initial commit

2026-09-17 21:39:08 +09:00 · 2026-08-07 15:56:42 +09:00
commit 91ad25aca9
1012 changed files with 159314 additions and 0 deletions
@@ -0,0 +1,93 @@
+% GET_PHASE_GRADIENT_2D get 2D gradient of phase of image IMG. 
+% Accept either complex image or just phase 
+%
+% [d_X, d_Y] = get_phase_gradient_2D(img, step=0, padding=8)
+%
+% Inputs
+%     **img     - stack of complex valued input images 
+% *optional*
+%     **step    - step used to calculate the central difference, default=0 (analytic expression)
+%     **padding - padding around edges to prevent periodic boundary artefacts 
+%
+% *returns*
+%     ++d_X,d_Y - horizontal and vertical phase gradient arrays 
+    
+
+%*-----------------------------------------------------------------------*
+%|                                                                       |
+%|  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 [d_X, d_Y] = get_phase_gradient_2D(img, step, padding)
+
+    import utils.*
+    import math.*
+
+    if isreal(img)
+        img = exp(1i*img);
+    end
+    if nargin < 2
+        step = 0;  % step of the difference (too small will amplify noise)
+    end
+    if nargin < 3
+         padding = 8; % pad arrays to avoid edge issues 
+    end
+    
+    
+    % suppress edge issues if phase ramp is not subtracted / there is no
+    % air around sample 
+    
+    if padding > 0
+        img = padarray(img,[padding, padding],'symmetric','both'); 
+        img = smooth_edges(img, padding, [1,2]);
+    end
+    
+    if step == 0
+        % analytic formula (sensitive to noise) but faster 
+        % img = img ./ (abs(img) + eps); 
+        [d_X, d_Y] = get_img_grad(img);  % img is assumed to be complex 
+        d_X = imag(conj(img).*d_X);
+        d_Y = imag(conj(img).*d_Y);
+    else
+        % finite difference based method 
+        d_X = angle( imshift_fft_ax(img,-step,2) .* conj( imshift_fft_ax(img,step,2)))/(2*step);
+        d_Y = angle( imshift_fft_ax(img,-step,1) .* conj( imshift_fft_ax(img,step,1)))/(2*step);
+    end
+    if padding > 0
+        % remove padding 
+        ind = {padding:size(d_X,1)-padding-1,padding:size(d_X,2)-padding-1, ':'};
+        d_X = d_X(ind{:}); 
+        d_Y = d_Y(ind{:}); 
+    end
+        
+
+end