Sep 19, 2023 · Sep 20, 2023 · Sep 20, 2023 · Sep 20, 2023 · Sep 20, 2023 · Sep 22, 2023
diff --git a/nibabel/pointset.py b/nibabel/pointset.py
        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):


 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`"""
diff --git a/nibabel/tests/test_pointset.py b/nibabel/tests/test_pointset.py
            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
    """
            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):
        )


 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',
            '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
Original file line number	Diff line number	Diff line change
Expand Up		@@ -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):
Expand All		@@ -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`"""
Expand Down
Original file line number	Diff line number	Diff line change
Expand Up		@@ -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
		"""
Expand All		@@ -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):
Expand DownExpand Up		@@ -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',
Expand All		@@ -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


Expand Down