adding interpolation order flag for shifting, default bicubic

py4DSTEM/process/phase/direct_ptychography.py

@@ -325,6 +325,7 @@ def preprocess(
         bf_disk_padding_px: int = 0,
         dp_mask: np.ndarray = None,
         in_place_datacube_modification: bool = False,
+        shifting_interpolation_order: int = 3,
         fit_function: str = "plane",
         plot_center_of_mass: str = "default",
         plot_rotation: bool = True,
@@ -354,6 +355,8 @@ def preprocess(
         in_place_datacube_modification: bool, optional
             If True, the datacube will be preprocessed in-place. Note this is not possible
             when either crop_patterns or positions_mask are used.
+        shifting_interpolation_order: int
+            Spline interpolation order used in shifting DPs to origin. Default is bi-cubic.
         fit_function: str, optional
             2D fitting function for CoM fitting. One of 'plane','parabola','bezier_two'
         plot_center_of_mass: str, optional
@@ -527,6 +530,7 @@ def preprocess(
             None,
             crop_patterns,
             in_place_datacube_modification,
+            shifting_interpolation_order=shifting_interpolation_order,
             return_intensities_instead=True,
         )
 
@@ -583,7 +587,7 @@ def preprocess(
                 self._vacuum_probe_intensity,
                 -probe_x0,
                 -probe_y0,
-                bilinear=False,
+                bilinear=True,
                 device=device,
             )
 

py4DSTEM/process/phase/magnetic_ptychographic_tomography.py

@@ -227,6 +227,7 @@ def preprocess(
         self,
         diffraction_intensities_shape: Tuple[int, int] = None,
         reshaping_method: str = "bilinear",
+        shifting_interpolation_order: int = 3,
         padded_diffraction_intensities_shape: Tuple[int, int] = None,
         region_of_interest_shape: Tuple[int, int] = None,
         dp_mask: np.ndarray = None,
@@ -264,6 +265,8 @@ def preprocess(
             If None, no resampling of diffraction intenstities is performed
         reshaping_method: str, optional
             Method to use for reshaping, either 'bin, 'bilinear', or 'fourier' (default)
+        shifting_interpolation_order: int
+            Spline interpolation order used in shifting DPs to origin. Default is bi-cubic.
         padded_diffraction_intensities_shape: (int,int), optional
             Padded diffraction intensities shape.
             If None, no padding is performed
@@ -496,6 +499,7 @@ def preprocess(
                 self._positions_mask[index],
                 crop_patterns,
                 in_place_datacube_modification,
+                shifting_interpolation_order=shifting_interpolation_order,
             )
 
             self._mean_diffraction_intensity.append(mean_diffraction_intensity_temp)

py4DSTEM/process/phase/magnetic_ptychography.py

@@ -205,6 +205,7 @@ def preprocess(
         self,
         diffraction_intensities_shape: Tuple[int, int] = None,
         reshaping_method: str = "bilinear",
+        shifting_interpolation_order: int = 3,
         padded_diffraction_intensities_shape: Tuple[int, int] = None,
         region_of_interest_shape: Tuple[int, int] = None,
         dp_mask: np.ndarray = None,
@@ -252,6 +253,8 @@ def preprocess(
             If None, no resampling of diffraction intenstities is performed
         reshaping_method: str, optional
             Method to use for reshaping, either 'bin, 'bilinear', or 'fourier' (default)
+        shifting_interpolation_order: int
+            Spline interpolation order used in shifting DPs to origin. Default is bi-cubic.
         padded_diffraction_intensities_shape: (int,int), optional
             Padded diffraction intensities shape.
             If None, no padding is performed
@@ -559,6 +562,7 @@ def preprocess(
                 self._positions_mask[index],
                 crop_patterns,
                 in_place_datacube_modification,
+                shifting_interpolation_order=shifting_interpolation_order,
             )
 
             self._mean_diffraction_intensity.append(mean_diffraction_intensity_temp)

py4DSTEM/process/phase/mixedstate_multislice_ptychography.py

@@ -264,6 +264,7 @@ def preprocess(
         self,
         diffraction_intensities_shape: Tuple[int, int] = None,
         reshaping_method: str = "bilinear",
+        shifting_interpolation_order: int = 3,
         padded_diffraction_intensities_shape: Tuple[int, int] = None,
         region_of_interest_shape: Tuple[int, int] = None,
         dp_mask: np.ndarray = None,
@@ -311,6 +312,8 @@ def preprocess(
             If None, no resampling of diffraction intenstities is performed
         reshaping_method: str, optional
             Method to use for reshaping, either 'bin, 'bilinear', or 'fourier' (default)
+        shifting_interpolation_order: int
+            Spline interpolation order used in shifting DPs to origin. Default is bi-cubic.
         padded_diffraction_intensities_shape: (int,int), optional
             Padded diffraction intensities shape.
             If None, no padding is performed
@@ -498,6 +501,7 @@ def preprocess(
             self._positions_mask,
             crop_patterns,
             in_place_datacube_modification,
+            shifting_interpolation_order=shifting_interpolation_order,
         )
 
         # explicitly transfer arrays to storage

py4DSTEM/process/phase/mixedstate_ptychography.py

@@ -210,6 +210,7 @@ def preprocess(
         self,
         diffraction_intensities_shape: Tuple[int, int] = None,
         reshaping_method: str = "bilinear",
+        shifting_interpolation_order: int = 3,
         padded_diffraction_intensities_shape: Tuple[int, int] = None,
         region_of_interest_shape: Tuple[int, int] = None,
         dp_mask: np.ndarray = None,
@@ -257,6 +258,8 @@ def preprocess(
             If None, no resampling of diffraction intenstities is performed
         reshaping_method: str, optional
             Method to use for reshaping, either 'bin, 'bilinear', or 'fourier' (default)
+        shifting_interpolation_order: int
+            Spline interpolation order used in shifting DPs to origin. Default is bi-cubic.
         padded_diffraction_intensities_shape: (int,int), optional
             Padded diffraction intensities shape.
             If None, no padding is performed
@@ -444,6 +447,7 @@ def preprocess(
             self._positions_mask,
             crop_patterns,
             in_place_datacube_modification,
+            shifting_interpolation_order=shifting_interpolation_order,
         )
 
         # explicitly transfer arrays to storage

py4DSTEM/process/phase/multislice_ptychography.py

@@ -238,6 +238,7 @@ def preprocess(
         self,
         diffraction_intensities_shape: Tuple[int, int] = None,
         reshaping_method: str = "bilinear",
+        shifting_interpolation_order: int = 3,
         padded_diffraction_intensities_shape: Tuple[int, int] = None,
         region_of_interest_shape: Tuple[int, int] = None,
         dp_mask: np.ndarray = None,
@@ -285,6 +286,8 @@ def preprocess(
             If None, no resampling of diffraction intenstities is performed
         reshaping_method: str, optional
             Method to use for reshaping, either 'bin, 'bilinear', or 'fourier' (default)
+        shifting_interpolation_order: int
+            Spline interpolation order used in shifting DPs to origin. Default is bi-cubic.
         padded_diffraction_intensities_shape: (int,int), optional
             Padded diffraction intensities shape.
             If None, no padding is performed
@@ -472,6 +475,7 @@ def preprocess(
             self._positions_mask,
             crop_patterns,
             in_place_datacube_modification,
+            shifting_interpolation_order=shifting_interpolation_order,
         )
 
         # explicitly transfer arrays to storage

py4DSTEM/process/phase/parallax.py

@@ -32,7 +32,7 @@
 from py4DSTEM.process.utils.utils import electron_wavelength_angstrom
 from py4DSTEM.visualize import return_scaled_histogram_ordering
 from scipy.linalg import polar
-from scipy.ndimage import distance_transform_edt
+from scipy.ndimage import distance_transform_edt, shift
 from scipy.special import comb
 
 try:
@@ -316,6 +316,7 @@ def preprocess(
         normalize_images: bool = True,
         normalize_order=0,
         descan_correction_fit_function: str = None,
+        shifting_interpolation_order: int = 3,
         force_rotation_angle_deg: float = 0,
         force_transpose: bool = None,
         aligned_bf_image_guess: np.ndarray = None,
@@ -354,6 +355,8 @@ def preprocess(
         descan_correction_fit_function: str, optional
             If not None, descan correction will be performed using fit function.
             One of "constant", "plane", "parabola", or "bezier_two".
+        shifting_interpolation_order: int, optional
+            Spline interpolation order used in shifting DPs to origin. Default is bi-cubic.
         plot_average_bf: bool, optional
             If True, plots the average bright field image, using defocus_guess
         realspace_mask: np.array, optional
@@ -433,15 +436,25 @@ def preprocess(
 
             for rx in range(intensities_shifted.shape[0]):
                 for ry in range(intensities_shifted.shape[1]):
-                    intensity_shifted = get_shifted_ar(
-                        intensities_np[rx, ry],
-                        -com_fitted_x[rx, ry] + center_x,
-                        -com_fitted_y[rx, ry] + center_y,
-                        bilinear=False,
-                        device="cpu",
-                    )
-
-                    intensities_shifted[rx, ry] = intensity_shifted
+                    if shifting_interpolation_order == 1:
+                        # faster but may lead to gridding artifacts
+                        intensities_shifted[rx, ry] = get_shifted_ar(
+                            intensities_np[rx, ry].astype(np.float32),
+                            -com_fitted_x[rx, ry] + center_x,
+                            -com_fitted_y[rx, ry] + center_y,
+                            bilinear=True,
+                            device="cpu",
+                        )
+                    else:
+                        intensities_shifted[rx, ry] = shift(
+                            intensities_np[rx, ry].astype(np.float32),
+                            (
+                                -com_fitted_x[rx, ry] + center_x,
+                                -com_fitted_y[rx, ry] + center_y,
+                            ),
+                            order=shifting_interpolation_order,
+                            mode="grid-wrap",
+                        )
 
             intensities = xp.asarray(intensities_shifted, xp.float32)
 

py4DSTEM/process/phase/phase_base_class.py

@@ -9,7 +9,7 @@
 import numpy as np
 from mpl_toolkits.axes_grid1 import ImageGrid
 from py4DSTEM.visualize import show_complex
-from scipy.ndimage import zoom
+from scipy.ndimage import shift, zoom
 
 try:
     import cupy as cp
@@ -1352,6 +1352,7 @@ def _normalize_diffraction_intensities(
         positions_mask,
         crop_patterns,
         in_place_datacube_modification,
+        shifting_interpolation_order=3,
         return_intensities_instead=False,
     ):
         """
@@ -1371,6 +1372,10 @@ def _normalize_diffraction_intensities(
             If True, patterns are cropped to avoid wrap around of patterns
         in_place_datacube_modification: bool
             If True, the diffraction intensities are modified in-place
+        shifting_interpolation_order: int
+            Spline interpolation order used in shifting DPs to origin. Default is bi-cubic.
+        return_intensities_instead: bool
+            If True, function returns shifted intensities instead of amplitudes. Used in SSB.
 
         Returns
         -------
@@ -1434,13 +1439,22 @@ def _normalize_diffraction_intensities(
                 if not positions_mask[rx, ry]:
                     continue
 
-            intensities = get_shifted_ar(
-                diff_intensities[rx, ry],
-                -com_fitted_x[rx, ry],
-                -com_fitted_y[rx, ry],
-                bilinear=False,
-                device="cpu",
-            )
+            if shifting_interpolation_order == 1:
+                # faster but may lead to gridding artifacts
+                intensities = get_shifted_ar(
+                    diff_intensities[rx, ry].astype(np.float32),
+                    -com_fitted_x[rx, ry],
+                    -com_fitted_y[rx, ry],
+                    bilinear=True,
+                    device="cpu",
+                )
+            else:
+                intensities = shift(
+                    diff_intensities[rx, ry].astype(np.float32),
+                    (-com_fitted_x[rx, ry], -com_fitted_y[rx, ry]),
+                    order=shifting_interpolation_order,
+                    mode="grid-wrap",
+                )
 
             mean_intensity += np.sum(intensities)
             if return_intensities_instead:

py4DSTEM/process/phase/ptychographic_methods.py

@@ -1077,7 +1077,7 @@ def _initialize_probe(
                     vacuum_probe_intensity,
                     -probe_x0,
                     -probe_y0,
-                    bilinear=False,
+                    bilinear=True,
                     device=device,
                 )
 

py4DSTEM/process/phase/ptychographic_tomography.py

@@ -377,6 +377,7 @@ def preprocess(
         self,
         diffraction_intensities_shape: Tuple[int, int] = None,
         reshaping_method: str = "bilinear",
+        shifting_interpolation_order: int = 3,
         padded_diffraction_intensities_shape: Tuple[int, int] = None,
         region_of_interest_shape: Tuple[int, int] = None,
         dp_mask: np.ndarray = None,
@@ -416,6 +417,8 @@ def preprocess(
             If None, no resampling of diffraction intenstities is performed
         reshaping_method: str, optional
             Method to use for reshaping, either 'bin, 'bilinear', or 'fourier' (default)
+        shifting_interpolation_order: int
+            Spline interpolation order used in shifting DPs to origin. Default is bi-cubic.
         padded_diffraction_intensities_shape: (int,int), optional
             Padded diffraction intensities shape.
             If None, no padding is performed
@@ -652,6 +655,7 @@ def preprocess(
                 self._positions_mask[index],
                 crop_patterns,
                 in_place_datacube_modification,
+                shifting_interpolation_order=shifting_interpolation_order,
             )
 
             self._mean_diffraction_intensity.append(mean_diffraction_intensity_temp)

py4DSTEM/process/phase/singleslice_ptychography.py

@@ -192,6 +192,7 @@ def preprocess(
         self,
         diffraction_intensities_shape: Tuple[int, int] = None,
         reshaping_method: str = "bilinear",
+        shifting_interpolation_order: int = 3,
         padded_diffraction_intensities_shape: Tuple[int, int] = None,
         region_of_interest_shape: Tuple[int, int] = None,
         dp_mask: np.ndarray = None,
@@ -229,6 +230,8 @@ def preprocess(
             If None, no resampling of diffraction intenstities is performed
         reshaping_method: str, optional
             Method to use for reshaping, either 'bin, 'bilinear', or 'fourier' (default)
+        shifting_interpolation_order: int
+            Spline interpolation order used in shifting DPs to origin. Default is bi-cubic.
         padded_diffraction_intensities_shape: (int,int), optional
             Padded diffraction intensities shape.
             If None, no padding is performed
@@ -417,6 +420,7 @@ def preprocess(
             self._positions_mask,
             crop_patterns,
             in_place_datacube_modification,
+            shifting_interpolation_order=shifting_interpolation_order,
         )
 
         # explicitly transfer arrays to storage

py4DSTEM/process/phase/utils.py

@@ -179,7 +179,7 @@ def evaluate_aperture(
                     xp.asarray(self._vacuum_probe_intensity, dtype=xp.float32),
                     self._origin[0],
                     self._origin[1],
-                    bilinear=False,
+                    bilinear=True,
                     device=self._device,
                 )
             else:

py4DSTEM/process/phase/xray_magnetic_ptychography.py

@@ -203,6 +203,7 @@ def preprocess(
         self,
         diffraction_intensities_shape: Tuple[int, int] = None,
         reshaping_method: str = "bilinear",
+        shifting_interpolation_order: int = 3,
         padded_diffraction_intensities_shape: Tuple[int, int] = None,
         region_of_interest_shape: Tuple[int, int] = None,
         dp_mask: np.ndarray = None,
@@ -250,6 +251,8 @@ def preprocess(
             If None, no resampling of diffraction intenstities is performed
         reshaping_method: str, optional
             Method to use for reshaping, either 'bin, 'bilinear', or 'fourier' (default)
+        shifting_interpolation_order: int
+            Spline interpolation order used in shifting DPs to origin. Default is bi-cubic.
         padded_diffraction_intensities_shape: (int,int), optional
             Padded diffraction intensities shape.
             If None, no padding is performed
@@ -557,6 +560,7 @@ def preprocess(
                 self._positions_mask[index],
                 crop_patterns,
                 in_place_datacube_modification,
+                shifting_interpolation_order=shifting_interpolation_order,
             )
 
             self._mean_diffraction_intensity.append(mean_diffraction_intensity_temp)