def test_transfer_many(self):
n = 32
shape = (n, n)
ps = 1 * q.um
energies = np.arange(5, 30) * q.keV
energy = 10 * q.keV
lam = physics.energy_to_wavelength(energy)
# Delta causes phase shift between two adjacent pixels by Pi / 16
delta = (lam / (32 * ps)).simplified.magnitude
ri = np.ones_like(energies.magnitude, dtype=np.complex) * delta + 0j
material = Material('dummy', ri, energies)
wedge = np.tile(np.arange(n), [n, 1]) * ps
wedge = StaticBody(wedge, ps, material=material)
# Test more objects
u_many = physics.transfer_many([wedge, wedge], shape, ps, energy).get()
# 2 objects
u = wedge.transfer(shape, ps, energy).get()**2
np.testing.assert_almost_equal(u, u_many)
# Test exponent
u = physics.transfer_many([wedge], shape, ps, energy,
exponent=False).get()
u_exp = physics.transfer_many([wedge],
shape,
ps,
energy,
exponent=True).get()
np.testing.assert_almost_equal(u, np.exp(u_exp))
def _transfer(
self,
shape,
pixel_size,
energy,
offset,
exponent=False,
t=None,
queue=None,
out=None,
check=True,
block=False,
):
"""Transfer function implementation based on a refractive index."""
if out is None:
out = cl_array.zeros(queue, shape, dtype=cfg.PRECISION.np_cplx)
else:
# transmission_many adds values, make sure it start with a zeroed array
out.fill(0)
return transfer_many(
self.bodies,
shape,
pixel_size,
energy,
offset=offset,
exponent=exponent,
queue=queue,
out=out,
t=t,
check=check,
block=block,
)
def test_transmission_sampling(self):
def compute_transmission_function(n, ps, energy, material):
wedge = np.tile(np.arange(n), [n, 1]) * ps
wedge = StaticBody(wedge, ps, material=material)
return wedge.transfer((n, n), ps, energy, exponent=True)
def compute_distance(n, ps, lam, ps_per_lam):
ca = (lam / (ps_per_lam * ps)).simplified.magnitude
alpha = np.arccos(ca)
theta = np.pi / 2 - alpha
return (n * ps / (2 * np.tan(theta))).simplified
n = 32
ps = 1 * q.um
energies = np.arange(5, 30) * q.keV
energy = 10 * q.keV
lam = physics.energy_to_wavelength(energy)
# Delta causes phase shift between two adjacent pixels by 2 Pi
delta = (lam / ps).simplified.magnitude
ri = np.ones_like(energies.magnitude, dtype=np.complex) * delta + 0j
material = Material('dummy', ri, energies)
# Single object
u = compute_transmission_function(n, ps, energy, material)
self.assertFalse(physics.is_wavefield_sampling_ok(u))
# 4x supersampling => phase shift Pi/2
u = compute_transmission_function(4 * n, ps / 4, energy, material)
self.assertTrue(physics.is_wavefield_sampling_ok(u))
# 4x supersampling with 2 objects => phase shift Pi
n *= 4
ps /= 4
wedge = np.tile(np.arange(n), [n, 1]) * ps
wedge = StaticBody(wedge, ps, material=material)
u = physics.transfer_many([wedge, wedge], (n, n), ps, energy, exponent=True)
self.assertFalse(physics.is_wavefield_sampling_ok(u))
# X-ray source with a parabolic phase profile
n = 128
ps = 1 * q.um
trajectory = Trajectory([(n / 2, n / 2, 0)] * ps)
# 1 pixel per wavelength => insufficient sampling
d = compute_distance(n, ps, lam, 1)
source = BendingMagnet(2.5 * q.GeV, 150 * q.mA, 1.5 * q.T, d,
1, np.array([0.2, 0.8]) * q.mm, ps, trajectory,
phase_profile='parabola')
u = source.transfer((n, n), ps, energy, exponent=True)
self.assertFalse(physics.is_wavefield_sampling_ok(u))
# 4 pixel per wavelength => good sampling
d = compute_distance(n, ps, lam, 4)
source = BendingMagnet(2.5 * q.GeV, 150 * q.mA, 1.5 * q.T, d,
1, np.array([0.2, 0.8]) * q.mm, ps, trajectory,
phase_profile='parabola')
u = source.transfer((n, n), ps, energy, exponent=True)
self.assertTrue(physics.is_wavefield_sampling_ok(u))
def _transfer(self, shape, pixel_size, energy, offset, exponent=False, t=None,
queue=None, out=None, check=True, block=False):
"""Transfer function implementation based on a refractive index."""
if out is None:
out = cl_array.zeros(queue, shape, dtype=cfg.PRECISION.np_cplx)
else:
# transmission_many adds values, make sure it start with a zeroed array
out.fill(0)
return transfer_many(self.bodies, shape, pixel_size, energy, offset=offset,
exponent=exponent, queue=queue, out=out, t=t, check=check,
block=block)
def test_transfer_many(self):
n = 32
shape = (n, n)
ps = 1 * q.um
energies = np.arange(5, 30) * q.keV
energy = 10 * q.keV
lam = physics.energy_to_wavelength(energy)
# Delta causes phase shift between two adjacent pixels by Pi / 16
delta = (lam / (32 * ps)).simplified.magnitude
ri = np.ones_like(energies.magnitude, dtype=np.complex) * delta + 0j
material = Material('dummy', ri, energies)
wedge = np.tile(np.arange(n), [n, 1]) * ps
wedge = StaticBody(wedge, ps, material=material)
# Test more objects
u_many = physics.transfer_many([wedge, wedge], shape, ps, energy).get()
# 2 objects
u = wedge.transfer(shape, ps, energy).get() ** 2
np.testing.assert_almost_equal(u, u_many)
# Test exponent
u = physics.transfer_many([wedge], shape, ps, energy, exponent=False).get()
u_exp = physics.transfer_many([wedge], shape, ps, energy, exponent=True).get()
np.testing.assert_almost_equal(u, np.exp(u_exp))
def test_transmission_sampling(self):
def compute_transmission_function(n, ps, energy, material):
wedge = np.tile(np.arange(n), [n, 1]) * ps
wedge = StaticBody(wedge, ps, material=material)
return wedge.transfer((n, n), ps, energy, exponent=True)
def compute_distance(n, ps, lam, ps_per_lam):
ca = (lam / (ps_per_lam * ps)).simplified.magnitude
alpha = np.arccos(ca)
theta = np.pi / 2 - alpha
return (n * ps / (2 * np.tan(theta))).simplified
n = 32
ps = 1 * q.um
energies = np.arange(5, 30) * q.keV
energy = 10 * q.keV
lam = physics.energy_to_wavelength(energy)
# Delta causes phase shift between two adjacent pixels by 2 Pi
delta = (lam / ps).simplified.magnitude
ri = np.ones_like(energies.magnitude, dtype=np.complex) * delta + 0j
material = Material('dummy', ri, energies)
# Single object
u = compute_transmission_function(n, ps, energy, material)
self.assertFalse(physics.is_wavefield_sampling_ok(u))
# 4x supersampling => phase shift Pi/2
u = compute_transmission_function(4 * n, ps / 4, energy, material)
self.assertTrue(physics.is_wavefield_sampling_ok(u))
# 4x supersampling with 2 objects => phase shift Pi
n *= 4
ps /= 4
wedge = np.tile(np.arange(n), [n, 1]) * ps
wedge = StaticBody(wedge, ps, material=material)
u = physics.transfer_many([wedge, wedge], (n, n),
ps,
energy,
exponent=True)
self.assertFalse(physics.is_wavefield_sampling_ok(u))
# X-ray source with a parabolic phase profile
n = 128
ps = 1 * q.um
trajectory = Trajectory([(n / 2, n / 2, 0)] * ps)
# 1 pixel per wavelength => insufficient sampling
d = compute_distance(n, ps, lam, 1)
source = BendingMagnet(2.5 * q.GeV,
150 * q.mA,
1.5 * q.T,
d,
1,
np.array([0.2, 0.8]) * q.mm,
ps,
trajectory,
phase_profile='parabola')
u = source.transfer((n, n), ps, energy, exponent=True)
self.assertFalse(physics.is_wavefield_sampling_ok(u))
# 4 pixel per wavelength => good sampling
d = compute_distance(n, ps, lam, 4)
source = BendingMagnet(2.5 * q.GeV,
150 * q.mA,
1.5 * q.T,
d,
1,
np.array([0.2, 0.8]) * q.mm,
ps,
trajectory,
phase_profile='parabola')
u = source.transfer((n, n), ps, energy, exponent=True)
self.assertTrue(physics.is_wavefield_sampling_ok(u))