black formatting

py4DSTEM/io/filereaders/read_mib.py

@@ -163,7 +163,6 @@ def scan_size(path, scan):
     header_path = path[:-3] + "hdr"
     result = {}
     if os.path.exists(header_path):
-
         with open(header_path, encoding="UTF-8") as f:
             for line in f:
                 k, v = line.split("\t", 1)

py4DSTEM/process/diffraction/WK_scattering_factors.py

@@ -221,7 +221,9 @@ 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

py4DSTEM/process/diffraction/crystal_viz.py

@@ -453,7 +453,8 @@ 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,

py4DSTEM/process/diffraction/digital_dark_field.py

@@ -496,7 +496,7 @@ def DDFimage(points_array, aperture_positions, Rshape=None, tol=1):
 
 def radial_filtered_array(points_array_w_rphi, radius, tol=1):
     """
-    Calculates a Filtered points array from a list of detected diffraction peak positions in a points_array 
+    Calculates a Filtered points array from a list of detected diffraction peak positions in a points_array
     matching a specific qr radius, within a defined matching tolerance
 
     Parameters
@@ -579,7 +579,7 @@ def DDF_radial_image(points_array_w_rphi, radius, Rshape, tol=1):
 
 def DDFradialazimuthimage(points_array_w_rphi, radius, phi0, phi1, Rshape, tol=1):
     """
-    Calculates a Digital Dark Field image from a list of detected diffraction peak positions in a points_array 
+    Calculates a Digital Dark Field image from a list of detected diffraction peak positions in a points_array
     matching a specific qr radius, within a defined matching tolerance, and only within a defined azimuthal range
 
     Parameters

py4DSTEM/process/fit/fit.py

@@ -169,7 +169,8 @@ 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
     )
 
 

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

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

py4DSTEM/process/phase/parallax.py

@@ -884,15 +884,17 @@ def guess_common_aberrations(
         sampling = 1 / (
             np.array(self._reciprocal_sampling) * self._region_of_interest_shape
         )
-        aberrations_basis, aberrations_basis_du, aberrations_basis_dv = (
-            calculate_aberration_gradient_basis(
-                aberrations_mn,
-                sampling,
-                self._region_of_interest_shape,
-                self._wavelength,
-                rotation_angle=np.deg2rad(rotation_angle_deg),
-                xp=xp,
-            )
+        (
+            aberrations_basis,
+            aberrations_basis_du,
+            aberrations_basis_dv,
+        ) = calculate_aberration_gradient_basis(
+            aberrations_mn,
+            sampling,
+            self._region_of_interest_shape,
+            self._wavelength,
+            rotation_angle=np.deg2rad(rotation_angle_deg),
+            xp=xp,
         )
 
         # shifts
@@ -2432,7 +2434,6 @@ def score_CTF(coefs):
 
             # Plot the measured/fitted shifts comparison
             if plot_BF_shifts_comparison:
-
                 fitted_shifts = (
                     xp.tensordot(gradients, xp.array(self._aberrations_coefs), axes=1)
                     .reshape((2, -1))
@@ -3055,7 +3056,6 @@ def show_shifts(
         shifts = shifts_px * scale_arrows * xp.array(self._reciprocal_sampling)
 
         if plot_rotated_shifts and hasattr(self, "rotation_Q_to_R_rads"):
-
             if figax is None:
                 figsize = kwargs.pop("figsize", (8, 4))
                 fig, ax = plt.subplots(1, 2, figsize=figsize)

py4DSTEM/process/phase/ptychographic_methods.py

@@ -366,7 +366,9 @@ 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(

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

py4DSTEM/process/phase/utils.py

@@ -202,7 +202,9 @@ 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]

py4DSTEM/process/phase/xray_magnetic_ptychography.py

@@ -892,7 +892,6 @@ def _gradient_descent_adjoint(
 
         match (self._recon_mode, self._active_measurement_index):
             case (0, 0) | (1, 0):  # reverse
-
                 magnetic_conj = xp.exp(1.0j * xp.conj(object_patches[1]))
 
                 probe_magnetic_abs = xp.abs(shifted_probes * magnetic_conj)
@@ -930,7 +929,6 @@ def _gradient_descent_adjoint(
                 )
 
                 if not fix_probe:
-
                     electrostatic_magnetic_abs = xp.abs(
                         electrostatic_conj * magnetic_conj
                     )
@@ -962,7 +960,6 @@ def _gradient_descent_adjoint(
                     )
 
             case (0, 1) | (1, 2) | (2, 1):  # forward
-
                 magnetic_conj = xp.exp(-1.0j * xp.conj(object_patches[1]))
 
                 probe_magnetic_abs = xp.abs(shifted_probes * magnetic_conj)
@@ -992,7 +989,6 @@ def _gradient_descent_adjoint(
                 )
 
                 if not fix_probe:
-
                     electrostatic_magnetic_abs = xp.abs(
                         electrostatic_conj * magnetic_conj
                     )
@@ -1024,7 +1020,6 @@ def _gradient_descent_adjoint(
                     )
 
             case (1, 1) | (2, 0):  # neutral
-
                 probe_abs = xp.abs(shifted_probes)
                 probe_normalization = self._sum_overlapping_patches_bincounts(
                     probe_abs**2,
@@ -1047,7 +1042,6 @@ def _gradient_descent_adjoint(
                 )
 
                 if not fix_probe:
-
                     electrostatic_abs = xp.abs(electrostatic_conj)
                     electrostatic_normalization = xp.sum(
                         electrostatic_abs**2,
@@ -1482,20 +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

py4DSTEM/process/utils/utils.py

@@ -93,7 +93,12 @@ 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
 
 
@@ -102,8 +107,15 @@ 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