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 compare_with_file(fname, dx, NA, lam, n):
u1 = read3dTiff(fname)
Nz, Ny, Nx = u1.shape
u2 = psf((Nx, Ny, Nz), (dx, ) * 3, lam, NA, n0=n)
u1 *= 1. / np.amax(u1)
u2 *= 1. / np.amax(u2)
x = dx * (np.arange(Nx) - Nx / 2)
z = dx * (np.arange(Nz) - Nz / 2)
pylab.clf()
pylab.subplot(2, 1, 1)
pylab.title("NA = %s n = %s" % (NA, n))
pylab.plot(x, u1[Nz / 2, Ny / 2, :], label="file_x")
pylab.plot(x, u2[Nz / 2, Ny / 2, :], label="u_x")
pylab.plot(x, theory_x(x, lam, NA, n), color="k", label="theor_x")
pylab.legend()
pylab.subplot(2, 1, 2)
pylab.plot(z, u1[:, Ny / 2, Nx / 2], label="file_z")
pylab.plot(z, u2[:, Ny / 2, Nx / 2], label="u_z")
pylab.plot(z, theory_z(z, lam, NA, n), color="k", label="theor_z")
#pylab.plot(z,theory_debye_z(z,lam,NA,n),"o",color="r",label="debye_z")
pylab.legend()
pylab.show()
return u1, u2
def compare_with_theory(shape, dx, NA, lam, n):
Nz, Ny, Nx = shape
u2 = psf((Nx, Ny, Nz), (dx, ) * 3, lam, NA, n0=n)
u2 *= 1. / np.amax(u2)
x = dx * (np.arange(Nx) - Nx / 2)
z = dx * (np.arange(Nz) - Nz / 2)
# pylab.plot(x,u2[Nz/2,Ny/2,:],label="u2_x")
# pylab.plot(x,theory_x(x,lam,NA,n),color="k",label="theor_x")
#pylab.figure()
pylab.clf()
pylab.subplot(2, 1, 1)
pylab.plot(x, u2[Nz / 2, Ny / 2, :], label="u2_x")
pylab.plot(x, theory_x(x, lam, NA, n), label="theor_x")
#pylab.plot(x,theory_debye_x(x,lam,NA,n),label="debye_x")
pylab.title("NA = %s n = %s" % (NA, n))
pylab.legend()
pylab.subplot(2, 1, 2)
pylab.plot(z, u2[:, Ny / 2, Nx / 2], label="u2_z")
pylab.plot(z, theory_z(z, lam, NA, n), label="theor_z")
pylab.plot(z, theory_debye_z(z, lam, NA, n), label="debye_z")
pylab.legend()
pylab.show()
return u2
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 compare_with_theory(shape, dx, NA,lam,n):
Nz,Ny,Nx = shape
u2 = psf((Nx, Ny, Nz), (dx,) * 3, lam, NA, n0=n)
u2 *= 1./np.amax(u2)
x = dx*(np.arange(Nx)-Nx/2)
z = dx*(np.arange(Nz)-Nz/2)
# pylab.plot(x,u2[Nz/2,Ny/2,:],label="u2_x")
# pylab.plot(x,theory_x(x,lam,NA,n),color="k",label="theor_x")
#pylab.figure()
pylab.clf()
pylab.subplot(2,1,1)
pylab.plot(x,u2[Nz/2,Ny/2,:],label="u2_x")
pylab.plot(x,theory_x(x,lam,NA,n),label="theor_x")
#pylab.plot(x,theory_debye_x(x,lam,NA,n),label="debye_x")
pylab.title("NA = %s n = %s"%(NA,n))
pylab.legend()
pylab.subplot(2,1,2)
pylab.plot(z,u2[:,Ny/2,Nx/2],label="u2_z")
pylab.plot(z,theory_z(z,lam,NA,n),label="theor_z")
pylab.plot(z,theory_debye_z(z,lam,NA,n),label="debye_z")
pylab.legend()
pylab.show()
return u2
def compare_with_file(fname,dx, NA,lam,n):
u1 = read3dTiff(fname)
Nz,Ny,Nx = u1.shape
u2 = psf((Nx, Ny, Nz), (dx,) * 3, lam, NA, n0=n)
u1 *= 1./np.amax(u1)
u2 *= 1./np.amax(u2)
x = dx*(np.arange(Nx)-Nx/2)
z = dx*(np.arange(Nz)-Nz/2)
pylab.clf()
pylab.subplot(2,1,1)
pylab.title("NA = %s n = %s"%(NA,n))
pylab.plot(x,u1[Nz/2,Ny/2,:],label="file_x")
pylab.plot(x,u2[Nz/2,Ny/2,:],label="u_x")
pylab.plot(x,theory_x(x,lam,NA,n),color="k",label="theor_x")
pylab.legend()
pylab.subplot(2,1,2)
pylab.plot(z,u1[:,Ny/2,Nx/2],label="file_z")
pylab.plot(z,u2[:,Ny/2,Nx/2],label="u_z")
pylab.plot(z,theory_z(z,lam,NA,n),color="k",label="theor_z")
#pylab.plot(z,theory_debye_z(z,lam,NA,n),"o",color="r",label="debye_z")
pylab.legend()
pylab.show()
return u1, u2
def _get_error(shape, dx, NA,lam,n):
Nz,Ny,Nx = shape
u2 = psf((Nx, Ny, Nz), (dx,) * 3, lam, NA, n0=n)
u2 *= 1./np.amax(u2)
x = dx*(np.arange(Nx)-Nx/2)
z = dx*(np.arange(Nz)-Nz/2)
u2_z = u2[:,Ny/2,Nx/2]
u_z = theory_z(z,lam,NA,n)
u2_x = u2[Nz/2,Ny/2,:]
u_x = theory_x(x,lam,NA,n)
return np.sqrt(np.mean((u_x-u2_x)**2))+np.sqrt(np.mean((u_z-u2_z)**2))
def _get_error(shape, dx, NA, lam, n):
Nz, Ny, Nx = shape
u2 = psf((Nx, Ny, Nz), (dx, ) * 3, lam, NA, n0=n)
u2 *= 1. / np.amax(u2)
x = dx * (np.arange(Nx) - Nx / 2)
z = dx * (np.arange(Nz) - Nz / 2)
u2_z = u2[:, Ny / 2, Nx / 2]
u_z = theory_z(z, lam, NA, n)
u2_x = u2[Nz / 2, Ny / 2, :]
u_x = theory_x(x, lam, NA, n)
return np.sqrt(np.mean((u_x - u2_x)**2)) + np.sqrt(np.mean(
(u_z - u2_z)**2))
u = abs(ex)**2+abs(ey)**2+abs(ez)**2
return u,ex,ey,ez
if __name__ == '__main__':
NA = .95
lam = .5
Nx = 256
Ny = 164
Nz = 100
dx = 0.008
u, ex,ey,ez = psf((Nx,Ny,Nz),(dx,)*3,lam=lam, NA = NA, return_field=True)
#
x = dx*(np.arange(Nx)-Nx/2.)
y = dx*(np.arange(Ny)-Ny/2.)
ex0 = np.array([debye_integral_at_point(_x,.5*dx,.5*dx, 2*np.pi/lam,NA,
n_int = 1000)[1] for _x in x])
ex1 = np.array([debye_integral_at_point(.5*dx,_x,.5*dx, 2*np.pi/lam,NA,
n_int = 1000)[1] for _x in x])
#ex1 = ex[Nz/2,Ny/2,:]
u = abs(ex)**2 + abs(ey)**2 + abs(ez)**2
return u, ex, ey, ez
if __name__ == '__main__':
NA = .95
lam = .5
Nx = 256
Ny = 164
Nz = 100
dx = 0.008
u, ex, ey, ez = psf((Nx, Ny, Nz), (dx, ) * 3,
lam=lam,
NA=NA,
return_field=True)
#
x = dx * (np.arange(Nx) - Nx / 2.)
y = dx * (np.arange(Ny) - Ny / 2.)
ex0 = np.array([
debye_integral_at_point(_x,
.5 * dx,
.5 * dx,
2 * np.pi / lam,
NA,
n_int=1000)[1] for _x in x
])
ex1 = np.array([
