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,
npass=5,
norm=2)
#: visualize output field
viewer1 = dtmm.field_viewer(field_data_out,
mode="t",
n=1.5,
intensity=0.5,
focus=-20)
fig1, ax1 = viewer1.plot()
ax1.set_title("Transmitted field")
units of coefficient b are microns**2
"""
epsc = EpsilonCauchy(shape=(NLAYERS, HEIGHT, WIDTH), n=2)
epsc.coefficients[..., 0] = (epsv)**0.5 # a term, just set to refractive index
epsc.coefficients[..., 0:2,
1] = 0.005 * (epsv[..., 0:2])**0.5 # b term ordinary
epsc.coefficients[..., 2,
1] = 0.005 * (epsv[..., 2])**0.5 # b term extraordinary
#redefien optical data, setting epsc as
optical_data = [(d, epsc, epsa)]
#: create non-polarized input light
field_data_in = dtmm.field.illumination_data((HEIGHT, WIDTH),
WAVELENGTHS,
pixelsize=PIXELSIZE)
#: transfer input light through stack. We must split wavelength and compute for each wavelength.
#: the algorithm computes epsv values from the cauchy coefficient for each of the wavelengths.
field_data_out = dtmm.transfer_field(field_data_in,
optical_data,
split_wavelengths=True)
#: visualize output field
viewer = dtmm.pom_viewer(field_data_out)
viewer.set_parameters(polarizer="h", analyzer="v", focus=-18)
fig, ax = viewer.plot()
plt.show()
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,
diffraction=1,
betamax=1)
viewer2 = dtmm.field_viewer(field_data_out)
#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)
viewer_bulk.set_parameters(sample=0,
intensity=1,
polarizer=0,
focus=0,
analyzer=0)
fig, ax = viewer_bulk.plot()
"""Hello nematic droplet example."""
import dtmm
import numpy as np
import matplotlib.pyplot as plt
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)
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.field.illumination_data((HEIGHT, WIDTH), WAVELENGTHS,
pixelsize = PIXELSIZE)
#: transfer input light through stack
field_data_out = dtmm.transfer_field(field_data_in, optical_data)
#: visualize output field
viewer = dtmm.pom_viewer(field_data_out)
viewer.set_parameters(polarizer = "h", analyzer = "v", focus = -18)
fig,ax = viewer.plot()
plt.show()
"""Nematic droplet example using bulk data calculation and bulk viewer"""
import dtmm
import numpy as np
#: pixel size in nm
PIXELSIZE = 200
#: compute box dimensions
NLAYERS, HEIGHT, WIDTH = 60, 96, 96
#: illumination wavelengths in nm
WAVELENGTHS = [550]
#: 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 and compute bulk EM field
field_data_out = dtmm.transfer_field(field_data_in, optical_data, ret_bulk = True)
#: visualize output field
viewer = dtmm.field_viewer(field_data_out, bulk_data = True)
viewer.set_parameters(sample = 0, intensity = 2,
polarizer = 0, focus = 20, analyzer = 90)
fig,ax = viewer.plot()
#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,
polarizer=0,
focus=-30,
analyzer=90,
polarization="mode")
fig, ax = viewer.plot()
fig.show()
1 * np.sin(np.linspace(0, np.pi / 2048 * PIXELSIZE * WIDTH, WIDTH))**2)
mod = eps_periodic()
e[..., 2] = mod[None, None, :]
window = dtmm.aperture((HEIGHT, WIDTH), 0.1, 1)
#: create non-polarized input light
field_data_in = dtmm.illumination_data((HEIGHT, WIDTH),
WAVELENGTHS,
jones=(1, 0),
pixelsize=PIXELSIZE,
window=window)
#: transfer input light through stack
f, w, p = dtmm.transfer_field(field_data_in, (d, e, a),
betamax=np.inf,
diffraction=1)
ff = np.fft.fftshift(dtmm.fft.fft2(f), axes=(-2, -1))
i = dtmm.field2specter(ff)
cmf = dtmm.load_tcmf(w)
c = dtmm.specter2color(i, cmf, norm=True)
plt.imshow(c)
plt.title("far field - fft of the near field")
#: visualize output field
viewer1 = dtmm.field_viewer((f, w, p), betamax=1)
viewer1.set_parameters(sample=0,
intensity=2,
polarizer=None,
focus=0,
]
#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,
beta=beta)
fig, ax = viewer.plot()
fig.show()
window = dtmm.aperture((96, 96), 0.95, 0.)
window = None
#: create non-polarized input light
(fin2, w, p) = dtmm.illumination_data((HEIGHT, WIDTH),
WAVELENGTHS,
beta=0.,
pixelsize=PIXELSIZE,
window=window)
(fin4, w, p) = (fin2.copy(), w, p)
(f2, w, p) = dtmm.transfer_field((fin2, w, p),
optical_data,
beta=0.,
phi=0.,
betamax=betamax,
method="2x2",
ret_bulk=False,
npass=9,
reflection=2)
(f4, w, p) = dtmm.transfer_field((fin4, w, p),
optical_data,
beta=0.,
phi=0.,
betamax=betamax,
method="4x4",
ret_bulk=False,
npass=9,
reflection=2)
#: 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")
#: residual back propagating field is close to zero
viewer2 = dtmm.field_viewer(field_data_out, mode = "r",intensity = 1,n = 1.)
fig2,ax2 = viewer2.plot()
temp_director = dtmm.nematic_droplet_director(shape, radius, "r")
# Export the data to a text file
temp_director.tofile("director.txt", sep=",")
# --- Read in director and convert optical data
# Read director from text file
director = dtmm.read_director("director.txt", (n_layers, height, width, 3), sep=",")
# Create the mask for a spherical
mask = dtmm.sphere_mask(shape, radius)
# Covert director, mask, and physical parameters into optical data
optical_data = dtmm.director2data(director, mask, no, ne, nhost)
# ----
# Generate wavelengths
wavelengths = np.linspace(380, 780, 9)
# Size of each pixel in nm
pixel_size = 200
# Generate input light field
input_light_field = dtmm.field.illumination_data((height, width), wavelengths, pixel_size)
# Generate output light field using 4x4 method
output_light_field = dtmm.transfer_field(input_light_field, optical_data, method="4x4")
#: visualize output field
viewer = dtmm.field_viewer(output_light_field)
viewer.set_parameters(focus=-14, intensity=2,
sample=0, analyzer=90, polarizer=0)
fig, _ = viewer.plot()
# Show figure
fig.show()
None, :])
optical_data = (d, eps_values[:, None, None, :], eps_angles[:, None, None, :])
#: create non-polarized input light
field_data_in = dtmm.field.illumination_data((1, 1),
wavelengths,
beta=beta,
phi=phi,
diffraction=False,
pixelsize=step)
#: transfer input light through stack
field_data_out = dtmm.transfer_field(field_data_in,
optical_data,
beta=beta,
phi=phi,
method="2x2",
reflection=2,
diffraction=False)
f, w, p = field_data_out
Txx2 = field2poynting(dotmf(
x_polarizer,
f[0]))[..., 0,
0] * 2 #times two, because field_data_in[0][0] has intensity of 0.5
Tyx2 = field2poynting(dotmf(y_polarizer, f[0]))[..., 0, 0] * 2
Txy2 = field2poynting(dotmf(
x_polarizer,
f[1]))[..., 0,
0] * 2 #times two, because field_data_in[0][1] has intensity of 0.5
Tyy2 = field2poynting(dotmf(y_polarizer, f[1]))[..., 0, 0] * 2
"""Hello nematic droplet example."""
import dtmm
import numpy as np
import matplotlib.pyplot as plt
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)
optical_block = 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.field.illumination_data((HEIGHT, WIDTH), WAVELENGTHS,
pixelsize = PIXELSIZE)
#: transfer input light through stack
field_data_out = dtmm.transfer_field(field_data_in, [optical_block])
#: visualize output field
viewer = dtmm.pom_viewer(field_data_out)
viewer.set_parameters(polarizer = "h", analyzer = "v", focus = -18)
fig,ax = viewer.plot()
plt.show()
window = dtmm.aperture((HEIGHT, WIDTH), 1, 0.1)
field_data_in = dtmm.illumination_data((HEIGHT, WIDTH),
WAVELENGTHS,
PIXELSIZE,
beta,
phi,
intensity,
window=window,
n=1.3,
focus=30)
field_data_out = dtmm.transfer_field(field_data_in,
optical_data,
multiray=True,
split_rays=False,
nin=1.3,
nout=1.3,
betamax=1.,
diffraction=1,
reflection=1)
#: visualize output field
viewer = dtmm.field_viewer(field_data_out, betamax=1., n=1.3)
viewer.set_parameters(sample=0,
intensity=1,
polarizer=None,
focus=-14,
analyzer=None)
fig, ax = viewer.plot()
