def create_face_geom(
coord_vals: SoCoordValsListType,
face_indices: SoIndicesListType,
face_color: SoVectorType,
transparency: float,
translation: SoVectorType = None,
quaternion: SoQuaternionType = None
) -> ThreeJSSceneGraphObjectListType:
"""
Returns a pythreejs `Mesh` object that consists of the faces given by
face_indices and the coord_vals.
Additionally the attributes `Mesh.default_material` and `Mesh.geometry.default_color`
will be set before returning the Mesh. Those attributes contain references to the
default colors and materials that are set in this function to restore later changes.
"""
vertices = np.asarray(coord_vals, dtype='float32')
faces = np.asarray(face_indices, dtype='uint16')
normals = compute_normals(faces, vertices)
faces = faces.ravel()
vertexcolors = np.asarray([face_color] * len(coord_vals), dtype='float32')
face_geometry = BufferGeometry(
attributes=dict(position=BufferAttribute(vertices, normalized=False),
index=BufferAttribute(faces, normalized=False),
normal=BufferAttribute(normals, normalized=False),
color=BufferAttribute(vertexcolors, normalized=False)))
# this is used for returning to original state after highlighting
face_geometry.default_color = vertexcolors
# BUG: This is a bug in pythreejs and currently does not work
#faceGeometry.exec_three_obj_method('computeFaceNormals')
#faceGeometry.exec_three_obj_method('computeVertexNormals')
col = so_col_to_hex(face_color)
material = MeshPhongMaterial(color=col,
transparency=transparency,
depthTest=True,
depthWrite=True,
metalness=0)
object_mesh = Mesh(
geometry=face_geometry,
material=material,
position=[0, 0, 0] # Center the cube
)
object_mesh.default_material = material
if quaternion:
object_mesh.quaternion = quaternion
if translation:
object_mesh.position = translation
return [object_mesh]
def _get_cylinder_from_vec(v0, v1, d_args=None):
"""Draw the cylinder given the two endpoints.
Args:
v0 (list): one endpoint of line
v1 (list): other endpoint of line
d_args (dict): properties of the line (line_width and color)
Returns:
Mesh: Pythreejs object that displays the cylinders
"""
obj_args = update_object_args(d_args, "Cylinders", ['radius', 'color'])
v0 = np.array(v0)
v1 = np.array(v1)
vec = v1 - v0
mid_point = (v0 + v1) / 2.0
rot_vec = np.cross([0, 1, 0], vec)
rot_vec_len = np.linalg.norm(rot_vec)
rot_vec = rot_vec / rot_vec_len
rot_arg = np.arccos(np.dot([0, 1, 0], vec) / np.linalg.norm(vec))
new_bond = Mesh(
geometry=CylinderBufferGeometry(
radiusTop=obj_args['radius'],
radiusBottom=obj_args['radius'],
height=np.linalg.norm(v1 - v0),
radialSegments=12,
heightSegments=10,
),
material=MeshLambertMaterial(color=obj_args['color']),
position=tuple(mid_point),
)
rot = R.from_rotvec(rot_arg * rot_vec)
quat = tuple(rot.as_quat())
if any(isnan(itr_q) for itr_q in quat):
new_bond.quaternion = (0, 0, 0, 0)
else:
new_bond.quaternion = quat
return new_bond
def _get_cylinder_from_vec(v0, v1, radius=0.15, color="#FFFFFF"):
v0 = np.array(v0)
v1 = np.array(v1)
vec = v1 - v0
mid_point = (v0 + v1) / 2.
rot_vec = np.cross([0, 1, 0], vec)
rot_vec_len = np.linalg.norm(rot_vec)
rot_vec = rot_vec / rot_vec_len
rot_arg = np.arccos(np.dot([0, 1, 0], vec) / np.linalg.norm(vec))
new_bond = Mesh(geometry=CylinderBufferGeometry(radiusTop=radius,
radiusBottom=radius,
height=np.linalg.norm(v1 -
v0),
radialSegments=12,
heightSegments=10),
material=MeshLambertMaterial(color=color),
position=tuple(mid_point))
rot = R.from_rotvec(rot_arg * rot_vec)
new_bond.quaternion = tuple(rot.as_quat())
return new_bond