def _show_one_gaussian(self, gauss, engine, scale=1.0):
"""Plot one of the gaussians."""
from mayavi.sources.api import ParametricSurface
from mayavi.modules.api import Surface
source = ParametricSurface()
source.function = 'ellipsoid'
engine.add_source(source)
eigval, eigvec = np.linalg.eig(gauss.sigma)
angles = rotationMatrixToEulerAngles(eigvec.T) * 180.0 / np.pi
surface = Surface()
source.add_module(surface)
actor = surface.actor
actor.property.opacity = 0.5
actor.property.color = tuple(np.random.rand(3))
actor.mapper.scalar_visibility = False
actor.property.backface_culling = True
actor.actor.orientation = np.array([0.0, 0.0, 0.0])
actor.actor.origin = np.array([0.0, 0.0, 0.0])
actor.actor.position = np.array(gauss.mu)
actor.actor.scale = np.array(scale * np.sqrt(eigval))
actor.actor.rotate_x(angles[0])
actor.actor.rotate_y(angles[1])
actor.actor.rotate_z(angles[2])
return surface
def atomic_displacement_ellipsoids(self, ux, uy, uz,
Uxx, Uyy, Uzz, Uyz, Uxz, Uxy,
colors, p=0.99):
self.fig.scene.disable_render = True
n_atm = ux.shape[0]
for i in range(n_atm):
s, a = self.__probability_ellipsoid(Uxx[i], Uyy[i], Uzz[i],
Uyz[i], Uxz[i], Uxy[i], p)
source = ParametricSurface()
source.function = 'ellipsoid'
self.engine.add_source(source)
surface = Surface()
source.add_module(surface)
actor = surface.actor
actor.property.opacity = 1.0
actor.property.color = colors[i]
actor.mapper.scalar_visibility = False
actor.property.backface_culling = True
actor.property.diffuse = 1.0
actor.property.specular = 0.0
actor.actor.origin = np.array([0,0,0])
actor.actor.position = np.array([ux[i],uy[i],uz[i]])
actor.actor.scale = np.array([s[0],s[1],s[2]])
actor.actor.orientation = np.array([a[0],a[1],a[2]]) #ZXY
actor.enable_texture = True
actor.property.representation = 'surface'
self.fig.scene.disable_render = False
def tresdeizar(X, Y, anchox, anchoy, angulo):
engine = Engine()
engine.start()
scene = engine.new_scene()
scene.scene.disable_render = True # for speed
visual.set_viewer(scene)
surfaces = []
for k in range(0, len(X)):
source = ParametricSurface()
source.function = 'ellipsoid'
engine.add_source(source)
surface = Surface()
source.add_module(surface)
actor = surface.actor # mayavi actor, actor.actor is tvtk actor
actor.property.opacity = 0.7
actor.property.color = (0, 0, 1) # tuple(np.random.rand(3))
actor.mapper.scalar_visibility = False # don't colour ellipses by their scalar indices into colour map
actor.actor.orientation = np.array([90, angulo[k], 0
]) #* 90 #(angulo[k]) # in degrees
actor.actor.position = np.array([X[k], Y[k], 0])
actor.actor.scale = np.array(
[anchox[k] / 2, anchox[k] / 2, anchoy[k] / 2])
surfaces.append(surface)
source.scene.background = (1.0, 1.0, 1.0)
CellScann.set_img_3deizada(mlab)
return mlab.show()