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% show_reconstruction_quality - compare conventional reconstruction,
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% nonrigid reconstruction FBP and SART
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%
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% [rec_FBP, rec_NCT_FBP, rec_NCT_SART] = show_reconstruction_quality(sinogram, cfg, vectors, shift_3D_total, regularize_deform_evol)
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%
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% Inputs:
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% **sinogram current reconstruction
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% **vectors ASTRA configuration vectors
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% **cfg ASTRA configuration structure
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% **shift_3D_total recovered deformation vector field
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% **regularize_deform_evol regularization constant for the deformation field evolution calculation
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%
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% Outputs:
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% ++rec_FBP conventional FBP reconstruction
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% ++rec_NCT_FBP nonrigid FBP reconstruction
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% ++rec_NCT_SART nonrigid SART reconstruction
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%
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%*-----------------------------------------------------------------------*
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%| |
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%| Except where otherwise noted, this work is licensed under a |
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%| Creative Commons Attribution-NonCommercial-ShareAlike 4.0 |
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%| International (CC BY-NC-SA 4.0) license. |
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%| |
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%| Copyright (c) 2018 by Paul Scherrer Institute (http://www.psi.ch) |
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%| |
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%| Author: CXS group, PSI |
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%*-----------------------------------------------------------------------*
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% You may use this code with the following provisions:
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%
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% If the code is fully or partially redistributed, or rewritten in another
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% computing language this notice should be included in the redistribution.
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%
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% If this code, or subfunctions or parts of it, is used for research in a
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% publication or if it is fully or partially rewritten for another
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% computing language the authors and institution should be acknowledged
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% in written form in the publication: “Data processing was carried out
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% using the “cSAXS matlab package” developed by the CXS group,
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% Paul Scherrer Institut, Switzerland.”
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% Variations on the latter text can be incorporated upon discussion with
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% the CXS group if needed to more specifically reflect the use of the package
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% for the published work.
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%
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% A publication that focuses on describing features, or parameters, that
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% are already existing in the code should be first discussed with the
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% authors.
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%
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% This code and subroutines are part of a continuous development, they
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% are provided “as they are” without guarantees or liability on part
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% of PSI or the authors. It is the user responsibility to ensure its
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% proper use and the correctness of the results.
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function [rec_FBP, rec_NCT_FBP, rec_NCT_SART] = show_reconstruction_quality(sinogram, cfg, vectors, shift_3D_total, regularize_deform_evol)
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Nangles = cfg.iProjAngles;
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reset(gpuDevice)
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Nblocks = length(shift_3D_total);
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split = astra.ASTRA_find_optimal_split(cfg);
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Bsize = ceil(Nangles/Nblocks);
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if any(split(1:3)) > 1
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warning('Sample volume seems too large, try to reduce the reconstructed volume size')
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split(1:3) = 1; % at least try to make it work without splitting, otherwise recontruction will be poor
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end
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rec_FBP = gather(tomo.FBP(sinogram, cfg, vectors)) ;
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% generate deformation tensors from the shift tensors
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[deform_tensors, inv_deform_tensors] = nonrigid.get_deformation_fields(shift_3D_total, regularize_deform_evol, size(rec_FBP));
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%% FBP
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rec_NCT_FBP = nonrigid.FBP_deform(sinogram, cfg, vectors,Bsize, inv_deform_tensors);
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[SART_cache, cfg_SART] = tomo.SART_prepare(cfg, vectors, Bsize, split);
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SART_cache.R = min(1,SART_cache.R);
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%% SART - solve it using all constraints
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[~,rec_mask] = utils.apply_3D_apodization(rec_NCT_FBP,0);
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rec_NCT_SART = rec_NCT_FBP;
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Niter_SART = 10;
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clear err_sart
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disp('====== SART ==========')
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for kk = 1:Niter_SART
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utils.progressbar(kk, Niter_SART)
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[rec_NCT_SART,err_sart(kk,:)] = tomo.SART(rec_NCT_SART, sinogram, cfg_SART, vectors, SART_cache, split, ...
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'relax',0, 'deformation_fields', deform_tensors,'inv_deformation_fields', inv_deform_tensors, ...
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'constraint', @(x)(max(0,x.*rec_mask)), 'verbose',0);
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% figure(1343)
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% subplot(1,2,1)
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% plot(err_sart)
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% hold all
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% plot(mean(err_sart'),'k', 'LineWidth',2)
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% hold off
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% set(gca, 'xscale', 'log')
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% set(gca, 'yscale', 'log')
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% grid on
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% axis tight
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% title('SART error evolution')
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% subplot(1,2,2)
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% plotting.imagesc3D(rec_NCT_SART, 'init_frame', floor(size(rec_NCT_SART,3)/2))
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% axis image
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% colormap bone
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% axis off image
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% drawnow
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end
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% remove edges
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rec_FBP = utils.apply_3D_apodization(rec_FBP, 0);
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rec_NCT_FBP = utils.apply_3D_apodization(rec_NCT_FBP,0);
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figure(10)
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if exist('orig_phantom', 'var') && ~isempty(orig_phantom)
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orig_phantom = utils.crop_pad(orig_phantom, [cfg.iVolX,cfg.iVolY]);
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orig_phantom = orig_phantom ./ mean(orig_phantom(:)) * mean(rec_FBP(:))*0.9;
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rec_all = gather(cat(2, orig_phantom,rec_FBP, rec_NCT_FBP, rec_NCT_SART));
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else
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rec_all = gather(cat(2, rec_FBP, rec_NCT_FBP, rec_NCT_SART));
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end
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range = quantile(rec_all(:), [1e-2, 1-1e-2]);
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plotting.imagesc3D(rec_all, 'init_frame', size(rec_all,3)/2)
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caxis(range);
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axis off image; colormap bone
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title('Original reconstruction / Deform FBP / Deform SART')
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end
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