def __add_line_geometry(self, lines, shading, obj=None):
lines = lines.astype("float32", copy=False)
mi = np.min(lines, axis=0)
ma = np.max(lines, axis=0)
geometry = p3s.LineSegmentsGeometry(positions=lines.reshape((-1, 2,
3)))
material = p3s.LineMaterial(linewidth=shading["line_width"],
color=shading["line_color"])
#, vertexColors='VertexColors'),
lines = p3s.LineSegments2(geometry=geometry,
material=material) #type='LinePieces')
line_obj = {
"geometry": geometry,
"mesh": lines,
"material": material,
"max": ma,
"min": mi,
"type": "Lines",
"wireframe": None
}
if obj:
return self.__add_object(line_obj, obj), line_obj
else:
return self.__add_object(line_obj)
def draw_lines(self, lines, colors, line_width=1):
positions = np.array(lines)
colors = [[colors[i], colors[i]] for i, line in enumerate(lines)]
g = p3js.LineSegmentsGeometry(positions=positions, colors=colors)
m = p3js.LineMaterial(linewidth=line_width, vertexColors='VertexColors')
lines = p3js.LineSegments2(g, m)
self.geometry.append(lines)
return lines
def draw_line(self, line, color, line_width=1):
positions = [[list(line[0]), list(line[1])]]
colors = [[color, color]]
g = p3js.LineSegmentsGeometry(positions=positions, colors=colors)
m = p3js.LineMaterial(linewidth=line_width, vertexColors='VertexColors')
line = p3js.LineSegments2(g, m)
self.geometry.append(line)
return line
def __init__(self, segment, color, **kwargs):
g = three.LineSegmentsGeometry(positions=self.getPositions(segment))
m = three.LineMaterial(linewidth=10, color=color, light=True)
super().__init__(g, m)
self.segment = segment
def generate_3js_render(
element_groups,
canvas_size,
zoom,
camera_fov=30,
background_color="white",
background_opacity=1.0,
reuse_objects=False,
use_atom_arrays=False,
use_label_arrays=False,
):
"""Create a pythreejs scene of the elements.
Regarding initialisation performance, see: https://github.com/jupyter-widgets/pythreejs/issues/154
"""
import pythreejs as pjs
key_elements = {}
group_elements = pjs.Group()
key_elements["group_elements"] = group_elements
unique_atom_sets = {}
for el in element_groups["atoms"]:
element_hash = (
("radius", el.sradius),
("color", el.color),
("fill_opacity", el.fill_opacity),
("stroke_color", el.get("stroke_color", "black")),
("ghost", el.ghost),
)
unique_atom_sets.setdefault(element_hash, []).append(el)
group_atoms = pjs.Group()
group_ghosts = pjs.Group()
atom_geometries = {}
atom_materials = {}
outline_materials = {}
for el_hash, els in unique_atom_sets.items():
el = els[0]
data = dict(el_hash)
if reuse_objects:
atom_geometry = atom_geometries.setdefault(
el.sradius,
pjs.SphereBufferGeometry(radius=el.sradius,
widthSegments=30,
heightSegments=30),
)
else:
atom_geometry = pjs.SphereBufferGeometry(radius=el.sradius,
widthSegments=30,
heightSegments=30)
if reuse_objects:
atom_material = atom_materials.setdefault(
(el.color, el.fill_opacity),
pjs.MeshLambertMaterial(color=el.color,
transparent=True,
opacity=el.fill_opacity),
)
else:
atom_material = pjs.MeshLambertMaterial(color=el.color,
transparent=True,
opacity=el.fill_opacity)
if use_atom_arrays:
atom_mesh = pjs.Mesh(geometry=atom_geometry,
material=atom_material)
atom_array = pjs.CloneArray(
original=atom_mesh,
positions=[e.position.tolist() for e in els],
merge=False,
)
else:
atom_array = [
pjs.Mesh(
geometry=atom_geometry,
material=atom_material,
position=e.position.tolist(),
name=e.info_string,
) for e in els
]
data["geometry"] = atom_geometry
data["material_body"] = atom_material
if el.ghost:
key_elements["group_ghosts"] = group_ghosts
group_ghosts.add(atom_array)
else:
key_elements["group_atoms"] = group_atoms
group_atoms.add(atom_array)
if el.get("stroke_width", 1) > 0:
if reuse_objects:
outline_material = outline_materials.setdefault(
el.get("stroke_color", "black"),
pjs.MeshBasicMaterial(
color=el.get("stroke_color", "black"),
side="BackSide",
transparent=True,
opacity=el.get("stroke_opacity", 1.0),
),
)
else:
outline_material = pjs.MeshBasicMaterial(
color=el.get("stroke_color", "black"),
side="BackSide",
transparent=True,
opacity=el.get("stroke_opacity", 1.0),
)
# TODO use stroke width to dictate scale
if use_atom_arrays:
outline_mesh = pjs.Mesh(
geometry=atom_geometry,
material=outline_material,
scale=(1.05, 1.05, 1.05),
)
outline_array = pjs.CloneArray(
original=outline_mesh,
positions=[e.position.tolist() for e in els],
merge=False,
)
else:
outline_array = [
pjs.Mesh(
geometry=atom_geometry,
material=outline_material,
position=e.position.tolist(),
scale=(1.05, 1.05, 1.05),
) for e in els
]
data["material_outline"] = outline_material
if el.ghost:
group_ghosts.add(outline_array)
else:
group_atoms.add(outline_array)
key_elements.setdefault("atom_arrays", []).append(data)
group_elements.add(group_atoms)
group_elements.add(group_ghosts)
group_labels = add_labels(element_groups, key_elements, use_label_arrays)
group_elements.add(group_labels)
if len(element_groups["cell_lines"]) > 0:
cell_line_mat = pjs.LineMaterial(
linewidth=1,
color=element_groups["cell_lines"].group_properties["color"])
cell_line_geo = pjs.LineSegmentsGeometry(positions=[
el.position.tolist() for el in element_groups["cell_lines"]
])
cell_lines = pjs.LineSegments2(geometry=cell_line_geo,
material=cell_line_mat)
key_elements["cell_lines"] = cell_lines
group_elements.add(cell_lines)
if len(element_groups["bond_lines"]) > 0:
bond_line_mat = pjs.LineMaterial(
linewidth=element_groups["bond_lines"].
group_properties["stroke_width"],
vertexColors="VertexColors",
)
bond_line_geo = pjs.LineSegmentsGeometry(
positions=[
el.position.tolist() for el in element_groups["bond_lines"]
],
colors=[[Color(c).rgb for c in el.color]
for el in element_groups["bond_lines"]],
)
bond_lines = pjs.LineSegments2(geometry=bond_line_geo,
material=bond_line_mat)
key_elements["bond_lines"] = bond_lines
group_elements.add(bond_lines)
group_millers = pjs.Group()
if len(element_groups["miller_lines"]) or len(
element_groups["miller_planes"]):
key_elements["group_millers"] = group_millers
if len(element_groups["miller_lines"]) > 0:
miller_line_mat = pjs.LineMaterial(
linewidth=3,
vertexColors="VertexColors" # TODO use stroke_width
)
miller_line_geo = pjs.LineSegmentsGeometry(
positions=[
el.position.tolist() for el in element_groups["miller_lines"]
],
colors=[[Color(el.stroke_color).rgb] * 2
for el in element_groups["miller_lines"]],
)
miller_lines = pjs.LineSegments2(geometry=miller_line_geo,
material=miller_line_mat)
group_millers.add(miller_lines)
for el in element_groups["miller_planes"]:
vertices = el.position.tolist()
faces = [(
0,
1,
2,
triangle_normal(vertices[0], vertices[1], vertices[2]),
"black",
0,
)]
if len(vertices) == 4:
faces.append((
2,
3,
0,
triangle_normal(vertices[2], vertices[3], vertices[0]),
"black",
0,
))
elif len(vertices) != 3:
raise NotImplementedError("polygons with more than 4 points")
plane_geom = pjs.Geometry(vertices=vertices, faces=faces)
plane_mat = pjs.MeshBasicMaterial(
color=el.fill_color,
transparent=True,
opacity=el.fill_opacity,
side="DoubleSide",
)
plane_mesh = pjs.Mesh(geometry=plane_geom, material=plane_mat)
group_millers.add(plane_mesh)
group_elements.add(group_millers)
scene = pjs.Scene(background=None)
scene.add([group_elements])
view_width, view_height = canvas_size
minp, maxp = element_groups.get_position_range()
# compute a minimum camera distance, that is guaranteed to encapsulate all elements
camera_dist = maxp[2] + sqrt(maxp[0]**2 + maxp[1]**2) / tan(
radians(camera_fov / 2))
camera = pjs.PerspectiveCamera(
fov=camera_fov,
position=[0, 0, camera_dist],
aspect=view_width / view_height,
zoom=zoom,
)
scene.add([camera])
ambient_light = pjs.AmbientLight(color="lightgray")
key_elements["ambient_light"] = ambient_light
direct_light = pjs.DirectionalLight(position=(maxp * 2).tolist())
key_elements["direct_light"] = direct_light
scene.add([camera, ambient_light, direct_light])
camera_control = pjs.OrbitControls(controlling=camera,
screenSpacePanning=True)
atom_picker = pjs.Picker(controlling=group_atoms, event="dblclick")
key_elements["atom_picker"] = atom_picker
material = pjs.SpriteMaterial(
map=create_arrow_texture(right=False),
transparent=True,
depthWrite=False,
depthTest=False,
)
atom_pointer = pjs.Sprite(material=material,
scale=(4, 3, 1),
visible=False)
scene.add(atom_pointer)
key_elements["atom_pointer"] = atom_pointer
renderer = pjs.Renderer(
camera=camera,
scene=scene,
controls=[camera_control, atom_picker],
width=view_width,
height=view_height,
alpha=True,
clearOpacity=background_opacity,
clearColor=background_color,
)
return renderer, key_elements
def create_world_axes(camera,
controls,
initial_rotation=np.eye(3),
length=30,
width=3,
camera_fov=10):
"""Create a renderer, containing an axes and camera that is synced to another camera.
adapted from http://jsfiddle.net/aqnL1mx9/
Parameters
----------
camera : pythreejs.PerspectiveCamera
controls : pythreejs.OrbitControls
initial_rotation : list or numpy.array
initial rotation of the axes
length : int
length of axes lines
width : int
line width of axes
Returns
-------
pythreejs.Renderer
"""
import pythreejs as pjs
canvas_width = length * 2
canvas_height = length * 2
ax_scene = pjs.Scene()
group_ax = pjs.Group()
# NOTE: could use AxesHelper, but this does not allow for linewidth seletion
# TODO: add arrow heads (ArrowHelper doesn't seem to work)
ax_line_mat = pjs.LineMaterial(linewidth=width,
vertexColors="VertexColors")
ax_line_geo = pjs.LineSegmentsGeometry(
positions=[[[0, 0, 0], length * r / np.linalg.norm(r)]
for r in initial_rotation],
colors=[[Color(c).rgb] * 2 for c in ("red", "green", "blue")],
)
ax_lines = pjs.LineSegments2(geometry=ax_line_geo, material=ax_line_mat)
group_ax.add(ax_lines)
ax_scene.add([group_ax])
camera_dist = length / tan(radians(camera_fov / 2))
ax_camera = pjs.PerspectiveCamera(fov=camera_fov,
aspect=canvas_width / canvas_height,
near=1,
far=1000)
ax_camera.up = camera.up
ax_renderer = pjs.Renderer(
scene=ax_scene,
camera=ax_camera,
width=canvas_width,
height=canvas_height,
alpha=True,
clearOpacity=0.0,
clearColor="white",
)
def align_axes(change=None):
"""Align axes to world."""
# TODO: this is not working correctly for TrackballControls, when rotated upside-down
# (OrbitControls enforces the camera up direction,
# so does not allow the camera to rotate upside-down).
# TODO how could this be implemented on the client (js) side?
new_position = np.array(camera.position) - np.array(controls.target)
new_position = camera_dist * new_position / np.linalg.norm(
new_position)
ax_camera.position = new_position.tolist()
ax_camera.lookAt(ax_scene.position)
align_axes()
camera.observe(align_axes, names="position")
controls.observe(align_axes, names="target")
ax_scene.observe(align_axes, names="position")
return ax_renderer