def test_focus(size, units, NA=.3, n0=1.):
""" propagates a focused wave freely to the center
"""
Nx, Ny, Nz = size
dx, dy, dz = .1, .1, .1
lam = .5
_, u_debye, _, _ = psf(size,
units,
n0=n0,
lam=lam,
NA=NA,
return_field=True)
u0 = u_debye[0]
u0 = psf_u0(size[:2],
units[:2],
zfoc=.5 * units[-1] * (size[-1] - 1),
n0=n0,
lam=lam,
NA=NA)
u = bpm_3d(size, units=units, lam=lam, n0=n0, u0=u0, absorbing_width=0)
return u, u_debye
def test_focus(size, units, NA = .3, n0 = 1.):
""" propagates a focused wave freely to the center
"""
Nx, Ny, Nz = size
dx, dy , dz = .1, .1, .1
lam = .5
_, u_debye, _, _ = psf(size, units, n0= n0, lam=lam, NA=NA, return_field = True)
u0 = u_debye[0]
u0 = psf_u0(size[:2],units[:2],
zfoc = .5*units[-1]*(size[-1]-1),
n0 = n0,
lam = lam,
NA = NA)
u = bpm_3d(size,units= units, lam = lam,
n0 = n0,
u0 = u0,
absorbing_width = 0)
return u, u_debye
NA = .3
lam = .5
w = .8
dn0 = 0.1
x = dx*(np.arange(-Nx/2, Nx/2)+.5)
y = dx*(np.arange(-Nx/2, Nx/2)+.5)
z = dx*(np.arange(-Nz/2, Nz/2)+.5)
Z,Y,X = np.meshgrid(z,y,x,indexing="ij")
Z,X = np.cos(w)*Z-np.sin(w)*X, np.cos(w)*X+np.sin(w)*Z
dn = dn0*(Z>0)
u0 = psf_u0((Nx,Nx), units = (dx,)*2,zfoc = dx*(Nz-1.)/2.,lam = lam, NA= NA)
u = bpm_3d((Nx,Nx,Nz), units=(dx,)*3, lam=lam, dn =dn,
u0=u0)
u1 = np.abs(u[:Nz/2,...])[::-1,...]**2
u2 = gputools.rotate(abs(u[Nz/2:,...])**2, center = (0,Nx/2,Nx/2),
axis = (0.,1.,0),
angle = phi(dn0,w),
mode = "linear")
pylab.figure(1)
pylab.clf()
pylab.plot(u1[Nz/10,Nx/2,:])
pylab.plot(u2[Nz/10,Nx/2,:])
from six.moves import range
if __name__ == '__main__':
Nx, Nz = 256,512
dx = .5
#n = 0.05*dx*np.random.uniform(0,1.,(Nz,Nx,Nx))
#n = .05*gputools.perlin3((Nx,Nx,Nz),(4.,)*3)
n = np.zeros((Nz,Nx,Nx))
m = Bpm3d((Nx,Nx,Nz),(dx,)*3)
u = ones((Nz,Nx,Nx),complex64)
u[0] = bpm.psf_u0((Nx,Nx),(dx,dx),dx*Nz/2.,NA=.1)
u[0] *= 1./np.sqrt(np.mean(abs(u[0])**2))
t = time()
x = np.linspace(-Nx,Nx,Nx+1)[:Nx]
Y,X = np.meshgrid(x,x,indexing = "ij")
h0 = np.exp(-.1*(X**2+Y**2))
h0 *= 1./sum(h0)
h0_f = np.fft.fftn(h0)
for i in range(Nz-1):
_u = u[i]
_u = fft.fftn(_u)
_u *= m._H
_u = fft.ifftn(_u)
#_u *= exp(-dx*1.j*m.k0*n[i+1])
#dn[Nz/2:,...] = 0.0
m = Bpm3d((Nx,Nx,Nz),(dx,)*3)
def prop(n0):
H0 = np.sqrt(n0**2*m.k0**2-m._KX**2-m._KY**2)
outsideInds = np.isnan(H0)
H = np.exp(-1.j*dx*H0)
H[outsideInds] = 0.
return H
u0 = bpm.psf_u0((Nx,Nx),(dx,dx),dx*Nz/2.,NA=.3)
u0 *= 1./np.sqrt(np.mean(abs(u0)**2))
#u0 = ones((Nx,Nx),complex64)
u1 = ones((Nz,Nx,Nx),complex64)
u1[0] = u0
H1 = prop(1.)
t = time()
n0 = 1.
for i in range(Nz-1):
_u = u1[i]
_u = fft.fftn(_u)
_u *= H1
_u = fft.ifftn(_u)
_u *= exp(-dx*1.j*m.k0*(n[i+1]-n0))
from six.moves import range
if __name__ == '__main__':
Nx, Nz = 256, 512
dx = .5
#n = 0.05*dx*np.random.uniform(0,1.,(Nz,Nx,Nx))
#n = .05*gputools.perlin3((Nx,Nx,Nz),(4.,)*3)
n = np.zeros((Nz, Nx, Nx))
m = Bpm3d((Nx, Nx, Nz), (dx, ) * 3)
u = ones((Nz, Nx, Nx), complex64)
u[0] = bpm.psf_u0((Nx, Nx), (dx, dx), dx * Nz / 2., NA=.1)
u[0] *= 1. / np.sqrt(np.mean(abs(u[0])**2))
t = time()
x = np.linspace(-Nx, Nx, Nx + 1)[:Nx]
Y, X = np.meshgrid(x, x, indexing="ij")
h0 = np.exp(-.1 * (X**2 + Y**2))
h0 *= 1. / sum(h0)
h0_f = np.fft.fftn(h0)
for i in range(Nz - 1):
_u = u[i]
_u = fft.fftn(_u)
_u *= m._H
_u = fft.ifftn(_u)
#_u *= exp(-dx*1.j*m.k0*n[i+1])
w = .8
dn0 = 0.1
x = dx * (np.arange(-Nx / 2, Nx / 2) + .5)
y = dx * (np.arange(-Nx / 2, Nx / 2) + .5)
z = dx * (np.arange(-Nz / 2, Nz / 2) + .5)
Z, Y, X = np.meshgrid(z, y, x, indexing="ij")
Z, X = np.cos(w) * Z - np.sin(w) * X, np.cos(w) * X + np.sin(w) * Z
dn = dn0 * (Z > 0)
u0 = psf_u0((Nx, Nx),
units=(dx, ) * 2,
zfoc=dx * (Nz - 1.) / 2.,
lam=lam,
NA=NA)
u = bpm_3d((Nx, Nx, Nz), units=(dx, ) * 3, lam=lam, dn=dn, u0=u0)
u1 = np.abs(u[:Nz / 2, ...])[::-1, ...]**2
u2 = gputools.rotate(abs(u[Nz / 2:, ...])**2,
center=(0, Nx / 2, Nx / 2),
axis=(0., 1., 0),
angle=phi(dn0, w),
mode="linear")
pylab.figure(1)
pylab.clf()
pylab.plot(u1[Nz / 10, Nx / 2, :])
subsample = 1,
n_volumes = 1,
return_scattering = True )
u2, dn2, p2 = bpm_3d_old((Nx,Nx,Nz),units= units,
lam = lam,
dn = dn,
return_scattering = True )
return u1, u2
if __name__ == '__main__':
# test_speed()
#u = test_sphere()
N = 256
dx = .05
from bpm import psf_u0
if not "dn" in locals():
dn = np.zeros((N,)*3,np.float32)
dn[:40,...] += .2
u0 = psf_u0((N,)*2,(dx,)*2,zfoc = N/2.*dx,NA = .4)
u1 = bpm_3d(dn.shape[::-1],(dx,)*3, u0=u0,dn = dn, n_volumes=1)
#u2 = _bpm_3d2(dn.shape[::-1],(dx,)*3, u0=u0,dn = dn)