ENH: Add interface to aggregate / sort surface files

Author: mgxd

smriprep/interfaces/surf.py

@@ -33,6 +33,8 @@
     SimpleInterface,
     File,
     isdefined,
+    InputMultiObject,
+    traits,
 )
 
 
@@ -114,6 +116,45 @@ def _run_interface(self, runtime):
         return runtime
 
 
+class AggregateSurfacesInputSpec(TraitedSpec):
+    surfaces = InputMultiObject(File(exists=True), desc="Input surfaces")
+    morphometrics = InputMultiObject(File(exists=True), desc="Input morphometrics")
+
+
+class AggregateSurfacesOutputSpec(TraitedSpec):
+    pial = traits.List(File(), maxlen=2, desc="Pial surfaces")
+    white = traits.List(File(), maxlen=2, desc="White surfaces")
+    inflated = traits.List(File(), maxlen=2, desc="Inflated surfaces")
+    midthickness = traits.List(File(), maxlen=2, desc="Midthickness (or graymid) surfaces")
+    thickness = traits.List(File(), maxlen=2, desc="Cortical thickness maps")
+    sulc = traits.List(File(), maxlen=2, desc="Sulcal depth maps")
+    curv = traits.List(File(), maxlen=2, desc="Curvature maps")
+
+
+class AggregateSurfaces(SimpleInterface):
+    """Aggregate and group surfaces & morphometrics into left/right pairs."""
+    input_spec = AggregateSurfacesInputSpec
+    output_spec = AggregateSurfacesOutputSpec
+
+    def _run_interface(self, runtime):
+        from collections import defaultdict
+        import os
+        import re
+
+        container = defaultdict(list)
+        inputs = (self.inputs.surfaces or []) + (self.inputs.morphometrics or [])
+        findre = re.compile(
+            r'(?:^|[^d])(?P<name>white|pial|inflated|midthickness|thickness|sulc|curv)'
+        )
+        for surface in sorted(inputs, key=os.path.basename):
+            match = findre.search(os.path.basename(surface))
+            if match:
+                container[match.group('name')].append(surface)
+        for name, files in container.items():
+            self._results[name] = files
+        return runtime
+
+
 def normalize_surfs(in_file: str, transform_file: str, newpath: Optional[str] = None) -> str:
     """
     Update GIFTI metadata and apply rigid coordinate correction.