def main():
args = parse_args()
syris.init()
n = 1024
d = args.propagation_distance * q.m
shape = (n, n)
ps = 1 * q.um
energy = 20 * q.keV
tr = Trajectory([(n / 2, n / 2, 0)] * ps, pixel_size=ps)
sample = make_sphere(n, n / 30 * ps, pixel_size=ps, material=get_material('air_5_30_kev.mat'))
bm = make_topotomo(pixel_size=ps, trajectory=tr)
print 'Source size FWHM (height x width): {}'.format(bm.size.rescale(q.um))
u = bm.transfer(shape, ps, energy, t=0 * q.s)
u = sample.transfer(shape, ps, energy)
intensity = propagate([sample], shape, [energy], d, ps).get()
incoh = bm.apply_blur(intensity, d, ps).get()
region = (n / 4, n / 4, n / 2, n / 2)
intensity = ip.crop(intensity, region).get()
incoh = ip.crop(incoh, region).get()
show(intensity, title='Coherent')
show(incoh, title='Applied source blur')
plt.show()
def main():
args = parse_args()
syris.init()
n = 1024
d = args.propagation_distance * q.m
shape = (n, n)
ps = 1 * q.um
energy = 20 * q.keV
tr = Trajectory([(n / 2, n / 2, 0)] * ps, pixel_size=ps)
sample = make_sphere(n,
n / 30 * ps,
pixel_size=ps,
material=get_material('air_5_30_kev.mat'))
bm = make_topotomo(pixel_size=ps, trajectory=tr)
print 'Source size FWHM (height x width): {}'.format(bm.size.rescale(q.um))
u = bm.transfer(shape, ps, energy, t=0 * q.s)
u = sample.transfer(shape, ps, energy)
intensity = propagate([sample], shape, [energy], d, ps).get()
incoh = bm.apply_blur(intensity, d, ps).get()
region = (n / 4, n / 4, n / 2, n / 2)
intensity = ip.crop(intensity, region).get()
incoh = ip.crop(incoh, region).get()
show(intensity, title='Coherent')
show(incoh, title='Applied source blur')
plt.show()
def compute_intensity(self, t_0, t_1, shape, pixel_size, queue=None, block=False):
"""Compute intensity between times *t_0* and *t_1*."""
exp_time = (t_1 - t_0).simplified.magnitude
image = propagate(self.samples, shape, self.energies, self.propagation_distance,
pixel_size, detector=self.detector, t=t_0) * exp_time
return image
def propagate_one(unused, queue, shape, energies, distance, ps, spheres):
# Make sure we use the sample created by this *queue*
sample = spheres[queue]
return propagate([sample],
shape,
energies,
distance,
ps,
mollified=False,
queue=queue,
block=True).real.get()
def main():
args = parse_args()
syris.init()
# Propagate to 20 cm
d = 5 * q.cm
# Compute grid
n_camera = 256
n = n_camera * args.supersampling
shape = (n, n)
material = get_material("pmma_5_30_kev.mat")
energy = 15 * q.keV
ps = 1 * q.um
ps_hd = ps / args.supersampling
radius = n / 4.0 * ps_hd
fmt = " Wavelength: {}"
print(fmt.format(energy_to_wavelength(energy)))
fmt = "Pixel size used for propagation: {}"
print(fmt.format(ps_hd.rescale(q.um)))
print(" Field of view: {}".format(n *
ps_hd.rescale(q.um)))
fmt = " Sphere diameter: {}"
print(fmt.format(2 * radius))
sample = make_sphere(n, radius, pixel_size=ps_hd, material=material)
projection = sample.project((n, n), ps_hd).get() * 1e6
projection = decimate(projection, (n_camera, n_camera), average=True).get()
# Propagation with a monochromatic plane incident wave
hd = propagate([sample], shape, [energy], d, ps_hd).get()
ld = decimate(hd, (n_camera, n_camera), average=True).get()
kernel = compute_tie_kernel(n_camera, ps, d, material, energy)
mju = material.get_attenuation_coefficient(energy).rescale(1 /
q.m).magnitude
f_ld = fft_2(ld)
f_ld *= get_array(kernel.astype(cfg.PRECISION.np_float))
retrieved = ifft_2(f_ld).get().real
retrieved = -1 / mju * np.log(retrieved) * 1e6
if args.output_thickness:
imageio.imwrite(args.output_thickness, projection)
if args.output_projection:
imageio.imwrite(args.output_projection, ld)
if args.output_retrieved:
imageio.imwrite(args.output_retrieved, retrieved)
show(hd, title="High resolution")
show(ld, title="Low resolution (detector)")
show(retrieved, title="Retrieved [um]")
show(projection, title="Projection [um]")
show(projection - retrieved, title="Projection - retrieved")
plt.show()
def main():
syris.init()
energies = np.arange(10, 30) * q.keV
n = 1024
pixel_size = 0.4 * q.um
distance = 2 * q.m
material = make_henke('PMMA', energies)
sample = make_sphere(n, n / 4 * pixel_size, pixel_size, material=material)
image = propagate([sample], (n, n), energies, distance, pixel_size).get()
show(image)
plt.show()
def main():
args = parse_args()
syris.init()
n = 1024
shape = (n, n)
ps = 1 * q.um
tr = Trajectory([(n / 2, n / 2, 0)] * ps, pixel_size=ps)
energy_center = args.energy_center * q.keV
fwhm = args.energy_resolution * energy_center
sigma = smath.fwnm_to_sigma(fwhm, n=2)
# Make sure we resolve the curve nicely
energies = np.arange(max(1 * q.keV, energy_center - 2 * fwhm),
energy_center + 2 * fwhm, fwhm / 25) * q.keV
dE = energies[1] - energies[0]
print 'Energy from, to, step, number:', energies[0], energies[-1], dE, len(
energies)
bm = make_topotomo(dE=dE, pixel_size=ps, trajectory=tr)
spectrum_energies = np.arange(1, 50, 1) * q.keV
native_spectrum = get_spectrum(bm, spectrum_energies, ps)
fltr = GaussianFilter(energies, energy_center, sigma)
gauss = get_gauss(energies.magnitude, energy_center.magnitude,
sigma.magnitude)
filtered_spectrum = get_spectrum(bm, energies, ps) * gauss
intensity = propagate([bm, fltr], shape, energies, 0 * q.m, ps).get()
show(intensity,
title='Intensity for energy range {} - {}'.format(
energies[0], energies[-1]))
plt.figure()
plt.plot(spectrum_energies.magnitude, native_spectrum)
plt.title('Source Spectrum')
plt.xlabel('Energy [keV]')
plt.ylabel('Intensity')
plt.figure()
plt.plot(energies.magnitude, gauss)
plt.title('Gaussian Filter')
plt.xlabel('Energy [keV]')
plt.ylabel('Transmitted intensity')
plt.figure()
plt.plot(energies.magnitude, filtered_spectrum)
plt.title('Filtered Spectrum')
plt.xlabel('Energy [keV]')
plt.ylabel('Intensity')
plt.show()
def main():
args = parse_args()
syris.init()
n = 1024
shape = (n, n)
ps = 1 * q.um
tr = Trajectory([(n / 2, n / 2, 0)] * ps, pixel_size=ps)
energy_center = args.energy_center * q.keV
fwhm = args.energy_resolution * energy_center
sigma = smath.fwnm_to_sigma(fwhm, n=2)
# Make sure we resolve the curve nicely
energies = np.arange(max(1 * q.keV, energy_center - 2 * fwhm),
energy_center + 2 * fwhm,
fwhm / 25) * q.keV
dE = energies[1] - energies[0]
print 'Energy from, to, step, number:', energies[0], energies[-1], dE, len(energies)
bm = make_topotomo(dE=dE, pixel_size=ps, trajectory=tr)
spectrum_energies = np.arange(1, 50, 1) * q.keV
native_spectrum = get_spectrum(bm, spectrum_energies, ps)
fltr = GaussianFilter(energies, energy_center, sigma)
gauss = get_gauss(energies.magnitude, energy_center.magnitude, sigma.magnitude)
filtered_spectrum = get_spectrum(bm, energies, ps) * gauss
intensity = propagate([bm, fltr], shape, energies, 0 * q.m, ps).get()
show(intensity, title='Intensity for energy range {} - {}'.format(energies[0], energies[-1]))
plt.figure()
plt.plot(spectrum_energies.magnitude, native_spectrum)
plt.title('Source Spectrum')
plt.xlabel('Energy [keV]')
plt.ylabel('Intensity')
plt.figure()
plt.plot(energies.magnitude, gauss)
plt.title('Gaussian Filter')
plt.xlabel('Energy [keV]')
plt.ylabel('Transmitted intensity')
plt.figure()
plt.plot(energies.magnitude, filtered_spectrum)
plt.title('Filtered Spectrum')
plt.xlabel('Energy [keV]')
plt.ylabel('Intensity')
plt.show()
def compute_intensity(self,
t_0,
t_1,
shape,
pixel_size,
queue=None,
block=False):
"""Compute intensity between times *t_0* and *t_1*."""
exp_time = (t_1 - t_0).simplified.magnitude
image = propagate(self.samples,
shape,
self.energies,
self.propagation_distance,
pixel_size,
detector=self.detector,
t=t_0) * exp_time
return image
def main():
args = parse_args()
syris.init()
# Propagate to 20 cm
d = 20 * q.cm
# Compute grid
n_camera = 256
n = n_camera * args.supersampling
shape = (n, n)
material = get_material('pmma_5_30_kev.mat')
energies = material.energies
dE = energies[1] - energies[0]
# Lens with magnification 5 and numerical aperture 0.25
lens = Lens(5, na=0.25)
# Considered visible light wavelengths
vis_wavelengths = np.arange(500, 700) * q.nm
# Simple camera quantum efficiencies
cam_qe = 0.1 * np.ones(len(vis_wavelengths))
camera = Camera(10 * q.um, 0.1, 500, 23, 32, (256, 256), exp_time=args.exposure * q.ms,
fps=1 / q.s, quantum_efficiencies=cam_qe, wavelengths=vis_wavelengths,
dtype=np.float32)
# Scintillator emits visible light into a region given by a Gaussian distribution
x = camera.wavelengths.rescale(q.nm).magnitude
sigma = fwnm_to_sigma(50)
emission = np.exp(-(x - 600) ** 2 / (2 * sigma ** 2)) / (sigma * np.sqrt(2 * np.pi))
# Scintillator 50 um thick, light yield 14 and refractive index 1.84
luag = get_material('luag.mat')
scintillator = Scintillator(50 * q.um,
luag,
14 * np.ones(len(energies)) / q.keV,
energies,
emission / q.nm,
camera.wavelengths,
1.84)
detector = Detector(scintillator, lens, camera)
# Pixel size used for propagation
ps = detector.pixel_size / args.supersampling
fmt = 'Pixel size used for propagation: {}'
print fmt.format(ps.rescale(q.um))
fmt = ' Effective detector pixel size: {}'
print fmt.format(detector.pixel_size.rescale(q.um))
print ' Field of view: {}'.format(n * ps.rescale(q.um))
# Bending magnet source
trajectory = Trajectory([(n / 2, n / 2, 0)] * ps)
source = make_topotomo(dE=dE, trajectory=trajectory, pixel_size=ps)
sample = make_sphere(n, n / 4. * ps, pixel_size=ps, material=material)
# Propagation with a monochromatic plane incident wave
coherent = propagate([source, sample], shape, [15 * q.keV], d, ps, t=0 * q.s,
detector=detector).get()
coherent *= camera.exp_time.simplified.magnitude
# Decimate to fit the effective pixel size of the detector system
coherent_ld = camera.get_image(coherent, shot_noise=False, amplifier_noise=False)
# Propagation which takes into account polychromaticity
poly = propagate([source, sample], shape, range(10, 30) * q.keV, d, ps, t=0 * q.s,
detector=detector).get()
poly *= camera.exp_time.simplified.magnitude
poly_ld = camera.get_image(poly, shot_noise=args.noise, amplifier_noise=args.noise)
# Compute and show some of the used propagators
propagator_10 = get_propagator_psf(n, d, ps, 10 * q.keV)
propagator_30 = get_propagator_psf(n, d, ps, 30 * q.keV)
show(coherent, title='Coherent Supersampled')
show(coherent_ld, title='Coherent Detector')
show(propagator_10.real, title='Propagator PSF for 10 keV (real part)')
show(propagator_30.real, title='Propagator PSF for 30 keV (real part)')
show(poly, title='Polychromatic Supersampled')
show(poly_ld, title='Polychromatic Detector')
plt.show()
def propagate_one(unused, queue, shape, energies, distance, ps, spheres):
# Make sure we use the sample created by this *queue*
sample = spheres[queue]
return propagate([sample], shape, energies, distance, ps,
mollified=False, queue=queue, block=True).real.get()
