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tomo/+tomo/CGLS.m

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+% CGLS conjugate gradient tomo solver, solve tomography as least squares
+% tasks
+% Note: in contrast to SART, it does not accept additional constraints 
+% 
+% [rec] = CGLS(rec, sino, cfg, vectors, Niter, varargin)
+% Inputs:
+%     **rec         - initial guess of the reconstruction 
+%     **sino        - sinogram (Nlayers x width x Nangles)
+%     **cfg         - config struct from ASTRA_initialize
+%     **vectors     - vectors of projection rotation generated by ASTRA_initialize
+%     **Niter       - number of iterations
+%     **varargin    - see the code + parameters of tomo.Atx_sup_partial
+% *returns*
+%     ++rec         - tomography reconstruction 
+
+%*-----------------------------------------------------------------------*
+%|                                                                       |
+%|  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 [rec] = CGLS(rec, sino, cfg, vectors, Niter, varargin)
+
+
+    par = inputParser;
+    par.addOptional('split', 1)
+    par.addParameter('valid_angles', [])
+    par.addParameter('deformation_fields',  {} )  % cell 3x1 of deformation arrays 
+    par.addOptional('GPU', [])   % list of GPUs to be used in reconstruction
+    par.addOptional('split_sub', 1)   % splitting of the sub block on smaller tasks in the Atx_partial method , 1 == no splitting 
+    par.addOptional('verbose', 1)   % verbose = 0 : quiet, verbose : standard info , verbose = 2: debug 
+    par.parse(varargin{:})
+    res = par.Results;
+    
+    if Niter == 0
+        return
+    end
+    
+    if res.verbose
+        disp('====== CGLS ==========')
+    end
+    
+    if ~isempty(res.valid_angles)
+        sino = sino(:,:,res.valid_angles);
+        vectors = vectors(res.valid_angles,:);
+        try cfg.lamino_angle = cfg.lamino_angle(res.valid_angles); end 
+    end
+
+    [Nlayers,Nw,Nproj] = size(sino);
+    cfg.iProjAngles = Nproj;
+    assert(cfg.iProjU == Nw, 'Wrong sinogram width')
+    assert(cfg.iProjV == Nlayers, 'Wrong sinogram height')
+
+    
+    import tomo.*
+
+    varargin = {'deformation_fields',res.deformation_fields,'GPU',res.GPU, 'split_sub', res.split_sub,'verbose', res.verbose};
+
+    % r = sino - A*x
+    r = sino - Ax_sup_partial(rec, cfg, vectors, res.split, varargin{:});
+    % p = A'*r         
+    p =  Atx_sup_partial(r, cfg, vectors,res.split, varargin{:});
+
+    norm_sino = sqrt(mean(sino(:).^2));
+    
+    gamma_0 = sum(p(:).^2);
+    t0 = tic;
+    for i = 1:Niter 
+%         progressbar(i, Niter)
+        fprintf('CGLS Iter %i/%i\n', i, Niter)
+        q = Ax_sup_partial(p, cfg, vectors,  res.split, varargin{:});
+        alpha = gamma_0 / sum(q(:).^2);
+        rec = rec + alpha * p;
+        r = r - alpha * q;
+        err(i) = sqrt(mean(r(:).^2));
+        s = Atx_sup_partial(r, cfg, vectors, res.split, varargin{:});
+        gamma_1 = sum(s(:).^2);
+        beta = gamma_1 / gamma_0;
+        gamma_0 = gamma_1;
+        p = s + beta * p;
+        
+        if toc(t0) >10 && res.verbose % plot every 5s 
+            figure(239821)
+            subplot(1,2,1)
+            plotting.imagesc3D(-rec, 'init_frame', size(rec,3)/2 )
+            axis off image ; 
+            colormap bone 
+            title('CLGS reconstruction preview')
+            subplot(1,2,2)
+            loglog(err/norm_sino)
+            title('Relative data error')
+            axis tight 
+            drawnow
+            t0 = tic;
+        end
+        if i > 1 && err(i) > err(i-1)
+            disp('Error increased, finishing')
+            break
+        end
+            
+    end
+
+
+end
+
+
+