initial commit

2026-09-17 22:59:07 +09:00 · 2026-08-07 15:56:42 +09:00
commit 91ad25aca9
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+% IMSHIFT_GENERIC auxiliar function to be performed bu block_fun on GPU 
+% it applies imshift_fft on the provided image that was first upsampled
+% to Npix (if needed) and cropped to region ROI 
+% after shifting, the image is downsampled by the chosen interpolation
+% method "intep_method" that is more accurate than simple binning 
+% 
+% img = imshift_generic(img, shift, Npix, affine_matrix, smooth, ROI, downsample, intep_method, interp_sign)
+% 
+%  Inputs: 
+%   **img           2D stacked image 
+%   **shift         Nx2 vector of shifts applied on the image 
+%   **Npix          2x1 int, size of the img to be upsampled before shift, Npix = [] -> no upsampling 
+%   **affine_matrix affine metrix ! not implemented yet!
+%   **smooth        how many pixels around edges will be smoothed before shifting the array 
+%   **ROI           cell array, used to crop the array to smaller size 
+%   **downsample    downsample factor , 1 == no downsampling
+%   **intep_method  interpolation method: linear, fft 
+%   **interp_sign   sign used for subpixel shifts of the dataset, +1 for unwrapped phase, -1 for phase differene 
+%  *returns* 
+%   ++img           2D stacked image 
+
+function img = imshift_generic(img, shift, Npix, affine_matrix, smooth, ROI, downsample, intep_method, interp_sign)
+
+    if nargin < 9 
+        interp_sign = 0; 
+    end
+    
+    import math.*
+    import utils.*
+    
+    if isa(img, 'uint8') || (isa(img, 'gpuArray') && strcmpi(classUnderlying(img),'uint8'))
+        img = single(img) / 255; % assume that the provided image is only compressed into uint8
+    end
+    
+    % if needed upsample to the size of the projection 
+    if ~isempty(Npix) && any(Npix(1:2) ~= [size(img,1),size(img,2)])
+        switch intep_method
+            case 'linear', img = utils.interpolate_linear(img, Npix); 
+            case 'fft', img = utils.interpolateFT(img, Npix); 
+        end
+    end
+    
+    isReal = isreal(img); 
+   
+    if any(shift(:) ~=0 )
+        smooth_axis = 3-find(any(shift ~= 0)); 
+        img = smooth_edges(img, smooth, smooth_axis);
+        if ~ismatrix(img)
+            switch intep_method
+                case 'linear'
+                    img = utils.imshift_linear(img,shift);  % interpolation of the weights does not need such precision 
+                case 'fft'
+                    %%% APPLY SHIFT USING FFT -> periodic boundary 
+                    img = imshift_fft(img, shift);            
+            end
+        end
+    end
+
+    % crop the FOV after shift and before "downsample"
+    if ~isempty(ROI)
+       img = img(ROI{:},:);   % crop to smaller ROI if provided  
+                              % apply crop after imshift_fft
+    end
+    
+    Np = size(img); 
+    
+    % perform interpolation instead of downsample , it provides more accurate results 
+    if downsample > 1
+        img = utils.imgaussfilt3_conv(img,[downsample,downsample,0]); 
+        % correct for boundary effects of the convolution based smoothing
+        img = img ./ utils.imgaussfilt3_conv(ones(Np(1:2), 'like', img),[downsample,downsample,0]); 
+        switch intep_method
+            case 'linear', img = utils.interpolate_linear(img,ceil(Np(1:2)/downsample/2)*2);  % interpolation of the weights does not need such precision 
+            case 'fft',    img = utils.interpolateFT_centered(utils.smooth_edges(img, 2*downsample),ceil(Np(1:2)/downsample/2)*2, interp_sign); % accurate interpolation using FFT
+        end
+    end
+    if isReal; img = real(img); end
+    
+end