjectBrainExtracted,
@@ -62,6 +62,7 @@
 from ..interfaces.workbench import CreateSignedDistanceVolume
 
 
+@tag('anat.recon')
 def init_surface_recon_wf(
     *,
     omp_nthreads: int,
@@ -329,6 +330,7 @@ def init_surface_recon_wf(
     return workflow
 
 
+@tag('anat.mask-refine')
 def init_refinement_wf(
     *, image_type: ty.Literal['T1w', 'T2w'] = 'T1w', name: str = 'refinement_wf'
 ) -> Workflow:
@@ -420,6 +422,7 @@ def init_refinement_wf(
     return workflow
 
 
+@tag('anat.fs-autorecon-resume')
 def init_autorecon_resume_wf(*, omp_nthreads, name='autorecon_resume_wf'):
     r"""
     Resume recon-all execution, assuming the `-autorecon1` stage has been completed.
@@ -569,7 +572,6 @@ def _dedup(in_list):
             raise ValueError(f"Non-identical values can't be deduplicated:\n{in_list!r}")
         return vals.pop()
 
-    # fmt:off
     workflow.connect([
         (inputnode, cortribbon, [('use_T2', 'use_T2'),
                                  ('use_FLAIR', 'use_FLAIR')]),
@@ -587,12 +589,12 @@ def _dedup(in_list):
                                  (('subject_id', _dedup), 'subject_id')]),
         (autorecon3, outputnode, [('subjects_dir', 'subjects_dir'),
                                   ('subject_id', 'subject_id')]),
-    ])
-    # fmt:on
+    ])  # fmt:skip
 
     return workflow
 
 
+@tag('anat.surface-derivatives')
 def init_surface_derivatives_wf(
     *,
     image_type: ty.Literal['T1w', 'T2w'] = 'T1w',
@@ -703,6 +705,7 @@ def init_surface_derivatives_wf(
     return workflow
 
 
+@tag('anat.fslr-reg')
 def init_fsLR_reg_wf(*, name='fsLR_reg_wf'):
     """Generate GIFTI registration files to fsLR space"""
     from ..interfaces.workbench import SurfaceSphereProjectUnproject
@@ -743,6 +746,7 @@ def init_fsLR_reg_wf(*, name='fsLR_reg_wf'):
     return workflow
 
 
+@tag('anat.msm-sulc')
 def init_msm_sulc_wf(*, sloppy: bool = False, name: str = 'msm_sulc_wf'):
     """Run MSMSulc registration to fsLR surfaces, per hemisphere."""
     from ..interfaces.msm import MSM
@@ -835,6 +839,7 @@ def init_msm_sulc_wf(*, sloppy: bool = False, name: str = 'msm_sulc_wf'):
     return workflow
 
 
+@tag('anat.gifti-surfaces')
 def init_gifti_surfaces_wf(
     *,
     surfaces: list[str] = ('pial', 'midthickness', 'inflated', 'white'),
@@ -932,6 +937,7 @@ def init_gifti_surfaces_wf(
     return workflow
 
 
+@tag('anat.gifti-morphs')
 def init_gifti_morphometrics_wf(
     *,
     morphometrics: list[str] = ('thickness', 'curv', 'sulc'),
@@ -1024,6 +1030,7 @@ def init_gifti_morphometrics_wf(
     return workflow
 
 
+@tag('anat.hcp-morphs')
 def init_hcp_morphometrics_wf(
     *,
     omp_nthreads: int,
@@ -1167,6 +1174,7 @@ def init_hcp_morphometrics_wf(
     return workflow
 
 
+@tag('anat.segs-to-anat')
 def init_segs_to_native_wf(
     *,
     image_type: ty.Literal['T1w', 'T2w'] = 'T1w',
@@ -1247,6 +1255,7 @@ def init_segs_to_native_wf(
     return workflow
 
 
+@tag('anat.ribbon-mask')
 def init_anat_ribbon_wf(name='anat_ribbon_wf'):
     """Create anatomical ribbon mask
 
@@ -1296,26 +1305,23 @@ def init_anat_ribbon_wf(name='anat_ribbon_wf'):
 
     make_ribbon = pe.Node(MakeRibbon(), name='make_ribbon', mem_gb=DEFAULT_MEMORY_MIN_GB)
 
-    # fmt: off
-    workflow.connect(
-        [
-            (inputnode, create_wm_distvol, [
-                ('white', 'surf_file'),
-                ('ref_file', 'ref_file'),
-            ]),
-            (inputnode, create_pial_distvol, [
-                ('pial', 'surf_file'),
-                ('ref_file', 'ref_file'),
-            ]),
-            (create_wm_distvol, make_ribbon, [('out_file', 'white_distvols')]),
-            (create_pial_distvol, make_ribbon, [('out_file', 'pial_distvols')]),
-            (make_ribbon, outputnode, [('ribbon', 'anat_ribbon')]),
-        ]
-    )
-    # fmt: on
+    workflow.connect([
+        (inputnode, create_wm_distvol, [
+            ('white', 'surf_file'),
+            ('ref_file', 'ref_file'),
+        ]),
+        (inputnode, create_pial_distvol, [
+            ('pial', 'surf_file'),
+            ('ref_file', 'ref_file'),
+        ]),
+        (create_wm_distvol, make_ribbon, [('out_file', 'white_distvols')]),
+        (create_pial_distvol, make_ribbon, [('out_file', 'pial_distvols')]),
+        (make_ribbon, outputnode, [('ribbon', 'anat_ribbon')]),
+    ])  # fmt:skip
     return workflow
 
 
+@tag('anat.resample-surfs')
 def init_resample_surfaces_wf(
     surfaces: list[str],
     grayord_density: ty.Literal['91k', '170k'],
@@ -1423,6 +1429,7 @@ def init_resample_surfaces_wf(
     return workflow
 
 
+@tag('anat.resample-morphs-grayords')
 def init_morph_grayords_wf(
     grayord_density: ty.Literal['91k', '170k'],
     omp_nthreads: int,
@@ -1636,10 +1643,6 @@ def _sorted_by_basename(inlist):
     return sorted(inlist, key=lambda x: str(basename(x)))
 
 
-def _collate(files):
-    return [files[i : i + 2] for i in range(0, len(files), 2)]
-
-
 def _extract_fs_fields(filenames: str | list[str]) -> tuple[str, str]:
     from pathlib import Path