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tomo/+nonrigid/show_sinograms.m

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+% show_sinograms - compare reconstructed and mesaured projections
+%
+%   show_sinograms(rec_avg,dphase, vectors,cfg, angles,  shift_3D_total, par, show_derivative = false )
+%
+% Inputs:
+%    **rec_avg - optimal NCT reconstruction       
+%    **dphase    phase difference calculated from the measured data 
+%    **vectors   ASTRA configuration vectors
+%    **cfg       ASTRA configuration structure
+%    **angles    angles of the projections 
+%    **shift_3D_total  recovered deformation vector field 
+%    **par       parameter structure of the nonrigid tomo 
+%  *optional*
+%    ++show_derivative  if false, show directly the recovered signal otherwise the phase derivative  
+
+%*-----------------------------------------------------------------------*
+%|                                                                       |
+%|  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 show_sinograms(rec_avg,dphase, vectors,cfg, angles,  shift_3D_total, par, show_derivative )
+    if nargin < 8
+        show_derivative = false;  % show directly the recovered signal 
+    end
+
+    Nangles = cfg.iProjAngles;
+    Nblocks = length(shift_3D_total); 
+    Bsize = ceil(Nangles/Nblocks); 
+
+    % generate deformation tensors from the shift tensors 
+    deform_tensors = nonrigid.get_deformation_fields(shift_3D_total, par.regularize_deform_evol, size(rec_avg));
+
+    
+
+    % SHOW ANIMATION OF PROJECTIONS 
+    rec_avg = gather(rec_avg);
+
+    split = astra.ASTRA_find_optimal_split(cfg,1,Nblocks); 
+        
+    for ll = 1:Nblocks
+        ids = 1+(ll-1)*Bsize:min(Nangles, ll*Bsize); 
+        sinogram_corr(:,:,ids) = gather(tomo.Ax_sup_partial(rec_avg,cfg, vectors(ids,:),split, 'deformation_fields', deform_tensors{ll}));
+    end
+
+    split = astra.ASTRA_find_optimal_split(cfg); 
+    sinogram_ideal = tomo.Ax_sup_partial(rec_avg,cfg, vectors,split); 
+    
+    if show_derivative
+        dphase_avg = math.get_phase_gradient_1D(exp(-1i*sinogram_ideal),2);
+        dphase_corr = math.get_phase_gradient_1D(exp(-1i*sinogram_corr),2);
+        sino_diff =  dphase_corr - math.sum2(dphase_corr .* dphase) ./ math.sum2(dphase.^2) .* dphase ; 
+%         sino_diff =  dphase_corr - dphase ; 
+        dsino_range = math.sp_quantile(sino_diff,[0.001, 0.999],10);
+        sino_diff = max(min(sino_diff, dsino_range(2)), dsino_range(1));
+        sino_range = math.sp_quantile(dphase_avg,[0.001,0.999],10);
+        sino_diff = (sino_diff-dsino_range(1))/diff(dsino_range)*sino_range(2);
+        sino_all=  cat(2,dphase_corr, dphase, sino_diff);  
+    else
+        phase = -math.unwrap2D_fft(dphase, 2, par.air_gap); 
+        sino_diff =  sinogram_corr - math.sum2(sinogram_corr .* phase) ./ math.sum2(phase.^2) .* phase ; 
+        sino_range = math.sp_quantile(sinogram_corr,[0.001,0.999],10);
+        sino_all=  cat(2,sinogram_corr,phase, sino_diff+sino_range(2)/2);  
+    end
+
+    [~,order] = sort(angles);
+    figure(45864)
+    plotting.imagesc3D(sino_all, 'order', order)
+    axis off image xy
+    colormap bone 
+    set(gca, 'clim', sino_range)
+    str = 'Model / Data / Difference'; 
+    if show_derivative
+        str = [str, ' - showing phase-gradient'];
+    else
+        str = [str, ' - showing unwrapped phase'];
+    end
+    title(str)
+    drawnow 
+    
+    
+    
+end