brain_deer.infrastructure.io.mesh

Load cortical / anatomical surface meshes for 3D display (GIfTI, OBJ, STL, VTK, FreeSurfer ASCII).

Functions

apply_mesh_to_reference_space(→ vtk.vtkPolyData)	Map mesh vertices from NIfTI world mm into BrainDeer centred scene mm.
resolve_mesh_reference(→ Optional[tuple[tuple[int, ...)	Normalize a NIfTI image or explicit shape/spacing/affine into a scene reference.
load_mesh_for_3d(→ MeshLoadResult)	Load a surface mesh into vtkPolyData for Simple3DPlanes.

Module Contents

brain_deer.infrastructure.io.mesh.apply_mesh_to_reference_space(poly: vtk.vtkPolyData, *, reference_shape: tuple[int, int, int], reference_spacing: tuple[float, float, float], reference_affine: numpy.ndarray) → vtk.vtkPolyData

Map mesh vertices from NIfTI world mm into BrainDeer centred scene mm.

brain_deer.infrastructure.io.mesh.resolve_mesh_reference(*, reference_nifti: Any = None, reference_shape: tuple[int, int, int] | None = None, reference_spacing: tuple[float, float, float] | None = None, reference_affine: Any = None) → tuple[tuple[int, int, int], tuple[float, float, float], numpy.ndarray] | None

Normalize a NIfTI image or explicit shape/spacing/affine into a scene reference.

brain_deer.infrastructure.io.mesh.load_mesh_for_3d(path: str, *, center: bool = False, reference_nifti: Any = None, reference_shape: tuple[int, int, int] | None = None, reference_spacing: tuple[float, float, float] | None = None, reference_affine: Any = None, bake_reference_transform: bool = True) → MeshLoadResult

Load a surface mesh into vtkPolyData for Simple3DPlanes.

Vertices are treated as RAS+ world millimetres (same convention as NIfTI affines / FreeSurfer / GIfTI). When a reference is provided and bake_reference_transform is True, they are mapped into the centred VTK scene frame used by slice planes. Prefer leaving vertices in world mm and applying Simple3DPlanes.world_to_scene_user_matrix() on the actor when the reference volume may change.