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+utils/apply_3D_apodization.m

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+% APPLY_3D_APODIZATION Smoothly apodize tomogram to avoid sharp edges and air affecting
+% the FRC analysis 
+%
+% [tomogram,circulo] = apply_3D_apodization(tomogram, rad_apod, axial_apod, radial_smooth)
+%
+% Inputs:
+%     **tomogram - volume to be apodized 
+%     **rad_apod - number of pixels to be zeroed from edge of the tomogram 
+%     **axial_apod - roughly number of pixels to be zeroed from top / bottom 
+%     **radial_smooth - smoothness of the apodization in pixels, default = Npix/10
+%     **layer_dim
+% Outputs: 
+%     ++tomogram - apodized volume 
+%     ++circulo -apodization mask 
+% MODIFIED BY YJ TO ALLOW UNEVEN SIZES
+
+function [tomogram,circulo] = apply_3D_apodization(tomogram, rad_apod, axial_apod, radial_smooth )
+    import utils.*
+    [Npix_y,Npix_x,Nlayers] = size(tomogram);
+    Npix = max(Npix_y,Npix_x);
+    if nargin < 4 
+        radial_smooth = Npix/10;
+    end
+
+    if nargin < 3
+        axial_apod = [];
+    end
+    if ~isempty(rad_apod) 
+        xt = -Npix/2:Npix/2-1;
+        [X,Y] = meshgrid(xt,xt);
+        radial_smooth = max(radial_smooth,1); % prevent division by zero 
+        circulo= single(1-radtap(X,Y,radial_smooth,round(Npix/2-rad_apod-radial_smooth)));
+        if Npix_y~=Npix_x 
+            circulo= crop_pad( circulo, [Npix_y,Npix_x]);
+        end
+        tomogram = bsxfun(@times, tomogram, circulo);
+    end
+    if ~isempty(axial_apod) && Nlayers > 1
+        filters = fract_hanning_pad(Nlayers,Nlayers,max(0,round(Nlayers-2*axial_apod)));
+        filters = ifftshift(filters(:,1));
+        tomogram = bsxfun(@times,tomogram,reshape(filters,1,1,[]));
+    end
+    
+end