def setUp(self):
syris.init(device_index=0)
wavelengths = np.arange(10) * q.nm
qe = np.ones(len(wavelengths))
self.camera = Camera(1e-3 * q.um,
1.0,
10.0,
0,
10, (64, 64),
wavelengths=wavelengths,
quantum_efficiencies=qe,
exp_time=1 * q.s,
fps=1 / q.s)
def setUp(self):
default_syris_init()
lens = Lens(3.0, f_number=1.4, focal_length=100.0 * q.mm)
camera = Camera(1 * q.um, 0.1, 10, 1.0, 12, (64, 64))
detector = Detector(None, lens, camera)
ps = detector.pixel_size
t = np.linspace(0, 1, 10) * q.mm
x = t
y = np.zeros(len(t))
z = np.zeros(len(t))
points = list(zip(x, y, z)) * q.mm
mb_0 = MetaBall(
Trajectory(points,
pixel_size=ps,
furthest_point=1 * q.um,
velocity=1 * q.mm / q.s),
1 * q.um,
)
mb_1 = MetaBall(
Trajectory(points,
pixel_size=ps,
furthest_point=1 * q.um,
velocity=2 * q.mm / q.s),
1 * q.um,
)
self.experiment = Experiment([mb_0, mb_1], None, detector, 0 * q.m,
None)
def setUp(self):
syris.init(device_index=0)
wavelengths = np.arange(10) * q.nm
qe = np.ones(len(wavelengths))
self.camera = Camera(1e-3 * q.um,
1.0,
10.0,
0,
10,
(64, 64),
wavelengths=wavelengths,
quantum_efficiencies=qe,
exp_time=1 * q.s,
fps=1 / q.s)
def test_constructor(self):
Camera(1 * q.um, 0.1, 10, 1, 12, None)
Camera(1 * q.um, 0.1, 10, 1, 12, (64, 64))
# Exposure time priority
cam = Camera(1 * q.um,
0.1,
10,
1,
12,
None, (64, 64),
exp_time=1 * q.ms,
fps=10000 / q.s)
self.assertEqual(cam.fps.simplified, 1000 / q.s)
# Shorter exposure time than 1 / FPS
cam = Camera(1 * q.um,
0.1,
10,
1,
12, (64, 64),
exp_time=0.5 * q.s,
fps=1 / q.s)
self.assertEqual(cam.exp_time, .5 * q.s)
self.assertEqual(cam.fps, 1 / q.s)
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()
class TestCamera(SyrisTest):
def setUp(self):
syris.init(device_index=0)
wavelengths = np.arange(10) * q.nm
qe = np.ones(len(wavelengths))
self.camera = Camera(1e-3 * q.um,
1.0,
10.0,
0,
10,
(64, 64),
wavelengths=wavelengths,
quantum_efficiencies=qe,
exp_time=1 * q.s,
fps=1 / q.s)
def test_constructor(self):
Camera(1 * q.um, 0.1, 10, 1, 12, None)
Camera(1 * q.um, 0.1, 10, 1, 12, (64, 64))
# Exposure time priority
cam = Camera(1 * q.um, 0.1, 10, 1, 12, None, (64, 64), exp_time=1 * q.ms, fps=10000 / q.s)
self.assertEqual(cam.fps.simplified, 1000 / q.s)
# Shorter exposure time than 1 / FPS
cam = Camera(1 * q.um, 0.1, 10, 1, 12, (64, 64), exp_time = 0.5 * q.s, fps=1 / q.s)
self.assertEqual(cam.exp_time, .5 * q.s)
self.assertEqual(cam.fps, 1 / q.s)
def test_is_fps_feasible(self):
self.assertTrue(is_fps_feasible(1000 / q.s, 1 * q.ms))
self.assertTrue(is_fps_feasible(1000 / q.s, 0.5 * q.ms))
self.assertFalse(is_fps_feasible(1000 / q.s, 2 * q.ms))
def test_fps_setting(self):
self.camera.fps = 1000 / q.s
self.assertAlmostEqual(1e-3, self.camera.exp_time.simplified.magnitude)
def test_exp_time_setting(self):
self.camera.exp_time = 10 * q.s
self.assertAlmostEqual(.1, self.camera.fps.simplified.magnitude)
def test_bpp(self):
self.assertEqual(self.camera.max_grey_value, 2 ** self.camera.bpp - 1)
def test_dark(self):
photons = np.zeros(self.camera.shape, dtype=cfg.PRECISION.np_float)
res = self.camera.get_image(photons, shot_noise=True, psf=False)
self.assertNotEqual(np.var(res), 0.0)
self.assertNotEqual(np.sum(res), 0.0)
def test_saturation(self):
photons = np.ones(self.camera.shape, dtype=cfg.PRECISION.np_float) * 10 * \
self.camera.max_grey_value
res = self.camera.get_image(photons.astype(np.float32), shot_noise=False, psf=False)
self.assertEqual(np.var(res), 0)
diff = np.ones(self.camera.shape) * self.camera.max_grey_value - res
self.assertEqual(np.sum(diff), 0)
def setUp(self):
self.lens = Lens(3., f_number=1.4, focal_length=100.0 * q.mm)
self.camera = Camera(10 * q.um, 0.1, 10, 1, 12, None)
self.detector = Detector(None, self.lens, self.camera)
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
class TestCamera(SyrisTest):
def setUp(self):
syris.init(device_index=0)
wavelengths = np.arange(10) * q.nm
qe = np.ones(len(wavelengths))
self.camera = Camera(1e-3 * q.um,
1.0,
10.0,
0,
10, (64, 64),
wavelengths=wavelengths,
quantum_efficiencies=qe,
exp_time=1 * q.s,
fps=1 / q.s)
def test_constructor(self):
Camera(1 * q.um, 0.1, 10, 1, 12, None)
Camera(1 * q.um, 0.1, 10, 1, 12, (64, 64))
# Exposure time priority
cam = Camera(1 * q.um,
0.1,
10,
1,
12,
None, (64, 64),
exp_time=1 * q.ms,
fps=10000 / q.s)
self.assertEqual(cam.fps.simplified, 1000 / q.s)
# Shorter exposure time than 1 / FPS
cam = Camera(1 * q.um,
0.1,
10,
1,
12, (64, 64),
exp_time=0.5 * q.s,
fps=1 / q.s)
self.assertEqual(cam.exp_time, .5 * q.s)
self.assertEqual(cam.fps, 1 / q.s)
def test_is_fps_feasible(self):
self.assertTrue(is_fps_feasible(1000 / q.s, 1 * q.ms))
self.assertTrue(is_fps_feasible(1000 / q.s, 0.5 * q.ms))
self.assertFalse(is_fps_feasible(1000 / q.s, 2 * q.ms))
def test_fps_setting(self):
self.camera.fps = 1000 / q.s
self.assertAlmostEqual(1e-3, self.camera.exp_time.simplified.magnitude)
def test_exp_time_setting(self):
self.camera.exp_time = 10 * q.s
self.assertAlmostEqual(.1, self.camera.fps.simplified.magnitude)
def test_bpp(self):
self.assertEqual(self.camera.max_grey_value, 2**self.camera.bpp - 1)
def test_dark(self):
photons = np.zeros(self.camera.shape, dtype=cfg.PRECISION.np_float)
res = self.camera.get_image(photons, shot_noise=True, psf=False)
self.assertNotEqual(np.var(res), 0.0)
self.assertNotEqual(np.sum(res), 0.0)
def test_saturation(self):
photons = np.ones(self.camera.shape, dtype=cfg.PRECISION.np_float) * 10 * \
self.camera.max_grey_value
res = self.camera.get_image(photons.astype(np.float32),
shot_noise=False,
psf=False)
self.assertEqual(np.var(res), 0)
diff = np.ones(self.camera.shape) * self.camera.max_grey_value - res
self.assertEqual(np.sum(diff), 0)