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black formatting
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@bsavitzky
bsavitzky committed Nov 18, 2024
1 parent d3e227b commit 20917d0
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Showing 10 changed files with 64 additions and 84 deletions.
4 changes: 1 addition & 3 deletions py4DSTEM/process/diffraction/WK_scattering_factors.py
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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
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3 changes: 1 addition & 2 deletions py4DSTEM/process/diffraction/crystal_viz.py
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Original file line number Diff line number Diff line change
Expand Up @@ -453,8 +453,7 @@ 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,
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3 changes: 1 addition & 2 deletions py4DSTEM/process/fit/fit.py
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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
)


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28 changes: 14 additions & 14 deletions py4DSTEM/process/phase/magnetic_ptychographic_tomography.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1202,20 +1202,20 @@ 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
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28 changes: 14 additions & 14 deletions py4DSTEM/process/phase/magnetic_ptychography.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1510,20 +1510,20 @@ 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
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4 changes: 1 addition & 3 deletions py4DSTEM/process/phase/ptychographic_methods.py
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Original file line number Diff line number Diff line change
Expand Up @@ -366,9 +366,7 @@ 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(
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28 changes: 14 additions & 14 deletions py4DSTEM/process/phase/ptychographic_tomography.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1093,20 +1093,20 @@ 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
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4 changes: 1 addition & 3 deletions py4DSTEM/process/phase/utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -202,9 +202,7 @@ 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]
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28 changes: 14 additions & 14 deletions py4DSTEM/process/phase/xray_magnetic_ptychography.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1476,20 +1476,20 @@ 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
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18 changes: 3 additions & 15 deletions py4DSTEM/process/utils/utils.py
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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


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