Skip to content

Commit

Permalink
updating black version
Browse files Browse the repository at this point in the history
  • Loading branch information
@cophus
cophus committed Jul 18, 2024
1 parent 8899487 commit 0ecf427
Show file tree
Hide file tree
Showing 10 changed files with 62 additions and 82 deletions.
4 changes: 1 addition & 3 deletions py4DSTEM/process/diffraction/WK_scattering_factors.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -221,9 +221,7 @@ def RI1(BI, BJ, G):
ri1[sub] = np.pi * (BI * np.log((BI + BJ) / BI) + BJ * np.log((BI + BJ) / BJ))

sub = np.logical_and(eps <= 0.1, G > 0.0)
temp = 0.5 * BI**2 * np.log(BI / (BI + BJ)) + 0.5 * BJ**2 * np.log(
BJ / (BI + BJ)
)
temp = 0.5 * BI**2 * np.log(BI / (BI + BJ)) + 0.5 * BJ**2 * np.log(BJ / (BI + BJ))
temp += 0.75 * (BI**2 + BJ**2) - 0.25 * (BI + BJ) ** 2
temp -= 0.5 * (BI - BJ) ** 2
ri1[sub] += np.pi * G[sub] ** 2 * temp
Expand Down
3 changes: 1 addition & 2 deletions py4DSTEM/process/diffraction/crystal_viz.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -454,8 +454,7 @@ def plot_scattering_intensity(
int_sf_plot = calc_1D_profile(
k,
self.g_vec_leng,
(self.struct_factors_int**int_power_scale)
* (self.g_vec_leng**k_power_scale),
(self.struct_factors_int**int_power_scale) * (self.g_vec_leng**k_power_scale),
remove_origin=True,
k_broadening=k_broadening,
int_scale=int_scale,
Expand Down
3 changes: 1 addition & 2 deletions py4DSTEM/process/fit/fit.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -169,8 +169,7 @@ def polar_gaussian_2D(
# t2 = np.min(np.vstack([t,1-t]))
t2 = np.square(t - mu_t)
return (
I0 * np.exp(-(t2 / (2 * sigma_t**2) + (q - mu_q) ** 2 / (2 * sigma_q**2)))
+ C
I0 * np.exp(-(t2 / (2 * sigma_t**2) + (q - mu_q) ** 2 / (2 * sigma_q**2))) + C
)


Expand Down
28 changes: 14 additions & 14 deletions py4DSTEM/process/phase/magnetic_ptychographic_tomography.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -1196,20 +1196,20 @@ def reconstruct(

# position correction
if not fix_positions and a0 > 0:
self._positions_px_all[
batch_indices
] = self._position_correction(
object_sliced,
vectorized_patch_indices_row,
vectorized_patch_indices_col,
shifted_probes,
overlap,
amplitudes_device,
positions_px,
positions_px_initial,
positions_step_size,
max_position_update_distance,
max_position_total_distance,
self._positions_px_all[batch_indices] = (
self._position_correction(
object_sliced,
vectorized_patch_indices_row,
vectorized_patch_indices_col,
shifted_probes,
overlap,
amplitudes_device,
positions_px,
positions_px_initial,
positions_step_size,
max_position_update_distance,
max_position_total_distance,
)
)

measurement_error += batch_error
Expand Down
28 changes: 14 additions & 14 deletions py4DSTEM/process/phase/magnetic_ptychography.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -1497,20 +1497,20 @@ def reconstruct(

# position correction
if not fix_positions and a0 > 0:
self._positions_px_all[
batch_indices
] = self._position_correction(
self._object,
vectorized_patch_indices_row,
vectorized_patch_indices_col,
shifted_probes,
overlap,
amplitudes_device,
positions_px,
positions_px_initial,
positions_step_size,
max_position_update_distance,
max_position_total_distance,
self._positions_px_all[batch_indices] = (
self._position_correction(
self._object,
vectorized_patch_indices_row,
vectorized_patch_indices_col,
shifted_probes,
overlap,
amplitudes_device,
positions_px,
positions_px_initial,
positions_step_size,
max_position_update_distance,
max_position_total_distance,
)
)

measurement_error += batch_error
Expand Down
24 changes: 12 additions & 12 deletions py4DSTEM/process/phase/parallax.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -2202,16 +2202,16 @@ def score_CTF(coefs):
measured_shifts_sx = xp.zeros(
self._region_of_interest_shape, dtype=xp.float32
)
measured_shifts_sx[
self._xy_inds[:, 0], self._xy_inds[:, 1]
] = self._xy_shifts_Ang[:, 0]
measured_shifts_sx[self._xy_inds[:, 0], self._xy_inds[:, 1]] = (
self._xy_shifts_Ang[:, 0]
)

measured_shifts_sy = xp.zeros(
self._region_of_interest_shape, dtype=xp.float32
)
measured_shifts_sy[
self._xy_inds[:, 0], self._xy_inds[:, 1]
] = self._xy_shifts_Ang[:, 1]
measured_shifts_sy[self._xy_inds[:, 0], self._xy_inds[:, 1]] = (
self._xy_shifts_Ang[:, 1]
)

fitted_shifts = (
xp.tensordot(gradients, xp.array(self._aberrations_coefs), axes=1)
Expand All @@ -2222,16 +2222,16 @@ def score_CTF(coefs):
fitted_shifts_sx = xp.zeros(
self._region_of_interest_shape, dtype=xp.float32
)
fitted_shifts_sx[
self._xy_inds[:, 0], self._xy_inds[:, 1]
] = fitted_shifts[:, 0]
fitted_shifts_sx[self._xy_inds[:, 0], self._xy_inds[:, 1]] = (
fitted_shifts[:, 0]
)

fitted_shifts_sy = xp.zeros(
self._region_of_interest_shape, dtype=xp.float32
)
fitted_shifts_sy[
self._xy_inds[:, 0], self._xy_inds[:, 1]
] = fitted_shifts[:, 1]
fitted_shifts_sy[self._xy_inds[:, 0], self._xy_inds[:, 1]] = (
fitted_shifts[:, 1]
)

max_shift = xp.max(
xp.array(
Expand Down
4 changes: 1 addition & 3 deletions py4DSTEM/process/phase/ptychographic_methods.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -356,9 +356,7 @@ def _precompute_propagator_arrays(
propagators[i] = xp.exp(
1.0j * (-(kx**2)[:, None] * np.pi * wavelength * dz)
)
propagators[i] *= xp.exp(
1.0j * (-(ky**2)[None] * np.pi * wavelength * dz)
)
propagators[i] *= xp.exp(1.0j * (-(ky**2)[None] * np.pi * wavelength * dz))

if theta_x is not None:
propagators[i] *= xp.exp(
Expand Down
28 changes: 14 additions & 14 deletions py4DSTEM/process/phase/ptychographic_tomography.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -1088,20 +1088,20 @@ def reconstruct(

# position correction
if not fix_positions:
self._positions_px_all[
batch_indices
] = self._position_correction(
object_sliced,
vectorized_patch_indices_row,
vectorized_patch_indices_col,
shifted_probes,
overlap,
amplitudes_device,
positions_px,
positions_px_initial,
positions_step_size,
max_position_update_distance,
max_position_total_distance,
self._positions_px_all[batch_indices] = (
self._position_correction(
object_sliced,
vectorized_patch_indices_row,
vectorized_patch_indices_col,
shifted_probes,
overlap,
amplitudes_device,
positions_px,
positions_px_initial,
positions_step_size,
max_position_update_distance,
max_position_total_distance,
)
)

measurement_error += batch_error
Expand Down
4 changes: 1 addition & 3 deletions py4DSTEM/process/phase/utils.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -203,9 +203,7 @@ def evaluate_gaussian_envelope(
self, alpha: Union[float, np.ndarray]
) -> Union[float, np.ndarray]:
xp = self._xp
return xp.exp(
-0.5 * self._gaussian_spread**2 * alpha**2 / self._wavelength**2
)
return xp.exp(-0.5 * self._gaussian_spread**2 * alpha**2 / self._wavelength**2)

def evaluate_spatial_envelope(
self, alpha: Union[float, np.ndarray], phi: Union[float, np.ndarray]
Expand Down
18 changes: 3 additions & 15 deletions py4DSTEM/process/utils/utils.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -93,12 +93,7 @@ def electron_wavelength_angstrom(E_eV):
c = 299792458
h = 6.62607 * 10**-34

lam = (
h
/ ma.sqrt(2 * m * e * E_eV)
/ ma.sqrt(1 + e * E_eV / 2 / m / c**2)
* 10**10
)
lam = h / ma.sqrt(2 * m * e * E_eV) / ma.sqrt(1 + e * E_eV / 2 / m / c**2) * 10**10
return lam


Expand All @@ -107,15 +102,8 @@ def electron_interaction_parameter(E_eV):
e = 1.602177 * 10**-19
c = 299792458
h = 6.62607 * 10**-34
lam = (
h
/ ma.sqrt(2 * m * e * E_eV)
/ ma.sqrt(1 + e * E_eV / 2 / m / c**2)
* 10**10
)
sigma = (
(2 * np.pi / lam / E_eV) * (m * c**2 + e * E_eV) / (2 * m * c**2 + e * E_eV)
)
lam = h / ma.sqrt(2 * m * e * E_eV) / ma.sqrt(1 + e * E_eV / 2 / m / c**2) * 10**10
sigma = (2 * np.pi / lam / E_eV) * (m * c**2 + e * E_eV) / (2 * m * c**2 + e * E_eV)
return sigma


Expand Down

0 comments on commit 0ecf427

Please sign in to comment.