rescaleDefocusSeries: new mode which avoids cropping of data

functions/phaseRetrieval/utilities/rescaleDefocusSeries.m

@@ -45,6 +45,8 @@ function [imAligned,fresnelNumbersRescaled,imFiltered] = rescaleDefocusSeries(im
 % alignReconstructedImages : Default = false
 %     Should alignment be performed for single-distance CTF reconstructed
 %     projections? 
+% noCropOutput : Default = false
+%     Output the full holograms after rescaling without cropping. 
 % ctfsettings : Default = []
 %     Settings for the CTF reconstruction, if alignReconstructedImages is true. If it is
 %     empty, the settings betaDeltaRatio = 1/100, lim1 = 0.01 and lim2 = 0.1 are
@@ -145,6 +147,8 @@ defaults.cutBottom = 0;
 defaults.alignMethod = 'dftreg';   
 defaults.registrationMode = 'shift';            
 defaults.registrationAccuracy = 10;            
+defaults.noCropOutput = false;  
+
 
 defaults.givestatus = 0;
 defaults.alignReconstructedImages = false;
@@ -236,6 +240,11 @@ fresnelNumbersRescaled = fresnelNumbers .* (magnifications ./ maxMagnification).
 % determine scaling factors with respect to image with largest magnification
 scalings = maxMagnification ./ magnifications;
 
+if (settings.noCropOutput)
+    [imAligned, imFiltered] = rescaleNoCrop();
+    return
+end
+
 if (settings.givestatus)
     disp (['Aligning image 1 / ' num2str(numHolos)])
 end
@@ -299,6 +308,72 @@ for imageIdx = idxMaxMagnification+direction:direction:idxMaxMagnification+direc
                                     shifts, rotAngleDegree, scalings(:,imageIdx));
 end
 
+
+function [imAligned,imFiltered] = rescaleNoCrop()
+% for the no crop option it makes sense to do everything the other way
+% round. starting at the smallest magnification but the largest scaling.
+% since this is what determines the output.
+
+[maxScaling, maxScalingIdx] = max(scalings(1,:));
+
+% image with largest scaling is reference --> no alignment needed
+ imReference = imresize(images(:,:,maxScalingIdx), scalings(1,maxScalingIdx), 'lanczos3');  
+ outputSize = size(imReference);
+ 
+ imAligned = zeros([outputSize numHolos]);
+ imAligned(:,:,maxScalingIdx) = imReference;
+
+ 
+% all other images are aligned to the predecessor
+shift = 0; number = 1;
+direction = direction*-1;
+for imageIdx = maxScalingIdx+direction:direction:maxScalingIdx+direction*(numHolos-1)
+    
+    if (settings.givestatus)
+        number = number+1;
+        disp (['Aligning image ' num2str(number) ' / ' num2str(numHolos)])
+end
+    
+    % scale all images to the pixelsize of the one with the largest
+    % magnification
+%     imScaled = magnifyImage(images(:,:,imageIdx), scalings(:,imageIdx));  
+    imScaled = imresize(images(:,:,imageIdx), scalings(1,imageIdx), 'lanczos3');  
+    imScaled = padToSize(imScaled, outputSize, 0);
+        
+    % optional CTF reconstruction to better align images to each other as
+    % holograms might look too different
+    if settings.alignReconstructedImages
+        imScaled = phaserec_ctf(imScaled, fresnelNumbersRescaled(:,imageIdx), settings.ctfsettings);
+    end
+           
+    % identify feature for manually determining shifts between images
+    if strcmp(settings.alignMethod,'manualFeature')
+        imagesc(imScaled)
+        colormap gray
+        axis equal tight off
+        % get coordinates (y, x)
+        featureCoords(imageIdx,:) = fliplr(ginput(1)) - ...
+            [(size(imScaled,1)-size(images(:,:,idxMaxMagnification),1))/2 ...
+            (size(imScaled,2)-size(images(:,:,idxMaxMagnification),2))/2];
+        shift_diff = featureCoords(imageIdx-direction,:) - featureCoords(imageIdx,:);
+        shift = shift+shift_diff;
+        
+        imFiltered = imScaled;
+    else
+        % align the cropped image to the reference using alignImages and dftregistration
+        [~, shifts, rotAngleDegree, imFiltered] = alignImages(imScaled, imReference ,settings);
+        shifts
+        rotAngleDegree
+    end
+    imScaled = padToSize(imScaled, ceil(outputSize*1.1), 0);
+    imScaled = circshiftSubPixel(imScaled, shifts);
+    imScaled = cropToCenter(imScaled, outputSize);
+    imAligned(:,:, imageIdx) = imScaled;
+                           
 end
 
+end % end rescaleNoCrop 
+
+end % end RescaleDefocusSeries
+