def make_motion(args):
syris.init()
n = 256
shape = (n, n)
energies = np.arange(5, 30, 1) * q.keV
bm, detector = make_devices(n, energies)
mb = create_sample(n, detector.pixel_size, velocity=20 * q.mm / q.s)
mb_2 = create_sample(n, detector.pixel_size, velocity=10 * q.mm / q.s)
mb.material = get_material('pmma_5_30_kev.mat')
mb_2.material = mb.material
cube = make_cube() / q.m * 30 * detector.pixel_size + 0.1 * detector.pixel_size
fov = detector.pixel_size * n
circle = make_circle().magnitude * fov / 30000 + fov / 2
tr = Trajectory(circle, velocity=10 * q.um / q.s)
glass = get_material('glass.mat')
mesh = Mesh(cube, tr, material=glass)
ex = Experiment([bm, mb, mb_2, mesh], bm, detector, 0 * q.m, energies)
for sample in ex.samples:
if sample != bm:
sample.trajectory.bind(detector.pixel_size)
if args.show_flat:
show(get_flat(shape, energies, detector, bm), title='Counts')
plt.show()
if args.conduct:
if args.output is not None and not os.path.exists(args.output):
os.makedirs(args.output, mode=0o755)
t_0 = 0 * q.s
if args.num_images:
t_1 = args.num_images / detector.camera.fps
else:
t_1 = ex.time
st = time.time()
mpl_im = None
for i, proj in enumerate(ex.make_sequence(t_0, t_1)):
image = get_host(proj)
if args.show:
if mpl_im is None:
plt.figure()
mpl_im = plt.imshow(image)
plt.show(False)
else:
mpl_im.set_data(image)
plt.draw()
if args.output:
path = os.path.join(args.output, 'projection_{:>05}.png').format(i)
scipy.misc.imsave(path, image)
print 'Maximum intensity:', image.max()
print 'Duration: {} s'.format(time.time() - st)
plt.show()
def make_devices(n, energies, camera=None, highspeed=True, scintillator=None):
"""Create devices with image shape (*n*, *n*), X-ray *energies*, *camera* and use the high speed
setup if *highspeed* is True.
"""
shape = (n, n)
dE = energies[1] - energies[0]
if not camera:
vis_wavelengths = np.arange(500, 700) * q.nm
camera = Camera(11 * q.um, .1, 500, 23, 32, shape, exp_time=1 * q.ms, fps=1000 / q.s,
quantum_efficiencies=0.5 * np.ones(len(vis_wavelengths)),
wavelengths=vis_wavelengths, dtype=np.float32)
else:
vis_wavelengths = camera.wavelengths.rescale(q.nm)
x = vis_wavelengths.rescale(q.nm).magnitude
dx = x[1] - x[0]
if scintillator == 'lso' or not (scintillator or highspeed):
sigma = fwnm_to_sigma(50)
emission = np.exp(-(x - 545) ** 2 / (2 * sigma ** 2)) / (sigma * np.sqrt(2 * np.pi))
lso = get_material('lso_5_30_kev.mat')
scintillator = Scintillator(13 * q.um,
lso,
36 * np.ones(len(energies)) / q.keV,
energies,
emission / q.nm,
vis_wavelengths,
1.82)
elif scintillator == 'luag' or (not scintillator and highspeed):
sigma = fwnm_to_sigma(50)
emission = np.exp(-(x - 450) ** 2 / (2 * sigma ** 2)) / (sigma * np.sqrt(2 * np.pi))
luag = get_material('luag.mat')
scintillator = Scintillator(50 * q.um,
luag,
14 * np.ones(len(energies)) / q.keV,
energies,
emission / q.nm,
vis_wavelengths,
1.84)
if highspeed:
# High speed setup
lens = Lens(3, f_number=1.4, focal_length=50 * q.mm, transmission_eff=0.7, sigma=None)
else:
# High resolution setup
lens = Lens(9, na=0.28, sigma=None)
detector = Detector(scintillator, lens, camera)
source_trajectory = Trajectory([(n / 2, n / 2, 0)] * detector.pixel_size)
bm = make_topotomo(dE=dE, trajectory=source_trajectory, pixel_size=detector.pixel_size)
return bm, detector
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 make_topo_tomo_flat(args, highspeed=True, scintillator=None):
syris.init(device_index=0, loglevel='INFO')
dimax = make_pco_dimax()
n = dimax.shape[0]
energies = np.arange(5, 30) * q.keV
bm, detector = make_devices(n, energies, camera=dimax, highspeed=highspeed,
scintillator=scintillator)
# Customize the setup for the 2013_03_07-08 experiment
air = MaterialFilter(1 * q.m, get_material('air_5_30_kev.mat'))
filters = [air]
dimax.bpp = 32
dimax.dtype = np.float32
dimax.fps = 450 / q.s
detector.lens.f_number = 2.8
bm.el_current = 130 * q.mA
# Compte the flat field
flat = get_flat(dimax.shape, energies, detector, bm, filters=filters, shot_noise=True,
amplifier_noise=True)
fmt = 'min: {}, max: {}, mean: {}, middle row std: {}'
print fmt.format(flat.min(), flat.max(), flat.mean(), flat[n / 2].std())
show(flat)
plt.show()
return flat
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()
# 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. * 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
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 make_topo_tomo_flat(args, highspeed=True, scintillator=None):
syris.init(device_index=0, loglevel='INFO')
dimax = make_pco_dimax()
n = dimax.shape[0]
energies = np.arange(5, 30) * q.keV
bm, detector = make_devices(n,
energies,
camera=dimax,
highspeed=highspeed,
scintillator=scintillator)
# Customize the setup for the 2013_03_07-08 experiment
air = MaterialFilter(1 * q.m, get_material('air_5_30_kev.mat'))
filters = [air]
dimax.bpp = 32
dimax.dtype = np.float32
dimax.fps = 450 / q.s
detector.lens.f_number = 2.8
bm.el_current = 130 * q.mA
# Compte the flat field
flat = get_flat(dimax.shape,
energies,
detector,
bm,
filters=filters,
shot_noise=True,
amplifier_noise=True)
fmt = 'min: {}, max: {}, mean: {}, middle row std: {}'
print fmt.format(flat.min(), flat.max(), flat.mean(), flat[n / 2].std())
show(flat)
plt.show()
return flat
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 make_devices(n, energies, camera=None, highspeed=True, scintillator=None):
"""Create devices with image shape (*n*, *n*), X-ray *energies*, *camera* and use the high speed
setup if *highspeed* is True.
"""
shape = (n, n)
dE = energies[1] - energies[0]
if not camera:
vis_wavelengths = np.arange(500, 700) * q.nm
camera = Camera(11 * q.um,
.1,
500,
23,
32,
shape,
exp_time=1 * q.ms,
fps=1000 / q.s,
quantum_efficiencies=0.5 *
np.ones(len(vis_wavelengths)),
wavelengths=vis_wavelengths,
dtype=np.float32)
else:
vis_wavelengths = camera.wavelengths.rescale(q.nm)
x = vis_wavelengths.rescale(q.nm).magnitude
dx = x[1] - x[0]
if scintillator == 'lso' or not (scintillator or highspeed):
sigma = fwnm_to_sigma(50)
emission = np.exp(-(x - 545)**2 /
(2 * sigma**2)) / (sigma * np.sqrt(2 * np.pi))
lso = get_material('lso_5_30_kev.mat')
scintillator = Scintillator(13 * q.um, lso,
36 * np.ones(len(energies)) / q.keV,
energies, emission / q.nm, vis_wavelengths,
1.82)
elif scintillator == 'luag' or (not scintillator and highspeed):
sigma = fwnm_to_sigma(50)
emission = np.exp(-(x - 450)**2 /
(2 * sigma**2)) / (sigma * np.sqrt(2 * np.pi))
luag = get_material('luag.mat')
scintillator = Scintillator(50 * q.um, luag,
14 * np.ones(len(energies)) / q.keV,
energies, emission / q.nm, vis_wavelengths,
1.84)
if highspeed:
# High speed setup
lens = Lens(3,
f_number=1.4,
focal_length=50 * q.mm,
transmission_eff=0.7,
sigma=None)
else:
# High resolution setup
lens = Lens(9, na=0.28, sigma=None)
detector = Detector(scintillator, lens, camera)
source_trajectory = Trajectory([(n / 2, n / 2, 0)] * detector.pixel_size)
bm = make_topotomo(dE=dE,
trajectory=source_trajectory,
pixel_size=detector.pixel_size)
return bm, detector
def make_motion(args):
syris.init()
n = 256
shape = (n, n)
energies = np.arange(5, 30, 1) * q.keV
bm, detector = make_devices(n, energies)
mb = create_sample(n, detector.pixel_size, velocity=20 * q.mm / q.s)
mb_2 = create_sample(n, detector.pixel_size, velocity=10 * q.mm / q.s)
mb.material = get_material('pmma_5_30_kev.mat')
mb_2.material = mb.material
cube = make_cube(
) / q.m * 30 * detector.pixel_size + 0.1 * detector.pixel_size
fov = detector.pixel_size * n
circle = make_circle().magnitude * fov / 30000 + fov / 2
tr = Trajectory(circle, velocity=10 * q.um / q.s)
glass = get_material('glass.mat')
mesh = Mesh(cube, tr, material=glass)
ex = Experiment([bm, mb, mb_2, mesh], bm, detector, 0 * q.m, energies)
for sample in ex.samples:
if sample != bm:
sample.trajectory.bind(detector.pixel_size)
if args.show_flat:
show(get_flat(shape, energies, detector, bm), title='Counts')
plt.show()
if args.conduct:
if args.output is not None and not os.path.exists(args.output):
os.makedirs(args.output, mode=0o755)
t_0 = 0 * q.s
if args.num_images:
t_1 = args.num_images / detector.camera.fps
else:
t_1 = ex.time
st = time.time()
mpl_im = None
for i, proj in enumerate(ex.make_sequence(t_0, t_1)):
image = get_host(proj)
if args.show:
if mpl_im is None:
plt.figure()
mpl_im = plt.imshow(image)
plt.show(False)
else:
mpl_im.set_data(image)
plt.draw()
if args.output:
path = os.path.join(args.output,
'projection_{:>05}.png').format(i)
scipy.misc.imsave(path, image)
print 'Maximum intensity:', image.max()
print 'Duration: {} s'.format(time.time() - st)
plt.show()
## == GAUSIAN FILTER (MONOCHROMATOR APPROX) ==
fwhm = dE_mono * energy * q.eV
sigma = smath.fwnm_to_sigma(fwhm, n=2)
fltr = GaussianFilter(energies, energy * q.eV, sigma)
# == SAMPLE ===
meshes = read_collada(OBJ_PATH, [(n / 2, n / 2, 0)] * detector.pixel_size,
iterations=1)
tr = Trajectory([(0 / 2, 0 / 2, 0)] * detector.pixel_size)
cb = CompositeBody(tr, bodies=meshes)
cb.bind_trajectory(detector.pixel_size)
airm = get_material('air_dry.mat')
cu = get_material('cu.mat')
air_gap = MaterialFilter(3 * q.m, airm)
abs_fltr = MaterialFilter(100 * q.um, cu)
# === MAKE EXPERIMENT ===
ex = Tomography([undu, fltr, abs_fltr, air_gap, cb], cb, undu, detector,
[53.455, 0, 0, 32.477, 0.15] * q.m, energies)
# == CONDUCT EXPERIMENT
if OUTPUT is not None and not os.path.exists(OUTPUT):
os.makedirs(OUTPUT, mode=0o755)
t_0 = 0 * q.s
t_1 = NO_OF_IMAGES / detector.camera.fps
st = time.time()