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 __init__(self, color='pink', transparent=False):
Mesh.__init__(self,
geometry=PlaneGeometry(),
material=MeshBasicMaterial(color=color))
self.material.side = 'DoubleSide'
if transparent:
self.material.transparent = transparent
self.material.opacity = 0.5
def __init__(self, p1, p2, p3, color='yellow'):
geometry = BufferGeometry(
attributes={
'position':
BufferAttribute(np.vstack((
p1, p2, p3)).reshape(3, 3).astype(np.float32),
normalized=False)
})
material = MeshBasicMaterial(color=color)
material.side = 'DoubleSide'
Mesh.__init__(self, geometry=geometry, material=material)
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 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 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 faces_to_mesh(name, vertices, faces, colors, opacity=None):
"""
:param name:
:param vertices:
:param faces:
:param colors:
:param opacity:
:return:
"""
geometry = BufferGeometry(attributes=dict(
position=BufferAttribute(vertices, normalized=False),
index=BufferAttribute(faces, normalized=False),
color=BufferAttribute(colors),
))
mat_atts = dict(vertexColors="VertexColors", side="DoubleSide")
if opacity is not None:
mat_atts["opacity"] = opacity
mat_atts["transparent"] = True
material = MeshBasicMaterial(**mat_atts)
mesh = Mesh(
name=name,
geometry=geometry,
material=material,
)
return mesh
def animate_mesh(mesh, norm_displ_verts, displ_time, displ_magn):
from pythreejs import (
AnimationAction,
AnimationClip,
AnimationMixer,
NumberKeyframeTrack,
)
mesh.morphAttributes = {
"position": [
BufferAttribute(norm_displ_verts),
]
}
morphed_mesh = Mesh(
mesh,
MeshPhongMaterial(color="#ff3333", shininess=150, morphTargets=True))
pill_track = NumberKeyframeTrack(name=".morphTargetInfluences[0]",
times=displ_time,
values=displ_magn)
pill_clip = AnimationClip(tracks=[pill_track])
pill_action = AnimationAction(AnimationMixer(morphed_mesh), pill_clip,
morphed_mesh)
return pill_action
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 __init__(
self,
image: Union[str, np.ndarray],
center_pos: Coord3 = (0, 0, 0),
rotation: Coord3 = (0, 0, 0),
width: float = 10,
height: float = 10,
*args,
**kwargs
):
"""
Plot an image as a plane.
Arguments:
image (Union[str, np.ndarray]): The image to plot. This can be a
URL, a blob, or a numpy array. If it is a numpy array, it must
be either 2D (greyscale), 3D (RGB), or 4D (RGBA).
center_pos: Center pos
rotation: Rotation of the img
plane, in radians
width (float: 10): The width of the final rendered plane
height (float: 10): The height of the final rendered plane
"""
super().__init__(*args, **kwargs)
if isinstance(image, str):
tex = ImageTexture(imageUri=image)
elif isinstance(image, (list, np.ndarray)):
if len(image.shape) == 2:
# handle 2D (grayscale).
# broadcast to rgba channels:
image = np.array([image, image, image, np.ones(image.shape)]).T
elif image.shape[-1] == 3:
# handle RGB:
image = np.dstack([image, np.ones(image.shape)])
tex = DataTexture(data=image.astype(np.float32), type="FloatType")
else:
raise ValueError(f"Expected string or array, but got {type(image)}")
plane = PlaneGeometry(width=width, height=height)
mat = MeshBasicMaterial(map=tex)
mesh = Mesh(geometry=plane, material=mat, position=center_pos)
mesh.rotation = rotation if len(rotation) == 4 else [*rotation, "XYZ"]
self.center = center_pos
self.size = (width,height)
self._objects.append(mesh)
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 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 _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 _load_mesh(self, dae, scale):
materials = self._load_material(dae)
for geometry in dae.geometries:
for primitive in geometry.primitives:
vertices = primitive.vertex[primitive.vertex_index] * scale
normals = primitive.normal[primitive.normal_index]
buffer_geometry = BufferGeometry(
attributes={
'position': BufferAttribute(array=vertices),
'normal': BufferAttribute(array=normals)
})
material = materials[primitive.material]
mesh = Mesh(geometry=buffer_geometry, material=material)
self.add(mesh)
def occ_shape_to_threejs(self, shp: TopoDS_Shape, shape_color, edge_color,
transparency, opacity):
# first, compute the tesselation
from .renderer_occ import occ_shape_to_faces
from .threejs_utils import create_material
np_vertices, np_faces, np_normals, edges = occ_shape_to_faces(
shp, self.quality, self.render_edges, self.parallel)
# set geometry properties
buffer_geometry_properties = {
"position": BufferAttribute(np_vertices),
"index": BufferAttribute(np_faces),
}
if self.compute_normals_mode == NORMAL.SERVER_SIDE:
if np_normals.shape != np_vertices.shape:
raise AssertionError("Wrong number of normals/shapes")
buffer_geometry_properties["normal"] = BufferAttribute(np_normals)
# build a BufferGeometry instance
shape_geometry = BufferGeometry(attributes=buffer_geometry_properties)
# if the client has to render normals, add the related js instructions
if self.compute_normals_mode == NORMAL.CLIENT_SIDE:
shape_geometry.exec_three_obj_method("computeVertexNormals")
# then a default material
shp_material = create_material(shape_color,
transparent=transparency,
opacity=opacity)
# and to the dict of shapes, to have a mapping between meshes and shapes
mesh_id = "%s" % uuid.uuid4().hex
self.mesh_id = mesh_id
# finally create the mesh
shape_mesh = Mesh(geometry=shape_geometry,
material=shp_material,
name=mesh_id)
# edge rendering, if set to True
if self.render_edges:
edge_list = flatten(list(map(explode, edges)))
lines = LineSegmentsGeometry(positions=edge_list)
mat = LineMaterial(linewidth=1, color=edge_color)
edge_lines = LineSegments2(lines, mat, name=mesh_id)
else:
edge_lines = None
return shape_mesh, edge_lines
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 __init__(self, color='red', radius=0.025):
Mesh.__init__(self,
geometry=SphereGeometry(radius=radius),
material=MeshLambertMaterial(color=color))
def AddShapeToScene(
self,
shp,
shape_color=None, # the default
render_edges=False,
edge_color=None,
vertex_color=None,
quality=1.0,
transparency=False,
opacity=1.0,
):
# first, compute the tesselation
tess = ShapeTesselator(shp)
tess.Compute(compute_edges=render_edges,
mesh_quality=quality,
parallel=True)
# get vertices and normals
vertices_position = tess.GetVerticesPositionAsTuple()
number_of_triangles = tess.ObjGetTriangleCount()
number_of_vertices = len(vertices_position)
# number of vertices should be a multiple of 3
if number_of_vertices % 3 != 0:
raise AssertionError("Wrong number of vertices")
if number_of_triangles * 9 != number_of_vertices:
raise AssertionError("Wrong number of triangles")
# then we build the vertex and faces collections as numpy ndarrays
np_vertices = np.array(vertices_position, dtype="float32").reshape(
int(number_of_vertices / 3), 3)
# Note: np_faces is just [0, 1, 2, 3, 4, 5, ...], thus arange is used
np_faces = np.arange(np_vertices.shape[0], dtype="uint32")
# set geometry properties
buffer_geometry_properties = {
"position": BufferAttribute(np_vertices),
"index": BufferAttribute(np_faces),
}
if self._compute_normals_mode == NORMAL.SERVER_SIDE:
# get the normal list, converts to a numpy ndarray. This should not raise
# any issue, since normals have been computed by the server, and are available
# as a list of floats
np_normals = np.array(tess.GetNormalsAsTuple(),
dtype="float32").reshape(-1, 3)
# quick check
if np_normals.shape != np_vertices.shape:
raise AssertionError("Wrong number of normals/shapes")
buffer_geometry_properties["normal"] = BufferAttribute(np_normals)
# build a BufferGeometry instance
shape_geometry = BufferGeometry(attributes=buffer_geometry_properties)
# if the client has to render normals, add the related js instructions
if self._compute_normals_mode == NORMAL.CLIENT_SIDE:
shape_geometry.exec_three_obj_method("computeVertexNormals")
# then a default material
shp_material = self._material(shape_color,
transparent=transparency,
opacity=opacity)
# and to the dict of shapes, to have a mapping between meshes and shapes
mesh_id = "%s" % uuid.uuid4().hex
self._shapes[mesh_id] = shp
# finally create the mesh
shape_mesh = Mesh(geometry=shape_geometry,
material=shp_material,
name=mesh_id)
# edge rendering, if set to True
if render_edges:
edges = list(
map(
lambda i_edge: [
tess.GetEdgeVertex(i_edge, i_vert)
for i_vert in range(tess.ObjEdgeGetVertexCount(i_edge))
],
range(tess.ObjGetEdgeCount()),
))
edge_list = _flatten(list(map(_explode, edges)))
lines = LineSegmentsGeometry(positions=edge_list)
mat = LineMaterial(linewidth=1, color=edge_color)
edge_lines = LineSegments2(lines, mat, name=mesh_id)
self._displayed_non_pickable_objects.add(edge_lines)
return shape_mesh
"""
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 visualize(self):
"""Start the visualization and initialize widgets"""
from pythreejs import PlainGeometry, Mesh, LambertMaterial, \
PhongMaterial, DirectionalLight, \
PerspectiveCamera, Scene, AmbientLight, \
Renderer, OrbitControls, Line, \
LineBasicMaterial, BoxGeometry, make_text
from matplotlib import colors
from matplotlib import cm
from IPython.display import display
import numpy as np
import ipywidgets as widgets
bbox = self._compute_bounding_box()
diam = bbox[1, :] - bbox[0, :]
center = .5 * _np.sum(bbox, axis=0)
xmin, ymin, zmin = bbox[0, :]
xmax, ymax, zmax = bbox[1, :]
position = (center + 2.5 * diam).tolist()
# Generate coordinate system base
box = PlainGeometry(
vertices=_np.array([[xmin, ymin, zmin], [xmax, ymin, zmin],
[xmin, ymin, zmin], [xmin, ymax, zmin],
[xmin, ymin, zmin], [xmin, ymin, zmax]]),
colors=['red', 'red', 'green', 'green', 'blue', 'blue'])
self._coord_box = Line(geometry=box,
material=LineBasicMaterial(
linewidth=10, vertexColors='VertexColors'),
type='LinePieces')
if self.data is not None:
vis_data = self.data
if not self.is_real:
vis_data = _np.real(self.data)
if not self.is_scalar:
vis_data = _np.sum(_np.abs(self.data)**2, axis=2)
self._vis_data = vis_data
self._cmap = cm.jet
self._vmin = vis_data.min()
self._vmax = vis_data.max()
cnorm = colors.Normalize(vmin=self._vmin, vmax=self._vmax)
facecolors = self._convert_data_to_colors(self._cmap, cnorm,
vis_data)
else:
facecolors = self.elements.shape[0] * [
3 * [_np.array([1., 1., 1.])]
]
self._geom = PlainGeometry(vertices=self.vertices,
faces=self.elements,
faceColors=facecolors)
self._mesh = Mesh(
geometry=self._geom,
material=LambertMaterial(vertexColors='VertexColors'))
self._wireframe = Mesh(geometry=self._geom,
material=PhongMaterial(wireframe=True,
color='black'))
light = DirectionalLight(color='white',
position=position,
intensity=0.5)
camera = PerspectiveCamera(position=position, fov=20)
self._scene = Scene(children=[
self._coord_box, self._mesh, self._wireframe,
AmbientLight(color='white')
])
self._renderer = Renderer(camera=camera,
background='white',
background_opacity=1,
scene=self._scene,
controls=[OrbitControls(controlling=camera)])
self._axes_info = widgets.Label(value="x: red; y: green; z: blue")
coord_system_toggle = widgets.Checkbox(
value=self._coord_box.visible,
description='Show coordinate axes',
disabled=False)
coord_system_toggle.observe(self.on_toggle_coord_system, names='value')
if self.data is not None:
# Enable/Disable wireframe
wireframe_toggle = widgets.Checkbox(value=self._wireframe.visible,
description='Enable wireframe',
disabled=False)
wireframe_toggle.observe(self.on_toggle_wireframe, names='value')
# Change vmin/vmax
vmin_box = widgets.FloatText(value=self._vmin,
description='vmin:',
disabled=False)
vmin_box.observe(self.on_change_vmin, names='value')
vmax_box = widgets.FloatText(value=self._vmax,
description='vmax:',
disabled=False)
vmax_box.observe(self.on_change_vmax, names='value')
vmin_info = widgets.Label(
value='Lower bound: {0}'.format(self._vmin))
vmax_info = widgets.Label(
value='Upper bound: {0}'.format(self._vmax))
range_info_box = widgets.VBox([vmin_info, vmax_info])
range_change = widgets.HBox([vmin_box, vmax_box])
toggles = widgets.HBox([wireframe_toggle, coord_system_toggle])
vbox = widgets.VBox(
[self._axes_info, range_info_box, range_change, toggles])
display(self._renderer, vbox)
else:
display(self._renderer, self._axes_info, coord_system_toggle)
def _render_shape(self,
shape_index,
shape=None,
edges=None,
vertices=None,
mesh_color=None,
edge_color=None,
vertex_color=None,
render_edges=False,
edge_width=1,
vertex_width=5,
deflection=0.05,
transparent=False,
opacity=1.0):
edge_list = None
edge_lines = None
points = None
shape_mesh = None
if shape is not None:
if mesh_color is None:
mesh_color = self.default_mesh_color
if edge_color is None:
edge_color = self.default_edge_color
if vertex_color is None:
vertex_color = self.default_edge_color # same as edge_color
# BEGIN copy
# The next lines are copied with light modifications from
# https://github.com/tpaviot/pythonocc-core/blob/master/src/Display/WebGl/jupyter_renderer.py
# first, compute the tesselation
tess = Tesselator(shape)
tess.Compute(uv_coords=False,
compute_edges=render_edges,
mesh_quality=self.quality,
parallel=True)
# get vertices and normals
vertices_position = tess.GetVerticesPositionAsTuple()
number_of_triangles = tess.ObjGetTriangleCount()
number_of_vertices = len(vertices_position)
# number of vertices should be a multiple of 3
if number_of_vertices % 3 != 0:
raise AssertionError("Wrong number of vertices")
if number_of_triangles * 9 != number_of_vertices:
raise AssertionError("Wrong number of triangles")
# then we build the vertex and faces collections as numpy ndarrays
np_vertices = np.array(vertices_position, dtype='float32')\
.reshape(int(number_of_vertices / 3), 3)
# Note: np_faces is just [0, 1, 2, 3, 4, 5, ...], thus arange is used
np_faces = np.arange(np_vertices.shape[0], dtype='uint32')
# compute normals
np_normals = np.array(tess.GetNormalsAsTuple(),
dtype='float32').reshape(-1, 3)
if np_normals.shape != np_vertices.shape:
raise AssertionError("Wrong number of normals/shapes")
# build a BufferGeometry instance
shape_geometry = BufferGeometry(
attributes={
'position': BufferAttribute(np_vertices),
'index': BufferAttribute(np_faces),
'normal': BufferAttribute(np_normals)
})
shp_material = self._material(mesh_color,
transparent=True,
opacity=opacity)
shape_mesh = Mesh(geometry=shape_geometry,
material=shp_material,
name="mesh_%d" % shape_index)
if render_edges:
edge_list = list(
map(
lambda i_edge: [
tess.GetEdgeVertex(i_edge, i_vert)
for i_vert in range(
tess.ObjEdgeGetVertexCount(i_edge))
], range(tess.ObjGetEdgeCount())))
# END copy
if vertices is not None:
vertices_list = []
for vertex in vertices:
p = BRep_Tool.Pnt(vertex)
vertices_list.append((p.X(), p.Y(), p.Z()))
vertices_list = np.array(vertices_list, dtype=np.float32)
attributes = {
"position": BufferAttribute(vertices_list, normalized=False)
}
mat = PointsMaterial(color=vertex_color,
sizeAttenuation=False,
size=vertex_width)
geom = BufferGeometry(attributes=attributes)
points = Points(geometry=geom, material=mat)
if edges is not None:
edge_list = [discretize_edge(edge, deflection) for edge in edges]
if edge_list is not None:
edge_list = _flatten(list(map(_explode, edge_list)))
lines = LineSegmentsGeometry(positions=edge_list)
mat = LineMaterial(linewidth=edge_width, color=edge_color)
edge_lines = LineSegments2(lines,
mat,
name="edges_%d" % shape_index)
if shape_mesh is not None or edge_lines is not None or points is not None:
index_mapping = {"mesh": None, "edges": None, "shape": shape_index}
if shape_mesh is not None:
ind = len(self.pickable_objects.children)
self.pickable_objects.add(shape_mesh)
index_mapping["mesh"] = ind
if edge_lines is not None:
ind = len(self.pickable_objects.children)
self.pickable_objects.add(edge_lines)
index_mapping["edges"] = ind
if points is not None:
ind = len(self.pickable_objects.children)
self.pickable_objects.add(points)
index_mapping["mesh"] = ind
self.pick_mapping.append(index_mapping)
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)
def DisplayMesh(self,
mesh,
color=default_mesh_color):
""" Display a MEFISTO2 triangle mesh
"""
if not HAVE_SMESH:
print("SMESH not installed, DisplayMesh method unavailable.")
return
if not isinstance(mesh, SMESH_Mesh):
raise AssertionError("You mush provide an SMESH_Mesh instance")
mesh_ds = mesh.GetMeshDS() # the mesh data source
face_iter = mesh_ds.facesIterator()
# vertices positions are stored to a liste
vertices_position = []
for _ in range(mesh_ds.NbFaces()-1):
face = face_iter.next()
#print('Face %i, type %i' % (i, face.GetType()))
#print(dir(face))
# if face.GetType == 3 : triangle mesh, then 3 nodes
for j in range(3):
node = face.GetNode(j)
#print('Coordinates of node %i:(%f,%f,%f)'%(i, node.X(), node.Y(), node.Z()))
vertices_position.append(node.X())
vertices_position.append(node.Y())
vertices_position.append(node.Z())
number_of_vertices = len(vertices_position)
# then we build the vertex and faces collections as numpy ndarrays
np_vertices = np.array(vertices_position, dtype='float32').reshape(int(number_of_vertices / 3), 3)
# Note: np_faces is just [0, 1, 2, 3, 4, 5, ...], thus arange is used
np_faces = np.arange(np_vertices.shape[0], dtype='uint32')
# set geometry properties
buffer_geometry_properties = {'position': BufferAttribute(np_vertices),
'index' : BufferAttribute(np_faces)}
# build a BufferGeometry instance
mesh_geometry = BufferGeometry(attributes=buffer_geometry_properties)
mesh_geometry.exec_three_obj_method('computeVertexNormals')
# then a default material
mesh_material = MeshPhongMaterial(color=color,
polygonOffset=True,
polygonOffsetFactor=1,
polygonOffsetUnits=1,
shininess=0.5,
wireframe=False,
side='DoubleSide')
edges_material = MeshPhongMaterial(color='black',
polygonOffset=True,
polygonOffsetFactor=1,
polygonOffsetUnits=1,
shininess=0.5,
wireframe=True)
# create a mesh unique id
mesh_id = uuid.uuid4().hex
# finally create the mash
shape_mesh = Mesh(geometry=mesh_geometry,
material=mesh_material,
name=mesh_id)
edges_mesh = Mesh(geometry=mesh_geometry,
material=edges_material,
name=mesh_id)
# a special display for the mesh
camera_target = [0., 0., 0.] # the point to look at
camera_position = [0, 0., 100.] # the camera initial position
camera = PerspectiveCamera(position=camera_position,
lookAt=camera_target,
up=[0, 0, 1],
fov=50,
children=[DirectionalLight(color='#ffffff',
position=[50, 50, 50],
intensity=0.9)])
scene_shp = Scene(children=[shape_mesh, edges_mesh, camera, AmbientLight(color='#101010')])
renderer = Renderer(camera=camera,
background=self._background,
background_opacity=self._background_opacity,
scene=scene_shp,
controls=[OrbitControls(controlling=camera, target=camera_target)],
width=self._size[0],
height=self._size[1],
antialias=True)
display(renderer)
def _render_shape(
self,
shape_index,
shape=None,
edges=None,
vertices=None,
mesh_color=None,
edge_color=None,
vertex_color=None,
render_edges=False,
edge_width=1,
vertex_width=5,
transparent=False,
opacity=1.0,
):
edge_list = None
edge_lines = None
points = None
shape_mesh = None
start_render_time = self._start_timer()
if shape is not None:
if mesh_color is None:
mesh_color = self.default_mesh_color
if edge_color is None:
edge_color = self.default_edge_color
if vertex_color is None:
vertex_color = self.default_edge_color # same as edge_color
# Compute the tesselation
start_tesselation_time = self._start_timer()
np_vertices, np_triangles, np_normals = tessellate(
shape, self.quality, self.angular_tolerance
)
if np_normals.shape != np_vertices.shape:
raise AssertionError("Wrong number of normals/shapes")
self._stop_timer("tesselation time", start_tesselation_time)
# build a BufferGeometry instance
shape_geometry = BufferGeometry(
attributes={
"position": BufferAttribute(np_vertices),
"index": BufferAttribute(np_triangles.ravel()),
"normal": BufferAttribute(np_normals),
}
)
shp_material = self._material(mesh_color, transparent=True, opacity=opacity)
shape_mesh = Mesh(
geometry=shape_geometry, material=shp_material, name="mesh_%d" % shape_index
)
if render_edges:
edges = get_edges(shape)
if vertices is not None:
vertices_list = []
for vertex in vertices:
vertices_list.append(get_point(vertex))
vertices_list = np.array(vertices_list, dtype=np.float32)
attributes = {"position": BufferAttribute(vertices_list, normalized=False)}
mat = PointsMaterial(color=vertex_color, sizeAttenuation=False, size=vertex_width)
geom = BufferGeometry(attributes=attributes)
points = Points(geometry=geom, material=mat)
if edges is not None:
start_discretize_time = self._start_timer()
edge_list = [discretize_edge(edge, self.edge_accuracy) for edge in edges]
self._stop_timer("discretize time", start_discretize_time)
if edge_list is not None:
edge_list = flatten(list(map(explode, edge_list)))
lines = LineSegmentsGeometry(positions=edge_list)
mat = LineMaterial(linewidth=edge_width, color=edge_color)
edge_lines = LineSegments2(lines, mat, name="edges_%d" % shape_index)
if shape_mesh is not None or edge_lines is not None or points is not None:
index_mapping = {"mesh": None, "edges": None, "shape": shape_index}
if shape_mesh is not None:
ind = len(self.pickable_objects.children)
self.pickable_objects.add(shape_mesh)
index_mapping["mesh"] = ind
if edge_lines is not None:
ind = len(self.pickable_objects.children)
self.pickable_objects.add(edge_lines)
index_mapping["edges"] = ind
if points is not None:
ind = len(self.pickable_objects.children)
self.pickable_objects.add(points)
index_mapping["mesh"] = ind
self.pick_mapping.append(index_mapping)
self._stop_timer("shape render time", start_render_time)
def AddShapeToScene(self,
shp, # the TopoDS_Shape to be displayed
shape_color=default_shape_color, # the default
render_edges=False,
edge_color=default_edge_color,
compute_uv_coords=False,
quality=1.0,
transparency=False,
opacity=1.):
# first, compute the tesselation
tess = Tesselator(shp)
tess.Compute(uv_coords=compute_uv_coords,
compute_edges=render_edges,
mesh_quality=quality,
parallel=self._parallel)
# get vertices and normals
vertices_position = tess.GetVerticesPositionAsTuple()
number_of_triangles = tess.ObjGetTriangleCount()
number_of_vertices = len(vertices_position)
# number of vertices should be a multiple of 3
if number_of_vertices % 3 != 0:
raise AssertionError("Wrong number of vertices")
if number_of_triangles * 9 != number_of_vertices:
raise AssertionError("Wrong number of triangles")
# then we build the vertex and faces collections as numpy ndarrays
np_vertices = np.array(vertices_position, dtype='float32').reshape(int(number_of_vertices / 3), 3)
# Note: np_faces is just [0, 1, 2, 3, 4, 5, ...], thus arange is used
np_faces = np.arange(np_vertices.shape[0], dtype='uint32')
# set geometry properties
buffer_geometry_properties = {'position': BufferAttribute(np_vertices),
'index' : BufferAttribute(np_faces)}
if self._compute_normals_mode == NORMAL.SERVER_SIDE:
# get the normal list, converts to a numpy ndarray. This should not raise
# any issue, since normals have been computed by the server, and are available
# as a list of floats
np_normals = np.array(tess.GetNormalsAsTuple(), dtype='float32').reshape(-1, 3)
# quick check
if np_normals.shape != np_vertices.shape:
raise AssertionError("Wrong number of normals/shapes")
buffer_geometry_properties['normal'] = BufferAttribute(np_normals)
# build a BufferGeometry instance
shape_geometry = BufferGeometry(attributes=buffer_geometry_properties)
# if the client has to render normals, add the related js instructions
if self._compute_normals_mode == NORMAL.CLIENT_SIDE:
shape_geometry.exec_three_obj_method('computeVertexNormals')
# then a default material
shp_material = self._material(shape_color, transparent=transparency, opacity=opacity)
# create a mesh unique id
mesh_id = uuid.uuid4().hex
# finally create the mash
shape_mesh = Mesh(geometry=shape_geometry,
material=shp_material,
name=mesh_id)
# and to the dict of shapes, to have a mapping between meshes and shapes
self._shapes[mesh_id] = shp
# edge rendering, if set to True
edge_lines = None
if render_edges:
edges = list(map(lambda i_edge: [tess.GetEdgeVertex(i_edge, i_vert) for i_vert in range(tess.ObjEdgeGetVertexCount(i_edge))], range(tess.ObjGetEdgeCount())))
edges = list(filter(lambda edge: len(edge) == 2, edges))
np_edge_vertices = np.array(edges, dtype=np.float32).reshape(-1, 3)
np_edge_indices = np.arange(np_edge_vertices.shape[0], dtype=np.uint32)
edge_geometry = BufferGeometry(attributes={
'position': BufferAttribute(np_edge_vertices),
'index' : BufferAttribute(np_edge_indices)
})
edge_material = LineBasicMaterial(color=edge_color, linewidth=1)
edge_lines = LineSegments(geometry=edge_geometry, material=edge_material)
# Add geometries to pickable or non pickable objects
self._displayed_pickable_objects.add(shape_mesh)
if render_edges:
self._displayed_non_pickable_objects.add(edge_lines)