From 20917d07675de1de06ce6c9f124d280dd4effe0b Mon Sep 17 00:00:00 2001 From: bsavitzky Date: Mon, 18 Nov 2024 16:19:09 -0500 Subject: [PATCH] black formatting --- .../diffraction/WK_scattering_factors.py | 4 +-- py4DSTEM/process/diffraction/crystal_viz.py | 3 +- py4DSTEM/process/fit/fit.py | 3 +- .../magnetic_ptychographic_tomography.py | 28 +++++++++---------- .../process/phase/magnetic_ptychography.py | 28 +++++++++---------- .../process/phase/ptychographic_methods.py | 4 +-- .../process/phase/ptychographic_tomography.py | 28 +++++++++---------- py4DSTEM/process/phase/utils.py | 4 +-- .../phase/xray_magnetic_ptychography.py | 28 +++++++++---------- py4DSTEM/process/utils/utils.py | 18 ++---------- 10 files changed, 64 insertions(+), 84 deletions(-) diff --git a/py4DSTEM/process/diffraction/WK_scattering_factors.py b/py4DSTEM/process/diffraction/WK_scattering_factors.py index 70110a977..eb964de96 100644 --- a/py4DSTEM/process/diffraction/WK_scattering_factors.py +++ b/py4DSTEM/process/diffraction/WK_scattering_factors.py @@ -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 diff --git a/py4DSTEM/process/diffraction/crystal_viz.py b/py4DSTEM/process/diffraction/crystal_viz.py index 5c3c8303b..5bc16c1bc 100644 --- a/py4DSTEM/process/diffraction/crystal_viz.py +++ b/py4DSTEM/process/diffraction/crystal_viz.py @@ -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, diff --git a/py4DSTEM/process/fit/fit.py b/py4DSTEM/process/fit/fit.py index 9973ff79f..5c2d56a3c 100644 --- a/py4DSTEM/process/fit/fit.py +++ b/py4DSTEM/process/fit/fit.py @@ -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 ) diff --git a/py4DSTEM/process/phase/magnetic_ptychographic_tomography.py b/py4DSTEM/process/phase/magnetic_ptychographic_tomography.py index 3e13f09f6..8265c1325 100644 --- a/py4DSTEM/process/phase/magnetic_ptychographic_tomography.py +++ b/py4DSTEM/process/phase/magnetic_ptychographic_tomography.py @@ -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 diff --git a/py4DSTEM/process/phase/magnetic_ptychography.py b/py4DSTEM/process/phase/magnetic_ptychography.py index ce1c4795b..975f6ac84 100644 --- a/py4DSTEM/process/phase/magnetic_ptychography.py +++ b/py4DSTEM/process/phase/magnetic_ptychography.py @@ -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 diff --git a/py4DSTEM/process/phase/ptychographic_methods.py b/py4DSTEM/process/phase/ptychographic_methods.py index e7a332787..2e47a5e23 100644 --- a/py4DSTEM/process/phase/ptychographic_methods.py +++ b/py4DSTEM/process/phase/ptychographic_methods.py @@ -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( diff --git a/py4DSTEM/process/phase/ptychographic_tomography.py b/py4DSTEM/process/phase/ptychographic_tomography.py index e672e712e..037ef4849 100644 --- a/py4DSTEM/process/phase/ptychographic_tomography.py +++ b/py4DSTEM/process/phase/ptychographic_tomography.py @@ -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 diff --git a/py4DSTEM/process/phase/utils.py b/py4DSTEM/process/phase/utils.py index 95b7fca4e..bb960da62 100644 --- a/py4DSTEM/process/phase/utils.py +++ b/py4DSTEM/process/phase/utils.py @@ -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] diff --git a/py4DSTEM/process/phase/xray_magnetic_ptychography.py b/py4DSTEM/process/phase/xray_magnetic_ptychography.py index 62a4aeb4c..a89905a6c 100644 --- a/py4DSTEM/process/phase/xray_magnetic_ptychography.py +++ b/py4DSTEM/process/phase/xray_magnetic_ptychography.py @@ -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 diff --git a/py4DSTEM/process/utils/utils.py b/py4DSTEM/process/utils/utils.py index 60da616d1..ddeeb2c36 100644 --- a/py4DSTEM/process/utils/utils.py +++ b/py4DSTEM/process/utils/utils.py @@ -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 @@ -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