deleted changes-cropping is done in alignImages

functions/phaseRetrieval/utilities/rescaleDefocusSeries.m

@@ -290,13 +290,7 @@ for imageIdx = idxMaxMagnification+direction:direction:idxMaxMagnification+direc
         imFiltered = imScaled;
     else
         % align the cropped image to the reference using alignImages and dftregistration
-        [~, shifts, rotAngleDegree, imFiltered] = alignImages(imScaled(...
-            settings.cutTop + 1: size(imScaled,1)-settings.cutBottom ...
-            , settings.cutLeft + 1 : size(imScaled,2)-settings.cutRight) ...
-            , imReference(...
-            settings.cutTop + 1 : size(imReference,1)-settings.cutBottom ...
-            , settings.cutLeft + 1 : size(imReference,2)-settings.cutRight) ...
-            ,settings);
+        [~, shifts, rotAngleDegree, imFiltered] = alignImages(imScaled, imReference ,settings);
     end
     
     % Apply scaling and registered shifts/rotations to original image (performed in a single step