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2026-09-17 23:59:11 +09:00 · 2026-08-07 15:56:42 +09:00
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+% simple and fast phase ramp/offset removal from already unwrapped sinogram 
+% Assume the sample to contain air on both horizontal sides in stripes: 
+% 1:air_gap(1) and end-air_gap(2):end
+%
+% sinogram = remove_sinogram_ramp(sinogram,air_gap,polyfit_order )
+% 
+% using linear interpolation between air on both sides 
+% Inputs:
+%     **sinogram - unwrapped projections 
+%     **air_gap = [2x1] vector with number of pixels on both sides where can
+%               be assumed to be air 
+%     **polyfit_order:-1 = dont assume anything about the removed phase,
+%                       subtract linear offset from each horizontal line separately
+%                      0 = assume that removed degree of freedom is only a constant offset
+%                      1 = assume that removed degree of freedom is a 2D plane 
+% Outputs: 
+%     ++unwrapped phase after the ramp removal 
+
+
+%*-----------------------------------------------------------------------*
+%|                                                                       |
+%|  Except where otherwise noted, this work is licensed under a          |
+%|  Creative Commons Attribution-NonCommercial-ShareAlike 4.0            |
+%|  International (CC BY-NC-SA 4.0) license.                             |
+%|                                                                       |
+%|  Copyright (c) 2017 by Paul Scherrer Institute (http://www.psi.ch)    |
+%|                                                                       |
+%|       Author: CXS group, PSI                                          |
+%*-----------------------------------------------------------------------*
+% You may use this code with the following provisions:
+%
+% If the code is fully or partially redistributed, or rewritten in another
+%   computing language this notice should be included in the redistribution.
+%
+% If this code, or subfunctions or parts of it, is used for research in a 
+%   publication or if it is fully or partially rewritten for another 
+%   computing language the authors and institution should be acknowledged 
+%   in written form in the publication: “Data processing was carried out 
+%   using the “cSAXS matlab package” developed by the CXS group,
+%   Paul Scherrer Institut, Switzerland.” 
+%   Variations on the latter text can be incorporated upon discussion with 
+%   the CXS group if needed to more specifically reflect the use of the package 
+%   for the published work.
+%
+% A publication that focuses on describing features, or parameters, that
+%    are already existing in the code should be first discussed with the
+%    authors.
+%   
+% This code and subroutines are part of a continuous development, they 
+%    are provided “as they are” without guarantees or liability on part
+%    of PSI or the authors. It is the user responsibility to ensure its 
+%    proper use and the correctness of the results.
+
+
+function sinogram = remove_sinogram_ramp(sinogram,air_gap, polyfit_order)
+    if nargin < 3
+        polyfit_order = -1; 
+    end 
+    
+    air_gap  = ceil(air_gap);
+    [Nlayers,width_sinogram,~] = size(sinogram);
+    ax = 1:width_sinogram;
+    mask{1} = ax <= air_gap(1);
+    mask{2} = ax >= width_sinogram-air_gap(min(end,2));
+    %%%%%%%% get average sinogram to be subtracted 
+    for ii = 1:2
+        % get average values in the air_gap
+        air_values{ii}  = sum( bsxfun(@times,sinogram,mask{ii}),2)/sum(mask{ii});
+        if polyfit_order == 0
+            %% find phase offset value 
+            air_values{ii} = mean(air_values{ii}); 
+        elseif polyfit_order == 1
+            %% find 2D plane that fits the air region
+            ramp = linspace(-1,1,Nlayers)';
+            weight = 1; 
+            % iterativelly refine the ideal plane estiamte to ignore
+            % imperfect estimations of the air_gap paramter 
+            for jj = 1:10
+                % fit it with a linear plane, use for 2d unwrapping
+                plane_fit = mean(weight .*air_values{ii}) ./ mean(weight) +mean(weight.*air_values{ii}  .* ramp)./ mean(weight.*ramp.^2)  .*ramp; 
+                deviation = 5*mad(air_values{ii}(:) - plane_fit(:),0); 
+                % avoid outliers by adaptive weighting
+                weight = 1./(1+(abs(air_values{ii}-plane_fit)./deviation).^2  ); 
+            end
+            air_values{ii}  = plane_fit; 
+        end
+    end
+    % get a plane in between left and right side passing through
+    % air_values{1} and air_values{2}
+    ramp = permute(interp1([0,width_sinogram]', permute([air_values{:}],[2,1,3]), 1:width_sinogram), [2,1,3]);
+    %%%%%%%% remove ramp & sinogram offset
+    sinogram =  sinogram - ramp; 
+
+
+end