(NLAYERS, HEIGHT, WIDTH), radius=20, pitch=7, no=1.5, ne=1.65,
nhost=1.5) #approx 50*7*1.5 nm bragg reflection
#: create right-handed polarized input light
beta = 0.3 #make it off-axis
#window = dtmm.aperture((HEIGHT, WIDTH),0.9,0.)
window = None
#jones = dtmm.jonesvec((1,1j))
jones = None
focus = 20 #this will focus field diaphragm in the middle of the stack
field_data_in = dtmm.illumination_data((HEIGHT, WIDTH),
WAVELENGTHS,
jones=jones,
beta=beta,
pixelsize=PIXELSIZE,
n=1.5,
focus=focus,
window=window)
#: transfer input light through stackt
field_data_out = dtmm.transfer_field(field_data_in,
optical_data,
beta=beta,
phi=0,
diffraction=1,
method="4x4",
smooth=0.1,
reflection=2,
nin=1.5,
nout=1.5,
NLAYERS, HEIGHT, WIDTH = 60, 96, 96
#: illumination wavelengths in nm
WAVELENGTHS = np.linspace(380, 780, 9)
#: create some experimental data (stack)
optical_data = [
dtmm.nematic_droplet_data((NLAYERS, HEIGHT, WIDTH),
radius=30,
profile="r",
no=1.5,
ne=1.6,
nhost=1.5)
]
#: create non-polarized input light
field_data_in = dtmm.illumination_data((HEIGHT, WIDTH),
WAVELENGTHS,
pixelsize=PIXELSIZE)
#: transfer input light through stack
field_data_out = dtmm.transfer_field(field_data_in,
optical_data,
diffraction=0,
betamax=1)
#: visualize output field
# no diffraction to simulate output of standard jones method
viewer1 = dtmm.field_viewer(field_data_out, diffraction=False)
viewer1.set_parameters(sample=0, intensity=2, polarizer=0, analyzer=90)
fig, ax = viewer1.plot()
ax.set_title("diffraction = 0")
field_data_out = dtmm.transfer_field(field_data_in,
optical_data = dtmm.nematic_droplet_data((NLAYERS, HEIGHT, WIDTH),
radius=30,
profile="r",
no=1.5,
ne=1.6,
nhost=1.5)
#optical_data[0][...]=1
#optical_data[1][0,...]=1
#optical_data[1][-1,...]=1
window = dtmm.aperture((96, 96), 0.95, 0.)
window = None
#: create non-polarized input light
field_data_in = dtmm.illumination_data((HEIGHT, WIDTH),
WAVELENGTHS,
beta=0.,
pixelsize=PIXELSIZE,
window=window)
f, w, p = dtmm.transfer_field(field_data_in,
optical_data,
beta=0.,
phi=0.,
betamax=0.8,
method="4x4",
ret_bulk=True,
npass=4,
reflection=2,
smooth=0.1) #must be even for 4x4 method
viewer_bulk = dtmm.field_viewer((f, w, p), bulk_data=True)
"""EM field example"""
import dtmm
import numpy as np
import matplotlib.pyplot as plt
WAVELENGTHS = [500, 600]
SIZE = (128, 128)
window = dtmm.aperture((128, 128))
field_data = dtmm.illumination_data(SIZE,
WAVELENGTHS,
window=window,
jones=(1, 0),
pixelsize=200,
beta=(0, 0.1, 0.2),
phi=(0., 0., np.pi / 6))
field = field_data[0]
#500nm
Ex = field[:, 0, 0] #Ex of the x-polarized light
subplots1 = [plt.subplot(i) for i in (231, 232, 233)]
subplots2 = [plt.subplot(i) for i in (234, 235, 236)]
for i, ax in enumerate(subplots1):
ax.imshow(Ex[i].real, origin="lower")
d = np.ones(shape=(NLAYERS, ))
epsv = np.empty(shape=(NLAYERS, HEIGHT, 3), dtype=dtmm.conf.CDTYPE)
epsv[..., 0] = no**2
epsv[..., 1] = no**2
epsv[..., 2] = ne**2
beta, phi, intensity = 0, 0, 1
#we use 3D non-polarized data and convert it to 2D
field_data_in = dtmm.illumination_data((HEIGHT, 1),
WAVELENGTHS,
jones=None,
beta=beta,
phi=phi,
intensity=intensity,
pixelsize=PIXELSIZE,
n=nin,
betamax=0.8)
field_data_in2d = field_data_in[0][..., 0], field_data_in[1], field_data_in[2]
optical_data2d = [(d, epsv, epsa)]
f, w, p = field_data_in2d
shape = f.shape[-1]
k0 = wave.k0(w, p)
mask, fmode_in = field.field2modes1(f, k0)
radius=30,
profile="r",
no=1.5,
ne=1.6,
nhost=1.5)
#NA 0.25, diaphragm with diameter 4 pixels, around 2*2*pi rays
beta, phi, intensity = dtmm.illumination_rays(0.25, 4)
window = dtmm.aperture((HEIGHT, WIDTH), 1, 0.1)
field_data_in = dtmm.illumination_data((HEIGHT, WIDTH),
WAVELENGTHS,
PIXELSIZE,
beta,
phi,
intensity,
window=window,
n=1.5,
focus=30)
field_data_out = dtmm.transfer_field(field_data_in,
optical_data,
multiray=True,
nin=1.5,
nout=1.5)
viewer = dtmm.field_viewer(field_data_out,
sample=0,
intensity=2,
n=1.5,
radius=30,
profile="r",
no=1.5,
ne=1.6,
nhost=1.5)
]
#using annular aperture, approximate ratio of aperture dimaters is inner/outer = 6/7
#: max NA is set to 0.7., this means input rays from NA of 0.6 to 0.7
beta, phi, intensity = dtmm.illumination_rays(0.7, (6, 7))
#: care must be taken when using high NA light source, we must usee a high betamax parameter
field_data_in = dtmm.illumination_data((HEIGHT, WIDTH),
WAVELENGTHS,
PIXELSIZE,
beta,
phi,
intensity,
focus=30,
betamax=1)
#: also in the calculation, we must perform it at high betamax
field_data_out = dtmm.transfer_field(field_data_in,
optical_data,
multiray=True,
betamax=1)
# we must set the numarical aperture of the objective lower than the minimum NA of the illumination.
viewer = dtmm.pom_viewer(field_data_out,
intensity=10,
NA=0.5,
focus=-20,
r = _r(shape).flatten() #radial coordinate for fitting
def gauss(r, w, a):
return a * np.exp(-2 * (r / w)**2)
def beam_waist(z, w0, k):
z0 = w0**2 * k / 2.
return w0 * (1 + (z / z0)**2)**0.5
window = dtmm.window.gaussian_beam(shape, w0, dtmm.k0(600, 50), n=n, z=0)
field, w, p = dtmm.illumination_data(shape, [w],
pixelsize=50,
n=n,
window=window,
jones=(1, 0))
ks = dtmm.k0(w, p)
epsv = dtmm.refind2eps([n] * 3)
power = dtmm.field2intensity(field)
plt.subplot(121)
plt.imshow(power[0])
plt.title("z=0")
waist = []
z = np.linspace(-512, 512, 13)
for d in z:
import numpy as np
dtmm.conf.set_verbose(2)
#: pixel size in nm
PIXELSIZE = 200
#: compute box dimensions
NLAYERS, HEIGHT, WIDTH = 60,96,96
#: illumination wavelengths in nm
WAVELENGTHS = np.linspace(380,780,9)
#: create some experimental data (stack)
d, epsv, epsa = dtmm.nematic_droplet_data((NLAYERS, HEIGHT, WIDTH),
radius = 30, profile = "x", no = 1.5, ne = 1.6, nhost = 1.5)
#: create non-polarized input light
f,w,p = dtmm.illumination_data((HEIGHT, WIDTH), WAVELENGTHS,
pixelsize = PIXELSIZE, beta = 0., phi = 0.)
field_data_in = f,w,p
#transpose to field vector
ft = dtmm.field.field2fvec(f)
# build kd phase values
kd = [x*(dtmm.k0(WAVELENGTHS, PIXELSIZE))[...,None,None] for x in d]
#build stack matrix and transmit...
cmat = dtmm.tmm.stack_mat(kd, epsv, epsa, method = "2x2")
#convert field vector to E vector (assuming vacuum)
Ein_2x2 = dtmm.tmm.fvec2E(ft)
Eout_2x2 = dtmm.linalg.dotmv(cmat,Ein_2x2)
#convert E vector to field vector (assuming vacuum)
NLAYERS, HEIGHT, WIDTH = 1,96,96
#: illumination wavelengths in nm
WAVELENGTHS = np.linspace(400,700,9)
#: some experimental data
BETA = 0.4
epsv = dtmm.refind2eps([4,4,4]) #high reflective index medium, to increase reflections.
epsa = (0.,0.,0.)
optical_data = [(THICKNESS, epsv, epsa)]
window = dtmm.aperture((HEIGHT, WIDTH),0.2,1)
#illumination data is focused at the top (exit) surface (actual focus = focus * ref_ind = 25*4=100)
field_data_in = dtmm.illumination_data((HEIGHT, WIDTH), WAVELENGTHS, window = window,
beta = BETA, pixelsize = PIXELSIZE,focus = 25.,n=1)
#illumination filed is defined in vacuum, so we make input and output medium with n = 1.
field_data_out = dtmm.transfer_field(field_data_in, optical_data, beta = BETA, phi = 0.,
reflection = 2, diffraction =1, npass = 3, method = "2x2",nin = 1, nout = 1)
#we are viewing computed data in vacuum, so set n = 1.
viewer4 = dtmm.field_viewer(field_data_in, mode = "t", intensity = 1,n = 1.)
fig4,ax4 = viewer4.plot()
ax4.set_title("Input field")
#: visualize output field
viewer1 = dtmm.field_viewer(field_data_out, mode = "t",intensity = 1,n = 1.)
fig1,ax1 = viewer1.plot()
ax1.set_title("Transmitted field")
