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2026-09-17 21:49:08 +09:00 · 2026-08-07 15:56:42 +09:00
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+% nonrigid_registration - recovered DVF for given full reconstruction and
+% subreconstructions using optical flow method 
+%
+%[shift_3D_total, vol_err, img_deform] = nonrigid_registration(volume_deform, volume_reference, weight, par, smooth, Niter, shift_3D_total)
+%
+% Inputs:
+%    **volume_deform        low quality deformed volume to be matched with reference 
+%    **volume_reference     reference volume used for alignment 
+%    **weight               importance weights for the 3D volumes 
+%    **par                  tomography parameter structure 
+%    **smooth               constant to smooth the recovered DVF 
+%    **Niter                number of iterations for the optical flow method 
+%    **shift_3D_total       initial deformation field (zeros) 
+% Outputs: 
+%    ++shift_3D_all         recovered deformation for given full reconstruction and subreconstructions 
+%    ++vol_err              error between volume and subvolumes 
+
+%*-----------------------------------------------------------------------*
+%|                                                                       |
+%|  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) 2018 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 [shift_3D_total, vol_err] = nonrigid_registration(volume_deform, volume_reference, weight, par, smooth, Niter, shift_3D_total)
+    % estimate deformation fields to match two 3D volumes 
+
+    Npix = size(volume_deform);
+        
+    if ~exist('shift_3D_total', 'var')
+        for ii = 1:3
+            shift_3D_total{ii}= gpuArray.zeros( ceil(Npix/par.downsample_DVF) , 'single');
+        end
+    end
+    
+    img_deform =  utils.interp3_gpu(volume_deform, shift_3D_total{:});
+    
+    for iter = 1:Niter
+
+        % core : estimate of the deformation field 
+        [shift_3D,vol_err(iter)] = nonrigid.find_shift_3D_nonrigid(img_deform,volume_reference, weight, par.downsample_DVF, smooth, par.regular);
+        for ii = 1:3
+            shift_3D_total{ii} = shift_3D_total{ii}+ par.relax_pos_corr*shift_3D{ii};
+        end
+        % apply inverse deformations on the deformated object 
+        img_deform =  utils.interp3_gpu(volume_deform, -shift_3D_total{1}, -shift_3D_total{2},  -shift_3D_total{3} );
+        
+        if iter > 1 && vol_err(end) > vol_err(end-1)
+            break
+        end
+    end
+
+end