RF: Allow coordinate names to be set on init

Author: effigies

nibabel/pointset.py

@@ -169,17 +169,21 @@ def from_tuple(
         mesh: tuple[CoordinateArray, CoordinateArray],
         affine: np.ndarray | None = None,
         homogeneous: bool = False,
+        **kwargs,
     ) -> Self:
-        return cls(mesh[0], mesh[1], affine=affine, homogeneous=homogeneous)
+        return cls(mesh[0], mesh[1], affine=affine, homogeneous=homogeneous, **kwargs)
 
     @classmethod
     def from_object(
         cls,
         mesh: HasMeshAttrs,
         affine: np.ndarray | None = None,
         homogeneous: bool = False,
+        **kwargs,
     ) -> Self:
-        return cls(mesh.coordinates, mesh.triangles, affine=affine, homogeneous=homogeneous)
+        return cls(
+            mesh.coordinates, mesh.triangles, affine=affine, homogeneous=homogeneous, **kwargs
+        )
 
     @property
     def n_triangles(self):
@@ -198,9 +202,10 @@ def get_mesh(self, *, as_homogeneous: bool = False):
 
 
 class CoordinateFamilyMixin(Pointset):
-    def __init__(self, *args, **kwargs):
-        self._coords = {}
+    def __init__(self, *args, name='original', **kwargs):
+        mapping = kwargs.pop('mapping', {})
         super().__init__(*args, **kwargs)
+        self._coords = {name: self.coordinates, **mapping}
 
     def get_names(self):
         """List of surface names that can be passed to :meth:`with_name`"""

nibabel/tests/test_pointset.py

@@ -262,7 +262,7 @@ def __getitem__(self, slicer):
             return h5f[self.dataset_name][slicer]
 
 
-class H5Geometry(ps.TriangularMesh, ps.CoordinateFamilyMixin):
+class H5Geometry(ps.CoordinateFamilyMixin, ps.TriangularMesh):
     """Simple Geometry file structure that combines a single topology
     with one or more coordinate sets
     """
@@ -274,8 +274,7 @@ def from_filename(klass, pathlike):
             triangles = H5ArrayProxy(pathlike, '/topology')
             for name in h5f['coordinates']:
                 coords[name] = H5ArrayProxy(pathlike, f'/coordinates/{name}')
-        self = klass(next(iter(coords.values())), triangles)
-        self._coords.update(coords)
+        self = klass(next(iter(coords.values())), triangles, mapping=coords)
         return self
 
     def to_filename(self, pathlike):
@@ -336,13 +335,12 @@ def triangles(self):
         )
 
 
-class FreeSurferHemisphere(ps.TriangularMesh, ps.CoordinateFamilyMixin):
+class FreeSurferHemisphere(ps.CoordinateFamilyMixin, ps.TriangularMesh):
     @classmethod
     def from_filename(klass, pathlike):
         path = Path(pathlike)
         hemi, default = path.name.split('.')
-        self = klass.from_object(FSGeometryProxy(path))
-        self._coords[default] = self.coordinates
+        self = klass.from_object(FSGeometryProxy(path), name=default)
         mesh_names = (
             'orig',
             'white',
@@ -353,10 +351,12 @@ def from_filename(klass, pathlike):
             'midthickness',
             'graymid',
         )  # Often created
+
         for mesh in mesh_names:
-            fpath = path.parent / f'{hemi}.{mesh}'
-            if mesh not in self._coords and fpath.exists():
-                self.add_coordinates(mesh, FSGeometryProxy(fpath).coordinates)
+            if mesh != default:
+                fpath = path.parent / f'{hemi}.{mesh}'
+                if fpath.exists():
+                    self.add_coordinates(mesh, FSGeometryProxy(fpath).coordinates)
         return self