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tomo/+tomo/FBP_CPU.m

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+% FBP_CPU  wrapper around iradonfast_v3 that automatically splits the data into
+% smaller blocks to avoid too large memory allocation and emulate GPU based
+% function tomo.FBP
+%
+% tomogram = FBP_CPU(sinogram, cfg, vectors, varargin)
+% 
+% Inputs:
+%     **sino        - sinogram (Nlayers x width x Nangles)
+%     **cfg         - config struct from ASTRA_initialize
+%     **vectors     - vectors of projection rotation generated by ASTRA_initialize
+%  *optional*
+%     ** valid_angles =  []       - list of valid angles, []==all are valid
+%     ** filter =   'ram-lak'     - name of the FBP filter 
+%     ** filter_value =   1       - fitlering value for the FBP filter 
+%     ** verbose =  1             - verbose = 0 : quiet, verbose : standard info , verbose = 2: debug 
+%     ** use_derivative =  false  - calculate reconstruction from the phase derivative 
+% *returns*
+%     ++tomogram    - FBP 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 tomogram = FBP_CPU(sinogram, cfg, vectors, varargin)
+
+    par = inputParser;
+    par.addParameter('valid_angles', [])
+    par.addParameter('filter',  'ram-lak' )
+    par.addParameter('filter_value',  1 )
+    par.addOptional('verbose', 1)   % verbose = 0 : quiet, verbose : standard info , verbose = 2: debug 
+    par.addOptional('determine_weights', true)% reweight projections if the angles are not equidistant
+    par.addOptional('mask', [])   % apply mask on reconstruction 
+    par.addOptional('use_derivative', false)   % calculate reconstruction from the phase derivative 
+    par.KeepUnmatched = true; 
+    par.parse(varargin{:})
+    r = par.Results;
+    
+    if r.verbose
+        disp('====== FBP ==========')
+    end
+    if r.use_derivative
+        extra_args = {'derivative'};
+    else
+        extra_args = {};
+    end
+
+    
+    if ~isempty(r.valid_angles)
+        sinogram = sinogram(:,:,r.valid_angles);
+        vectors = vectors(r.valid_angles,:);
+    end
+    
+    % calculate the original angles 
+    theta = rad2deg(pi-atan2(vectors(:,2),-vectors(:,1)))'; 
+    lamino_angle = rad2deg(pi/2-atan2(vectors(:,3), vectors(:,1)./cos(theta))); 
+    if abs(lamino_angle - 90) > 1e-2
+       error('CPU implementation of FBP does not support laminography') 
+    end
+    
+    [Nlayers,tomo_size,Nangles] = size(sinogram) ; 
+    block_size = ceil(2e9/(tomo_size*Nangles*4)); % split the task into ~2GB blocks 
+    Nblocks = ceil(Nlayers / block_size ); 
+
+    % preallocate array to store results 
+    tomogram = zeros(tomo_size, tomo_size, Nlayers, 'single');
+    
+    for ii = 1:Nblocks
+        ind = 1+(ii-1)*block_size:min(ii*block_size, Nlayers);
+        tomogram(:,:,ind) =tomo.iradonfast_v3(permute(sinogram(ind,:,:),[2,3,1]), theta, 'linear', r.filter, tomo_size, r.filter_value, extra_args{:});   % Calculate slice
+    end
+    
+    % make the results equivalent to the GPU version
+    tomogram = utils.imshift_fft(tomogram, [0.5,0.5] ); 
+    tomogram = utils.crop_pad(tomogram, [cfg.iVolX, cfg.iVolY]);
+    
+    if ~isempty(r.mask)
+        tomogram = tomogram .* r.mask;
+    end
+    
+end