`interface_trimesh` - interface with `trimesh`

Convert ObjMesh to trimesh’s mesh class.

convert_to_trimesh


def convert_to_trimesh(
    mesh:ObjMesh,
    add_texture_info:NoneType=None, # Whether to add texture info to the trimesh.Trimesh. If None, texture is added if
available for at least one vertex.
)->Trimesh:

Convert tcmesh.ObjMesh to trimesh.Trimesh

See https://trimesh.org/trimesh.base.html Note: normal information is recalculated. Discards any non-triangle faces.

Texture is saved as a vertex attribute via v_tex_coords_matrix. Note that this discards information since a vertex can have multiple texture coordinates! For this reason, we also add the texture coordinates as a (n_faces, 3, s)-array attribute face_tex. Note: this will not be updated if you remesh etc.

mesh_fname_data = "datasets/registration_example/Drosophila_CAAX-mCherry_mesh_remeshed.obj"
mesh_fname_ref = "datasets/registration_example/Drosophila_reference.obj"
mesh_data = tcmesh.ObjMesh.read_obj(mesh_fname_data)
mesh_ref = tcmesh.ObjMesh.read_obj(mesh_fname_ref)

Warning: readOBJ() ignored non-comment line 4:
  o embryo_rect

trimesh_data = convert_to_trimesh(mesh_data)
np.allclose(mesh_data.vertices, trimesh_data.vertices)

True

trimesh_normals = trimesh_data.vertex_normals
trimesh_normals = (trimesh_normals.T / np.linalg.norm(trimesh_normals, axis=-1)).T

np.einsum('vi,vi->v', mesh_data.normals, trimesh_normals)

array([6.27953731, 6.26481851, 6.27572446, ..., 6.24734426, 6.22183872,
       6.25817202])

convert_from_trimesh


def convert_from_trimesh(
    mesh:Trimesh,
    reconstruct_texture_from_faces:bool=True, # Whether to reconstruct texture information from per-face data (True), or
per-vertex data (False)
    texture_vertex_decimals:int=10, # Texture vertices are rounded to texture_vertex_decimals decimals.
)->ObjMesh:

Convert trimesh mesh to ObjMesh.

Texture vertices can be reconstructed from face attribute face_tex or from vertex attribute vertex_tex_coord_matrix. Reconstruction from face texture can accommodate multiple texture coordinates per vertex (e.g. for UV maps with seams).

trimesh_ref = convert_to_trimesh(mesh_ref)

mesh_seams = tcmesh.ObjMesh.read_obj("datasets/drosophila_example/Drosophila_CAAX-mCherry_mesh_uv.obj")
trimesh_seams = convert_to_trimesh(mesh_seams,add_texture_info=True)

Warning: readOBJ() ignored non-comment line 4:
  o Drosophila_CAAX-mCherry_mesh_remeshed
Warning: readOBJ() ignored non-comment line 48073:
  l 2534 8160
/home/nikolas/Programs/miniconda3/envs/blender-tissue-cartography/lib/python3.11/site-packages/trimesh/grouping.py:99: RuntimeWarning: invalid value encountered in cast
  stacked = np.column_stack(stacked).round().astype(np.int64)

convert_from_trimesh(trimesh_seams, reconstruct_texture_from_faces=False).texture_vertices.shape, mesh_seams.texture_vertices.shape

((8159, 2), (8288, 2))