def _update_camera(self):
if np.sum(self.viewer.dims.display) == 3:
# Set a 3D camera
self.view.camera = ArcballCamera(name="ArcballCamera")
# flip y-axis to have correct alignment
self.view.camera.flip = (0, 1, 0)
min_shape, max_shape = self.viewer._calc_bbox()
centroid = np.add(max_shape, min_shape) / 2
size = np.subtract(max_shape, min_shape)
# Scale the camera to the contents in the scene
if len(centroid) > 0:
centroid = centroid[-3:]
self.view.camera.center = centroid[::-1]
self.view.camera.scale_factor = 1.5 * np.mean(size[-3:])
elif np.sum(self.viewer.dims.display) == 2:
# Set 2D camera
self.view.camera = PanZoomCamera(aspect=1, name="PanZoomCamera")
# flip y-axis to have correct alignment
self.view.camera.flip = (0, 1, 0)
# Scale the camera to the contents in the scene
self.view.camera.set_range()
else:
raise ValueError(
"Invalid display flags set in dimensions {}".format(
self.viewer.dims.display
)
)
self.view.camera.viewbox_key_event = viewbox_key_event
# TO DO: Remove
self.viewer._view = self.view
def __init__(self):
self._canvas = SceneCanvas()
self._viewbox = ViewBox(parent=self._canvas.scene)
self._canvas.central_widget.add_widget(self._viewbox)
self._viewbox.camera = ArcballCamera(fov=0)
self._atlas_volume = Volume(
array([[[1, 2]]]) * 1000,
parent=self._viewbox.scene) # , interpolation='nearest')
self._atlas_volume.attach(filters.ColorFilter((1., .5, 0., 1.)))
self._atlas_volume.set_gl_state('additive', depth_test=False)
self._section_image = Image(parent=self._viewbox.scene, cmap='grays')
self._section_image.attach(filters.ColorFilter((0., .5, 1., 1.)))
self._section_image.set_gl_state('additive', depth_test=False)
self._canvas.events.key_press.connect(
self._handle_vispy_key_press_events)
def _update_camera(self):
if self.viewer.dims.ndisplay == 3:
# Set a 3D camera
if not isinstance(self.view.camera, ArcballCamera):
self.view.camera = ArcballCamera(name="ArcballCamera", fov=0)
# flip y-axis to have correct alignment
# self.view.camera.flip = (0, 1, 0)
self.view.camera.viewbox_key_event = viewbox_key_event
self.viewer.reset_view()
else:
# Set 2D camera
if not isinstance(self.view.camera, PanZoomCamera):
self.view.camera = PanZoomCamera(aspect=1,
name="PanZoomCamera")
# flip y-axis to have correct alignment
self.view.camera.flip = (0, 1, 0)
self.view.camera.viewbox_key_event = viewbox_key_event
self.viewer.reset_view()
def __init__(self, _model: VolumeViewModel):
self._model = _model
self._model.register(self.update)
self._canvas = SceneCanvas()
self._viewbox = ViewBox(parent=self._canvas.scene)
self._canvas.central_widget.add_widget(self._viewbox)
self._viewbox.camera = ArcballCamera(fov=0)
self._atlas_volume = Volume(self._model.atlas_volume, parent=self._viewbox.scene) # , interpolation='nearest')
self._atlas_volume.attach(filters.ColorFilter((1., .5, 0., 1.)))
self._atlas_volume.set_gl_state('additive', depth_test=False)
self._section_image = Image(parent=self._viewbox.scene, cmap='grays')
self._section_image.attach(filters.ColorFilter((0., .5, 1., 1.)))
self._section_image.set_gl_state('additive', depth_test=False)
self._canvas.events.key_press.connect(lambda event: self._model.press_key(event.key.name))
def __init__(self, view, camera, dims):
self._view = view
self._camera = camera
self._dims = dims
# Create 2D camera
self._2D_camera = PanZoomCamera(aspect=1)
# flip y-axis to have correct alignment
self._2D_camera.flip = (0, 1, 0)
self._2D_camera.viewbox_key_event = viewbox_key_event
# Create 3D camera
self._3D_camera = ArcballCamera(fov=0)
self._3D_camera.viewbox_key_event = viewbox_key_event
self._dims.events.ndisplay.connect(self._on_ndisplay_change,
position='first')
self._camera.events.center.connect(self._on_center_change)
self._camera.events.zoom.connect(self._on_zoom_change)
self._camera.events.angles.connect(self._on_angles_change)
self._on_ndisplay_change(None)
# Prepare atomic data:
atoms = [atom for atom in structure.get_atoms()]
natoms = len(atoms)
coordinates = np.array([atom.coord for atom in atoms])
# Move to center of coordinates:
center = centroid(coordinates)
coordinates -= center
#atom color
color = [colorrgba(atom.get_id()) for atom in atoms]
#atom radius
radius = [vrad(atom.get_id()) for atom in atoms]
# Window size
W, H = 1200, 800
MySpheres = scene.visuals.create_visual_node(MySpheresVisual)
canvas = scene.SceneCanvas(keys='interactive',
app='pyqt4',
bgcolor='white',
size=(W, H),
show=True)
view = canvas.central_widget.add_view()
view.camera = ArcballCamera() #(fov=20, distance=300)
MySpheres(coordinates, color, radius, W, H, parent=view.scene)
canvas.app.run()
color = []
chains = []
chain_coords = []
chain_colors = []
chain_radius = []
for chain in structure.get_chains():
chains.append(chain)
can_coord = np.array([atom.coord for atom in chain.get_atoms() if atom.get_name() =='CA' or atom.get_name() =='N'])
can_coord -= center
chain_coords.append(can_coord)
chain_length = len(can_coord)
chain_color = np.random.rand(1,3)
chain_colors.append(chain_color)
color.append(np.tile(chain_color,(chain_length,1)))
chain_radius.append(np.array([4*vrad(atom.get_id()) for atom in chain.get_atoms() if atom.get_name() =='CA' or atom.get_name() =='N']))
if len(chains)>1:
color = np.concatenate(color)
W,H = 1200, 800
Plot3D = scene.visuals.create_visual_node(visuals.LinePlotVisual)
canvas = scene.SceneCanvas(keys='interactive', app='pyqt4', bgcolor='white', title='Spheres',
size=(W,H), show=True)
view = canvas.central_widget.add_view()
view.camera = ArcballCamera(fov=95, distance=(max(abs(np.concatenate(coordinates))) + 40))
for i in range(len(chains)):
Plot3D(chain_coords[i], marker_size=chain_radius[i], width=10.0, color=chain_colors[i], edge_color='b', symbol='o', face_color=chain_colors[i], parent=view.scene)
canvas.app.run()
def plot_sphere_shell_vispy(func,
rows=100,
cols=100,
radius=1.,
opacity=1.,
translation=(0., 0., 0.),
method='latitude',
edge_color=None,
cmap='hsv',
smooth=0,
cutoff=0.4,
cutoff_max=0.8,
transparent_side=True,
**kwargs):
'''func must be a function of sphere angles theta, phi'''
from vispy.scene import Sphere, ArcballCamera
s = Sphere(rows=rows,
cols=cols,
method=method,
edge_color=edge_color,
radius=radius)
mesh = s.mesh
md = mesh._meshdata
vertices = md.get_vertices()
md.set_vertices(vertices + n.array(translation))
values = n.zeros(len(vertices))
opacities = n.ones(len(vertices))
print('pre')
for i, vertex in enumerate(vertices):
if i % 10 == 0:
vprint('\ri = {} / {}'.format(i, len(vertices)), newline=False)
vertex = vertex / n.sqrt(n.sum(vertex * vertex))
theta = n.arccos(vertex[2])
phi = n.arctan2(vertex[1], vertex[0])
if n.isnan(theta):
theta = 0.0
values[i] = func(theta, phi)
distance = vertex[1] - cutoff
distance_frac = distance / (cutoff_max - cutoff)
opacity = max(0, 1. - distance_frac)
opacities[i] = 1. if vertex[1] < cutoff else opacity
vprint()
colours = n.zeros((len(values), 4))
max_val = n.max(values)
min_val = n.min(values)
unique_values = n.unique(colours)
# max_val += (1. + 1./len(unique_values))*(max_val - min_val)
diff = (max_val - min_val)
import matplotlib.pyplot as plt
cm = plt.get_cmap(cmap)
for i in range(len(colours)):
colours[i] = cm(((values[i] - min_val) / diff))
colours[:, -1] = opacity
faces = md.get_faces()
for si in range(smooth):
new_colours = [[n.array(row) for _ in range(3)] for row in colours]
for i, face in enumerate(faces):
new_colours[face[0]].append(colours[face[1]])
new_colours[face[0]].append(colours[face[2]])
new_colours[face[1]].append(colours[face[0]])
new_colours[face[1]].append(colours[face[2]])
new_colours[face[2]].append(colours[face[0]])
new_colours[face[2]].append(colours[face[1]])
new_colours = n.array([n.average(cs, axis=0) for cs in new_colours])
colours = new_colours
colours = [(c[0], c[1], c[2], o) for c, o in zip(colours, opacities)]
md.set_vertex_colors(colours)
ensure_vispy_canvas()
vispy_canvas.view.camera = ArcballCamera(fov=30)
vispy_canvas.view.add(s)
vispy_canvas.show()
return colours
