Thnks fr th Mmr(s)

py4DSTEM/process/phase/iterative_base_class.py

@@ -1163,6 +1163,12 @@ def _normalize_diffraction_intensities(
         mean_intensity = 0
 
         diffraction_intensities = self._asnumpy(diffraction_intensities)
+        if positions_mask is not None:
+            number_of_patterns = np.count_nonzero(self._positions_mask.ravel())
+            sx, sy = np.where(~self._positions_mask)
+        else:
+            number_of_patterns = np.prod(diffraction_intensities.shape[:2])
+
         if crop_patterns:
             crop_x = int(
                 np.minimum(
@@ -1181,8 +1187,7 @@ def _normalize_diffraction_intensities(
             region_of_interest_shape = (crop_w * 2, crop_w * 2)
             amplitudes = np.zeros(
                 (
-                    diffraction_intensities.shape[0],
-                    diffraction_intensities.shape[1],
+                    number_of_patterns,
                     crop_w * 2,
                     crop_w * 2,
                 ),
@@ -1198,13 +1203,19 @@ def _normalize_diffraction_intensities(
 
         else:
             region_of_interest_shape = diffraction_intensities.shape[-2:]
-            amplitudes = np.zeros(diffraction_intensities.shape, dtype=np.float32)
+            amplitudes = np.zeros(
+                (number_of_patterns,) + region_of_interest_shape, dtype=np.float32
+            )
 
         com_fitted_x = self._asnumpy(com_fitted_x)
         com_fitted_y = self._asnumpy(com_fitted_y)
 
+        counter = 0
         for rx in range(diffraction_intensities.shape[0]):
             for ry in range(diffraction_intensities.shape[1]):
+                if positions_mask is not None:
+                    if rx in sx and ry in sy:
+                        continue
                 intensities = get_shifted_ar(
                     diffraction_intensities[rx, ry],
                     -com_fitted_x[rx, ry],
@@ -1219,13 +1230,10 @@ def _normalize_diffraction_intensities(
                     )
 
                 mean_intensity += np.sum(intensities)
-                amplitudes[rx, ry] = np.sqrt(np.maximum(intensities, 0))
+                amplitudes[counter] = np.sqrt(np.maximum(intensities, 0))
+                counter += 1
 
-        amplitudes = xp.reshape(amplitudes, (-1,) + region_of_interest_shape)
         amplitudes = xp.asarray(amplitudes)
-        if positions_mask is not None:
-            amplitudes = amplitudes[positions_mask.ravel()]
-
         mean_intensity /= amplitudes.shape[0]
 
         return amplitudes, mean_intensity

py4DSTEM/process/phase/iterative_mixedstate_multislice_ptychography.py

@@ -189,7 +189,7 @@ def __init__(
                 f"object_type must be either 'potential' or 'complex', not {object_type}"
             )
 
-        if positions_mask.dtype != "bool":
+        if positions_mask is not None and positions_mask.dtype != "bool":
             warnings.warn(
                 ("`positions_mask` converted to `bool` array"),
                 UserWarning,

py4DSTEM/process/phase/iterative_mixedstate_ptychography.py

@@ -164,7 +164,7 @@ def __init__(
             raise ValueError(
                 f"object_type must be either 'potential' or 'complex', not {object_type}"
             )
-        if positions_mask.dtype != "bool":
+        if positions_mask is not None and positions_mask.dtype != "bool":
             warnings.warn(
                 ("`positions_mask` converted to `bool` array"),
                 UserWarning,

py4DSTEM/process/phase/iterative_multislice_ptychography.py

@@ -198,7 +198,7 @@ def __init__(
             raise ValueError(
                 f"object_type must be either 'potential' or 'complex', not {object_type}"
             )
-        if positions_mask.dtype != "bool":
+        if positions_mask is not None and positions_mask.dtype != "bool":
             warnings.warn(
                 ("`positions_mask` converted to `bool` array"),
                 UserWarning,

py4DSTEM/process/phase/iterative_overlap_magnetic_tomography.py

@@ -166,7 +166,7 @@ def __init__(
         if object_type != "potential":
             raise NotImplementedError()
 
-        if positions_mask.dtype != "bool":
+        if positions_mask is not None and positions_mask.dtype != "bool":
             warnings.warn(
                 ("`positions_mask` converted to `bool` array"),
                 UserWarning,

py4DSTEM/process/phase/iterative_overlap_tomography.py

@@ -175,7 +175,7 @@ def __init__(
         if object_type != "potential":
             raise NotImplementedError()
 
-        if positions_mask.dtype != "bool":
+        if positions_mask is not None and positions_mask.dtype != "bool":
             warnings.warn(
                 ("`positions_mask` converted to `bool` array"),
                 UserWarning,

py4DSTEM/process/phase/iterative_simultaneous_ptychography.py

@@ -153,7 +153,7 @@ def __init__(
             raise ValueError(
                 f"object_type must be either 'potential' or 'complex', not {object_type}"
             )
-        if positions_mask.dtype != "bool":
+        if positions_mask is not None and positions_mask.dtype != "bool":
             warnings.warn(
                 ("`positions_mask` converted to `bool` array"),
                 UserWarning,

py4DSTEM/process/phase/iterative_singleslice_ptychography.py

@@ -150,7 +150,7 @@ def __init__(
                 f"object_type must be either 'potential' or 'complex', not {object_type}"
             )
 
-        if positions_mask.dtype != "bool":
+        if positions_mask is not None and positions_mask.dtype != "bool":
             warnings.warn(
                 ("`positions_mask` converted to `bool` array"),
                 UserWarning,