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Merge remote-tracking branch 'origin/dev' into phase_contrast
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@gvarnavi
gvarnavi committed Jul 11, 2024
2 parents 6a48ab0 + cbadde3 commit d995f66
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164 changes: 75 additions & 89 deletions py4DSTEM/process/diffraction/crystal.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -975,6 +975,7 @@ def generate_projected_potential(
potential_radius_angstroms=3.0,
sigma_image_blur_angstroms=0.1,
thickness_angstroms=100,
max_num_proj=200,
power_scale=1.0,
plot_result=False,
figsize=(6, 6),
Expand All @@ -989,9 +990,6 @@ def generate_projected_potential(
"""
Generate an image of the projected potential of crystal in real space,
using cell tiling, and a lookup table of the atomic potentials.
Note that we round atomic positions to the nearest pixel for speed.
TODO - fix scattering prefactor so that output units are sensible.
Parameters
----------
Expand All @@ -1006,6 +1004,9 @@ def generate_projected_potential(
thickness_angstroms: float
Thickness of the sample in Angstroms.
Set thickness_thickness_angstroms = 0 to skip thickness projection.
max_num_proj: int
This value prevents this function from projecting a large number of unit
cells along the beam direction, which could be potentially quite slow.
power_scale: float
Power law scaling of potentials. Set to 2.0 to approximate Z^2 images.
plot_result: bool
Expand Down Expand Up @@ -1054,52 +1055,22 @@ def generate_projected_potential(
# Rotate unit cell into projection direction
lat_real = self.lat_real.copy() @ orientation_matrix

# Determine unit cell axes to tile over, by selecting 2/3 with largest in-plane component
inds_tile = np.argsort(np.linalg.norm(lat_real[:, 0:2], axis=1))[1:3]
# Determine unit cell axes to tile over, by selecting 2/3 with smallest out-of-plane component
inds_tile = np.argsort(np.abs(lat_real[:, 2]))[0:2]
m_tile = lat_real[inds_tile, :]

# Vector projected along optic axis
m_proj = np.squeeze(np.delete(lat_real, inds_tile, axis=0))

# Thickness
if thickness_angstroms > 0:
num_proj = np.round(thickness_angstroms / np.abs(m_proj[2])).astype("int")
if num_proj > 1:
vec_proj = m_proj[:2] / pixel_size_angstroms
shifts = np.arange(num_proj).astype("float")
shifts -= np.mean(shifts)
x_proj = shifts * vec_proj[0]
y_proj = shifts * vec_proj[1]
else:
num_proj = 1
else:
num_proj = 1

# Determine tiling range
if thickness_angstroms > 0:
# include the cell height
dz = m_proj[2] * num_proj * 0.5
p_corners = np.array(
[
[-im_size_Ang[0] * 0.5, -im_size_Ang[1] * 0.5, dz],
[im_size_Ang[0] * 0.5, -im_size_Ang[1] * 0.5, dz],
[-im_size_Ang[0] * 0.5, im_size_Ang[1] * 0.5, dz],
[im_size_Ang[0] * 0.5, im_size_Ang[1] * 0.5, dz],
[-im_size_Ang[0] * 0.5, -im_size_Ang[1] * 0.5, -dz],
[im_size_Ang[0] * 0.5, -im_size_Ang[1] * 0.5, -dz],
[-im_size_Ang[0] * 0.5, im_size_Ang[1] * 0.5, -dz],
[im_size_Ang[0] * 0.5, im_size_Ang[1] * 0.5, -dz],
]
)
else:
p_corners = np.array(
[
[-im_size_Ang[0] * 0.5, -im_size_Ang[1] * 0.5, 0.0],
[im_size_Ang[0] * 0.5, -im_size_Ang[1] * 0.5, 0.0],
[-im_size_Ang[0] * 0.5, im_size_Ang[1] * 0.5, 0.0],
[im_size_Ang[0] * 0.5, im_size_Ang[1] * 0.5, 0.0],
]
)

p_corners = np.array(
[
[-im_size_Ang[0] * 0.5, -im_size_Ang[1] * 0.5, 0.0],
[im_size_Ang[0] * 0.5, -im_size_Ang[1] * 0.5, 0.0],
[-im_size_Ang[0] * 0.5, im_size_Ang[1] * 0.5, 0.0],
[im_size_Ang[0] * 0.5, im_size_Ang[1] * 0.5, 0.0],
]
)
ab = np.linalg.lstsq(m_tile[:, :2].T, p_corners[:, :2].T, rcond=None)[0]
ab = np.floor(ab)
a_range = np.array((np.min(ab[0]) - 1, np.max(ab[0]) + 2))
Expand All @@ -1115,31 +1086,17 @@ def generate_projected_potential(
abc_atoms[:, inds_tile[0]] += a_ind.ravel()
abc_atoms[:, inds_tile[1]] += b_ind.ravel()
xyz_atoms_ang = abc_atoms @ lat_real
atoms_ID_all_0 = self.numbers[atoms_ind.ravel()]
atoms_ID_all = self.numbers[atoms_ind.ravel()]

# Center atoms on image plane
x0 = xyz_atoms_ang[:, 0] / pixel_size_angstroms + im_size[0] / 2.0
y0 = xyz_atoms_ang[:, 1] / pixel_size_angstroms + im_size[1] / 2.0

# if needed, tile atoms in the projection direction
if num_proj > 1:
x = (x0[:, None] + x_proj[None, :]).ravel()
y = (y0[:, None] + y_proj[None, :]).ravel()
atoms_ID_all = np.tile(atoms_ID_all_0, (num_proj, 1))
else:
x = x0
y = y0
atoms_ID_all = atoms_ID_all_0
# print(x.shape, y.shape)

# delete atoms outside the field of view
bound = potential_radius_angstroms / pixel_size_angstroms
x = xyz_atoms_ang[:, 0] / pixel_size_angstroms + im_size[0] / 2.0
y = xyz_atoms_ang[:, 1] / pixel_size_angstroms + im_size[1] / 2.0
atoms_del = np.logical_or.reduce(
(
x <= -bound,
y <= -bound,
x >= im_size[0] + bound,
y >= im_size[1] + bound,
x <= -potential_radius_angstroms / 2,
y <= -potential_radius_angstroms / 2,
x >= im_size[0] + potential_radius_angstroms / 2,
y >= im_size[1] + potential_radius_angstroms / 2,
)
)
x = np.delete(x, atoms_del)
Expand All @@ -1164,58 +1121,87 @@ def generate_projected_potential(
for a0 in range(atoms_ID.shape[0]):
atom_sf = single_atom_scatter([atoms_ID[a0]])
atoms_lookup[a0, :, :] = atom_sf.projected_potential(atoms_ID[a0], R_2D)

# if needed, apply gaussian blurring to each atom
if sigma_image_blur_angstroms > 0:
atoms_lookup[a0, :, :] = gaussian_filter(
atoms_lookup[a0, :, :],
sigma_image_blur_angstroms / pixel_size_angstroms,
mode="nearest",
)
atoms_lookup **= power_scale

# Thickness
if thickness_angstroms > 0:
thickness_proj = thickness_angstroms / m_proj[2]
vec_proj = thickness_proj / pixel_size_angstroms * m_proj[:2]
num_proj = (np.ceil(np.linalg.norm(vec_proj)) + 1).astype("int")
num_proj = np.minimum(num_proj, max_num_proj)

x_proj = np.linspace(-0.5, 0.5, num_proj) * vec_proj[0]
y_proj = np.linspace(-0.5, 0.5, num_proj) * vec_proj[1]

# initialize potential
im_potential = np.zeros(im_size)

# Add atoms to potential image
for a0 in range(atoms_ID_all.shape[0]):
ind = np.argmin(np.abs(atoms_ID - atoms_ID_all[a0]))

x_ind = np.round(x[a0]).astype("int") + R_ind
y_ind = np.round(y[a0]).astype("int") + R_ind
x_sub = np.logical_and(
x_ind >= 0,
x_ind < im_size[0],
)
y_sub = np.logical_and(
y_ind >= 0,
y_ind < im_size[1],
)
im_potential[x_ind[x_sub][:, None], y_ind[y_sub][None, :]] += atoms_lookup[
ind
][x_sub][:, y_sub]
if thickness_angstroms > 0:
for a1 in range(num_proj):
x_ind = np.round(x[a0] + x_proj[a1]).astype("int") + R_ind
y_ind = np.round(y[a0] + y_proj[a1]).astype("int") + R_ind
x_sub = np.logical_and(
x_ind >= 0,
x_ind < im_size[0],
)
y_sub = np.logical_and(
y_ind >= 0,
y_ind < im_size[1],
)

im_potential[
x_ind[x_sub][:, None], y_ind[y_sub][None, :]
] += atoms_lookup[ind][x_sub, :][:, y_sub]

else:
x_ind = np.round(x[a0]).astype("int") + R_ind
y_ind = np.round(y[a0]).astype("int") + R_ind
x_sub = np.logical_and(
x_ind >= 0,
x_ind < im_size[0],
)
y_sub = np.logical_and(
y_ind >= 0,
y_ind < im_size[1],
)

im_potential[
x_ind[x_sub][:, None], y_ind[y_sub][None, :]
] += atoms_lookup[ind][x_sub, :][:, y_sub]

if thickness_angstroms > 0:
im_potential /= num_proj

# if needed, apply gaussian blurring
if sigma_image_blur_angstroms > 0:
sigma_image_blur = sigma_image_blur_angstroms / pixel_size_angstroms
im_potential = gaussian_filter(
im_potential,
sigma_image_blur,
mode="nearest",
)

if plot_result:
# quick plotting of the result
int_vals = np.sort(im_potential.ravel())
int_range = np.array(
(
int_vals[np.round(0.02 * int_vals.size).astype("int")],
int_vals[np.round(0.999 * int_vals.size).astype("int")],
int_vals[np.round(0.98 * int_vals.size).astype("int")],
)
)

fig, ax = plt.subplots(figsize=figsize)
ax.imshow(
im_potential,
cmap="gray",
cmap="turbo",
vmin=int_range[0],
vmax=int_range[1],
)
# ax.scatter(y,x,c='r') # for testing
ax.set_axis_off()
ax.set_aspect("equal")

Expand Down
28 changes: 14 additions & 14 deletions py4DSTEM/process/polar/polar_fits.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -126,20 +126,20 @@ def fit_amorphous_ring(
sigma2 = (radial_range[1] - radial_range[0]) / 4

coefs = (x0, y0, a, b, t, int0, int12, k_bg, sigma0, sigma1, sigma2)
lb = (0, 0, radial_range[0], radial_range[0], -np.inf, 0, 0, 0, 1, 1, 1)
ub = (
im.shape[0],
im.shape[1],
radial_range[1],
radial_range[1],
np.inf,
np.inf,
np.inf,
np.inf,
np.inf,
np.inf,
np.inf,
)
lb = (0, 0, radial_range[0], radial_range[0], -np.inf, 0, 0, 0, 1, 1, 1)
ub = (
im.shape[0],
im.shape[1],
radial_range[1],
radial_range[1],
np.inf,
np.inf,
np.inf,
np.inf,
np.inf,
np.inf,
np.inf,
)

if show_fit_mask:
# show image preview of fitting mask
Expand Down
21 changes: 7 additions & 14 deletions py4DSTEM/process/utils/single_atom_scatter.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -57,30 +57,23 @@ def projected_potential(self, Z, R):
me = 9.10938356e-31
# Electron charge in Coulomb
qe = 1.60217662e-19
# Electron charge in V-Angstroms
# qe = 14.4
# Permittivity of vacuum
eps_0 = 8.85418782e-12
# Bohr's constant
a_0 = 5.29177210903e-11

fe = np.zeros_like(R)
for i in range(5):
# fe += ai[i] * (2 + bi[i] * gsq) / (1 + bi[i] * gsq) ** 2
pre = 2 * np.pi / bi[i] ** 0.5
fe += (ai[i] / bi[i] ** 1.5) * (kn(0, pre * R) + R * kn(1, pre * R))

# Scale output units
# kappa = (4*np.pi*eps_0) / (2*np.pi*a_0*qe)
# fe *= 2*np.pi**2 / kappa
# # # kappa = (4*np.pi*eps_0) / (2*np.pi*a_0*me)

# # kappa = (4*np.pi*eps_0) / (2*np.pi*a_0*me)
# # return fe * 2 * np.pi**2 # / kappa
# # if units == "VA":
# return h**2 / (2 * np.pi * me * qe) * 1e18 * fe
# # elif units == "A":
# # return fe * 2 * np.pi**2 / kappa
return fe
# kappa = (4*np.pi*eps_0) / (2*np.pi*a_0*me)
return fe * 2 * np.pi**2 # / kappa
# if units == "VA":
# return h**2 / (2 * np.pi * me * qe) * 1e18 * fe
# elif units == "A":
# return fe * 2 * np.pi**2 / kappa

def get_scattering_factor(
self, elements=None, composition=None, q_coords=None, units=None
Expand Down

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