def callback_f(change):
"""
This functions implements highlighting and displaying the name
of selected faces and edges as well as vertices. You seemingly can't
select nothing, it only triggers on objects.
"""
value = picker.object
value_freecad_name = freecad_name_from_obj3d(value)
last_value = picker.last_object
if value is None:
if not (last_value is None):
reset_object_highlighting(last_value)
html.value = "<b>No selection.</b>"
return
if isinstance(value, Line):
if not (last_value is None):
reset_object_highlighting(last_value)
value.material.color = so_col_to_hex(HIGHLIGHTING_COLOR)
html.value = "{} <b>Edge{}</b>".format(value_freecad_name,
value.edge_index)
return
face_index = int(picker.faceIndex)
part_index = part_index_by_name(get_name(value), part_indices)
shape_face_index = index_by_face_index(part_index, face_index)
if not (last_value is None):
# check for case of selecting the same freecad face
if (last_value.name == value.name) and (picker.shape_face_index_old
== shape_face_index):
return
reset_object_highlighting(last_value)
face_indices = value.geometry.attributes["index"].array
cols_default = value.geometry.default_color
cols_highlighted = vertices_col_highlight_face(shape_face_index,
cols_default,
part_index,
face_indices)
value.geometry.attributes["color"].array = cols_highlighted
value.geometry.attributes["color"].needsUpdate = True
material = MeshLambertMaterial(vertexColors='VertexColors',
shininess=1)
material.name = value.material.color
value.material = material
picker.shape_face_index_old = shape_face_index
picker.last_object = value
html.value = "{} <b>Face{}</b>".format(value_freecad_name,
shape_face_index)
def convert_object_to_pythreejs(object):
"""
Cases for the conversion
:return:
"""
obs = []
if object["type"] == "spheres":
for ipos in object["positions"]:
obj3d = Mesh(
geometry=SphereBufferGeometry(radius=object["radius"],
widthSegments=32,
heightSegments=16),
material=MeshLambertMaterial(color=object["color"]),
position=ipos,
)
obs.append(obj3d)
elif object["type"] == "cylinders":
for ipos in object["positionPairs"]:
obj3d = _get_cylinder_from_vec(ipos[0],
ipos[1],
color=object["color"])
obs.append(obj3d)
elif object["type"] == "lines":
for ipos, jpos in zip(object["positions"][::2],
object["positions"][1::2]):
obj3d = _get_line_from_vec(ipos, jpos)
obs.append(obj3d)
else:
warnings.warn(
f"Primitive type {object['type']} has not been implemented for this renderer."
)
return obs
def virtualHelixMesh(pos1,
pos2,
radius: float = 1.0,
color: str = 'red') -> Mesh:
pos1 = np.array(pos1, dtype=float)
pos2 = np.array(pos2, dtype=float)
delta = pos2 - pos1
dist = np.linalg.norm(delta)
c_geometry = CylinderBufferGeometry(radiusTop=radius,
radiusBottom=radius,
height=dist,
radiusSegments=16)
# print(c_geometry.height)
v2 = normalize(delta)
# NOTE default direction in Three.js is the Y direction for geometry
v1 = np.array((0, 1, 0))
# Calculate angle between Vectors
angle = math.atan2(np.dot(np.cross(v1, v2), v1), np.dot(v1, v2))
normal_vec = normalize(np.cross(v1, v2)).tolist()
mid_point = (pos2 + pos1) / 2
xAxis = [mid_point[0], 0, 0]
yAxis = [0, mid_point[1], 0]
zAxis = [0, 0, mid_point[2]]
mesh = Mesh(geometry=c_geometry, material=MeshLambertMaterial(color=color))
rotm = rotationMatrix(v2)
mesh.setRotationFromMatrix(threeMatrix(rotm))
mesh.position = mid_point.tolist()
return mesh, mid_point
def convert_object_to_pythreejs(object):
"""
Cases for the conversion
:return:
"""
obs = []
if object['type'] == 'spheres':
for ipos in object['positions']:
obj3d = Mesh(geometry=SphereBufferGeometry(radius=object['radius'],
widthSegments=32,
heightSegments=16),
material=MeshLambertMaterial(color=object["color"]),
position=ipos)
obs.append(obj3d)
elif object['type'] == 'cylinders':
for ipos in object['positionPairs']:
obj3d = _get_cylinder_from_vec(ipos[0],
ipos[1],
color=object['color'])
obs.append(obj3d)
elif object['type'] == 'lines':
for ipos, jpos in zip(object['positions'][::2],
object['positions'][1::2]):
obj3d = _get_line_from_vec(ipos, jpos)
obs.append(obj3d)
return obs
def pseudomaterial_render(atoms):
c = cm.get_cmap("plasma")
scale_axis_vertices = [[-1, -1, -1], [9, -1, -1]]
scale_line_geom = Geometry(vertices=scale_axis_vertices,
colors=['black'] * len(scale_axis_vertices))
scale_lines = Line(
geometry=scale_line_geom,
material=LineBasicMaterial(linewidth=50, vertexColors='VertexColors'),
type='LinePieces',
)
a = atoms.a[1]
cube_vertices = [[0, 0, 0], [a, 0, 0], [a, 0, a], [a, 0, 0], [a, a, 0],
[a, a, a], [a, a, 0], [0, a, 0], [0, a, a], [0, a, 0],
[0, 0, 0], [0, 0, a], [a, 0, a], [a, a, a], [0, a, a],
[0, 0, a]]
linesgeom = Geometry(vertices=cube_vertices,
colors=['black'] * len(cube_vertices))
lines = Line(
geometry=linesgeom,
material=LineBasicMaterial(linewidth=5, vertexColors='VertexColors'),
type='LinePieces',
)
balls = []
for p in atoms.itertuples():
positions = (p.x * p.a, p.y * p.a, p.z * p.a)
new_ball = Mesh(
geometry=SphereGeometry(radius=p.sigma,
widthSegments=32,
heightSegments=24),
material=MeshLambertMaterial(color=rgb2hex(c(p.epsilon_norm))),
position=positions)
balls.append(new_ball)
# [scale*2*a,scale*2*a,scale*2*a]
camera = PerspectiveCamera(position=[25, a, a],
up=[0, 1, 0],
children=[
DirectionalLight(color='white',
position=[3, 5, 1],
intensity=0.5)
])
scene = Scene(children=[
scale_lines, lines, *balls, camera,
AmbientLight(color='#777')
])
renderer = Renderer(
camera=camera,
scene=scene,
controls=[OrbitControls(controlling=camera, target=[a, a, a])])
return renderer
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
def _get_spheres(ctk_scene, d_args=None):
if ctk_scene.phiEnd and ctk_scene.phiStart:
phi_length = ctk_scene.phiEnd - ctk_scene.phiStart
else:
phi_length = np.pi * 2
return [
Mesh(
geometry=SphereBufferGeometry(
radius=ctk_scene.radius,
phiStart=ctk_scene.phiStart or 0,
phiLength=phi_length,
widthSegments=32,
heightSegments=32,
),
material=MeshLambertMaterial(color=ctk_scene.color),
position=tuple(ipos),
) for ipos in ctk_scene.positions
]
def _get_surface_from_positions(positions, d_args, draw_edges=False):
# get defaults
obj_args = update_object_args(d_args, "Surfaces", ["color", "opacity"])
num_triangle = len(positions) / 3.0
assert num_triangle.is_integer()
# make decision on transparency
if obj_args["opacity"] > 0.99:
transparent = False
else:
transparent = True
num_triangle = int(num_triangle)
index_list = [[itr * 3, itr * 3 + 1, itr * 3 + 2]
for itr in range(num_triangle)]
# Vertex ositions as a list of lists
surf_vertices = BufferAttribute(array=positions, normalized=False)
# Indices
surf_indices = BufferAttribute(array=np.array(index_list,
dtype=np.uint16).ravel(),
normalized=False)
geometry = BufferGeometry(attributes={
"position": surf_vertices,
"index": surf_indices
})
new_surface = Mesh(
geometry=geometry,
material=MeshLambertMaterial(
color=obj_args["color"],
side="DoubleSide",
transparent=transparent,
opacity=obj_args["opacity"],
),
)
if draw_edges == True:
edges = EdgesGeometry(geometry)
edges_lines = LineSegments(edges,
LineBasicMaterial(color=obj_args["color"]))
return new_surface, edges_lines
else:
return new_surface, None
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 __init__(self, color='red', radius=0.025):
Mesh.__init__(self,
geometry=SphereGeometry(radius=radius),
material=MeshLambertMaterial(color=color))
"""
Link up the StructureMoleculeComponent objects to pythreejs
Also includes some helper functions for draw addition objects using pythreejs
"""
from pythreejs import MeshLambertMaterial, Mesh, SphereBufferGeometry, CylinderBufferGeometry, Object3D, LineSegments2, LineSegmentsGeometry, LineMaterial, Scene, AmbientLight, Renderer, OrbitControls, OrthographicCamera, DirectionalLight
from crystal_toolkit.components.structure import StructureMoleculeComponent
from IPython.display import display
from scipy.spatial.transform import Rotation as R
import numpy as np
ball = Mesh(geometry=SphereBufferGeometry(radius=1,
widthSegments=32,
heightSegments=16),
material=MeshLambertMaterial(color='red'),
position=[0, 1, 0])
def traverse_scene_object(scene_data, parent=None):
"""
Recursivesly populate a scene object with tree of children
:param scene_data:
:param parent:
:return:
"""
for sub_object in scene_data["contents"]:
if "type" in sub_object.keys():
parent.add(convert_object_to_pythreejs(sub_object))
else:
new_parent = Object3D(name=sub_object["name"])
if parent is None:
parent = new_parent
def __init__(self,
mesh: trimesh.Trimesh = None,
obj: str = None,
normalize: bool =False,
color: Union[str,ColorRGB] ="#00bbee",
alpha: float=1.,
transform: Union[Callable, None] = None,
*args,
**kwargs
):
"""
Add a mesh to the scene.
Arguments:
mesh: Mesh object, with attributes verticies, faces
obj: object filename
normalize : Normalize the coordinates of the vertices
to be between -1 and 1
color: Color for the mesh
alpha: transparency of the mesh
transform: a function to transform the vertices
"""
if mesh is not None and obj is not None:
raise ValueError('Received both mesh and obj')
if isinstance(mesh, str):
# perhaps this is a filename?
try:
mesh = trimesh.load(args[0])
except Exception as e:
raise ValueError(
"Did not understand arguments to method Figure#mesh"
) from e
if isinstance(obj, np.ndarray):
obj_data = obj
elif isinstance(obj, list):
obj_data = np.asarray(obj)
# Do something with this obj_data?
elif isinstance(obj, str):
if "\n" in obj:
# this is the file contents.
raise NotImplementedError()
else:
try:
# open the mesh file
mesh = trimesh.load(obj)
except Exception as e:
raise ValueError("Could not read file as OBJ") from e
assert hasattr(mesh, "vertices") and hasattr(mesh, "faces"), "Invalid mesh object"
if mesh is None:
raise ValueError("Could not understand how to parse mesh.")
if transform is None:
transform = lambda x: x
verts = transform(mesh.vertices)
faces = mesh.faces
if normalize:
# Normalize the vertex indices to be between -1,1
# Shifting these does change the coordinate system,
# so visualizing multiple meshes won't work
verts[:, 0] = _normalize_shift(verts[:, 0])
verts[:, 1] = _normalize_shift(verts[:, 1])
verts[:, 2] = _normalize_shift(verts[:, 2])
geo = BufferGeometry(
attributes={
"position": BufferAttribute(
array=verts.astype("float32"),
normalized=False,
# dtype=np.float64
),
"index": BufferAttribute(
array=faces.astype("uint64").ravel(),
normalized=False,
# dtype=np.float64,
),
}
)
self._coords = verts
transparent = alpha != 1.
mat = MeshLambertMaterial(color=color, opacity=alpha, transparent=transparent)
mesh = Mesh(geometry=geo, material=mat)
geo.exec_three_obj_method("computeVertexNormals")
super().__init__(*args, **kwargs)
self._objects.append(mesh)