Merge pull request #386 from effigies/enh/multithread-mrisexpand

ENH: Annotate mris_expand with thread usage

smriprep/interfaces/freesurfer.py

@@ -293,13 +293,21 @@ def _gen_filename(self, name):
         return super()._gen_filename(name)
 
 
-class MakeMidthickness(nwfs.MakeMidthickness):
+class MakeMidthicknessInputSpec(nwfs._MakeMidthicknessInputSpec, fs.base.FSTraitedSpecOpenMP):
+    pass
+
+
+class MakeMidthickness(nwfs.MakeMidthickness, fs.base.FSCommandOpenMP):
     """Patched MakeMidthickness interface
 
     Ensures output filenames are specified with hemisphere labels, when appropriate.
     This may not cover all use-cases in MRIsExpand, but we're just making midthickness
     files.
 
+    This interface also sets the OMP_NUM_THREADS environment variable to floor(1.5x) the
+    number of threads requested by the user, as tests indicate that cores are underutilized
+    by a factor of 2/3.
+
     >>> from smriprep.interfaces.freesurfer import MakeMidthickness
     >>> mris_expand = MakeMidthickness(thickness=True, distance=0.5)
     >>> mris_expand.inputs.in_file = 'lh.white'
@@ -316,9 +324,17 @@ class MakeMidthickness(nwfs.MakeMidthickness):
     'mris_expand -thickness lh.white 0.5 rh.graymid'
     """
 
+    input_spec = MakeMidthicknessInputSpec
+
     def _format_arg(self, name, trait_spec, value):
         # FreeSurfer at some point changed whether it would add the hemi label onto the
         # surface. Therefore we'll do it ourselves.
         if name == "out_name":
             value = self._associated_file(self.inputs.in_file, value)
         return super()._format_arg(name, trait_spec, value)
+
+    def _num_threads_update(self):
+        if self.inputs.num_threads:
+            self.inputs.environ.update(
+                {"OMP_NUM_THREADS": str(self.inputs.num_threads * 3 // 2)}
+            )

smriprep/workflows/surfaces.py

@@ -220,6 +220,7 @@ def init_surface_recon_wf(
         MakeMidthickness(thickness=True, distance=0.5, out_name="midthickness"),
         iterfield="in_file",
         name="midthickness",
+        n_procs=min(omp_nthreads, 12),
     )
 
     save_midthickness = pe.Node(nio.DataSink(parameterization=False), name="save_midthickness")
@@ -232,7 +233,6 @@ def init_surface_recon_wf(
         name="sync",
     )
 
-    # fmt:off
     workflow.connect([
         # Configuration
         (inputnode, recon_config, [('t1w', 't1w_list'),
@@ -275,21 +275,18 @@ def init_surface_recon_wf(
         (save_midthickness, sync, [('out_file', 'filenames')]),
         (sync, outputnode, [('subjects_dir', 'subjects_dir'),
                             ('subject_id', 'subject_id')]),
-    ])
-    # fmt:on
+    ])  # fmt:skip
 
     if "fsnative" not in precomputed.get("transforms", {}):
         fsnative2t1w_xfm = pe.Node(
             RobustRegister(auto_sens=True, est_int_scale=True), name="fsnative2t1w_xfm"
         )
 
-        # fmt:off
         workflow.connect([
             (inputnode, fsnative2t1w_xfm, [('t1w', 'target_file')]),
             (autorecon1, fsnative2t1w_xfm, [('T1', 'source_file')]),
             (fsnative2t1w_xfm, outputnode, [('out_reg_file', 'fsnative2t1w_xfm')]),
-        ])
-        # fmt:on
+        ])  # fmt:skip
 
     return workflow