def __init__(self, data, xlabel='', title='', N=2**14, lmax=None):
self.data = np.array(data)
self.N = N # points on the sphere
# Plotting
self.xlabel = xlabel
self.title = title
# Setup renderer
self.ren, self.renWin, self.iren = utilvtk.setup_render()
# Calculate dimensions
if lmax is None:
self.lmax, mm = utilsh.j2lm(len(self.data) - 1)
else:
self.lmax = lmax
self.J = utilsh.maxl2maxj(self.lmax)
# Fill the rest of the last l band with zeros
if self.data.shape[-1] != self.J:
temp = np.zeros(self.J)
temp[:self.data.shape[-1]] = self.data
self.data = temp
else:
self.data = data
# Calc points for spherical plotting
self.xyz = utilsh.fibonacci_sphere(N, xyz=True)
self.B = utilsh.calcB(self.N, self.J)
self.Binv = np.linalg.pinv(self.B, rcond=1e-15)
def __init__(self, data_xyz, data_J, shape=[10,10,4], N=2**12, title=''):
self.data_xyz = np.array(data_xyz)
self.data_J = np.array(data_J)
self.M = self.data_xyz.shape[0]
self.N = N
self.shape = shape # um
self.xlabel = utilmpl.shape2xlabel(self.shape)
self.title = title
# Calculate dimensions
self.lmax, mm = utilsh.j2lm(self.data_J.shape[-1] - 1)
self.J = utilsh.maxl2maxj(self.lmax)
# Fill the rest of the last l band with zeros
if self.data_J.shape[-1] != self.J:
temp = np.zeros(self.J)
temp[:self.data_J.shape[-1]] = np.array(self.data_J)
self.data_J = temp
# Calc points for spherical plotting
self.xyz = utilsh.fibonacci_sphere(N, xyz=True)
self.B = utilsh.calcB(self.N, self.J)
def guv(center=[0,0,0], radius=0.5, N=2**10, M=2**10, ellip_ratio=0.5,
dist_type='ellipsoid'):
xyz_guv = utilsh.fibonacci_sphere(M/8, xyz=True) # Points on guv
# Respect D4 symmetry
xyz_guv_flip = np.vstack([xyz_guv[:,1], xyz_guv[:,0], xyz_guv[:,2]]).T
xyz_guv = np.vstack([xyz_guv,
xyz_guv*[-1,1,1],
xyz_guv*[1,-1,1],
xyz_guv*[-1,-1,1],
xyz_guv_flip,
xyz_guv_flip*[-1,1,1],
xyz_guv_flip*[1,-1,1],
xyz_guv_flip*[-1,-1,1]])
xyz_list = (xyz_guv*radius + center) # Scaled and center
j_list = np.zeros((M, N))
for m in tqdm(range(M)):
if dist_type == 'ellipsoid':
j_list[m,:] = uniaxial_ellipsoid(1, ellip_ratio, xyz_guv[m], N=N)
elif dist_type == 'uniform':
j_list[m,:] = np.ones((N,))
return xyz_list, j_list
def to_R3toR3_xyz(self, N=2**10):
xyz = utilsh.fibonacci_sphere(N, xyz=True)
max_indices = np.argmax(self.data_j, axis=1)
xyz_max = np.einsum('ij,i->ij', xyz[max_indices], np.max(self.data_j, axis=-1))
return R3toR3.xyz_list(self.data_xyz, xyz_max, shape=self.shape,
xlabel=self.xlabel, title='Peaks')
def ellipsoid(pradii, paxes, N=2**12):
xyz = utilsh.fibonacci_sphere(N, xyz=True)
xyz_rot = np.einsum('ij,kj->ik', xyz, paxes) # Rotate
return 1/np.linalg.norm(xyz_rot/np.array(pradii), ord=2, axis=-1)
def draw_sphere_field(ren, centers, radii, plot_negative=True):
M = radii.shape[0]
N = radii.shape[1]
vertices = utilsh.fibonacci_sphere(radii.shape[-1], xyz=True)
faces = ConvexHull(vertices).simplices
# Split into positive and negative
if plot_negative:
iradiis = [radii.clip(min=0), -radii.clip(max=0)]
else:
iradiis = [radii.clip(min=0)]
# For both positive and negative
for i, iradii in enumerate(iradiis):
# Calculate vertices
xyz_vertices = np.einsum('ij,ki->ikj', vertices, iradii) + centers
all_xyz = xyz_vertices.reshape(-1, xyz_vertices.shape[-1], order='F') # Reshape
all_xyz_vtk = numpy_support.numpy_to_vtk(all_xyz, deep=True) # Convert to vtk
# Calculate faces
all_faces = []
for j in range(M):
all_faces.append(faces + j*N)
all_faces = np.concatenate(all_faces)
all_faces = np.hstack((3 * np.ones((len(all_faces), 1)), all_faces))
all_faces = np.ascontiguousarray(all_faces.ravel(), dtype='i8')
all_faces_vtk = numpy_support.numpy_to_vtkIdTypeArray(all_faces, deep=True)
# Populate points
points = vtk.vtkPoints()
points.SetData(all_xyz_vtk)
# Calculate cells
ncells = len(all_faces)
cells = vtk.vtkCellArray()
cells.SetCells(ncells, all_faces_vtk)
# Populate polydata
polydata = vtk.vtkPolyData()
polydata.SetPoints(points)
polydata.SetPolys(cells)
# Calculate colors
# TODO: Generalize colormaps
cols = 255*np.ones(all_xyz.shape)
iradiif = radii.flatten()
if i == 0: # Red to white
cols[:,1] = 255*(1-iradiif/(np.max(iradiif) + 1e-5))
cols[:,2] = 255*(1-iradiif/(np.max(iradiif) + 1e-5))
else: # Blue to white
cols[:,0] = 255*(iradiif/(np.max(iradiif) + 1e-5))
cols[:,1] = 255*(iradiif/(np.max(iradiif) + 1e-5))
vtk_colors = numpy_support.numpy_to_vtk(cols, deep=True, array_type=vtk.VTK_UNSIGNED_CHAR)
polydata.GetPointData().SetScalars(vtk_colors)
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputData(polydata)
# Create actor
actor = vtk.vtkActor()
actor.SetMapper(mapper)
actor.GetProperty().SetAmbient(0.25)
ren.AddActor(actor)