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% SART tomography reconstruction code
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%
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% [rec] = SART(rec, sino, cfg, vectors, cache, varargin)
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%
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% Inputs:
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% **rec - initial guess of the reconstruction
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% **sino - sinogram (Nlayers x width x Nangles)
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% **cfg - config struct from ASTRA_initialize
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% **vectors - vectors of projection rotation generated by ASTRA_initialize
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% **cache - precalcualated cache by SART_prepare
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% *optional*
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% ** split =[1,1,1] - split the solved volume, split(3 is used to split in separated blocks, split(1:2) is used inside Atx_partial to du subplitting for ASTRA
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% ** valid_angles = [] - list of valid angles, []==all are valid
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% ** filter = 'ram-lak' - name of the FBP filter
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% ** filter_value = 1 - fitlering value for the FBP filter
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% ** deformation_fields = {} - cell 3x1 of deformation arrays
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% ** inv_deformation_fields={}-cell 3x1 of inverse deformation arrays
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% ** GPU = [] - list of GPUs to be used in reconstruction
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% ** split_sub = [1,1,1] - splitting of the sub block on smaller tasks in the Atx_partial method , 1 == no splitting
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% ** verbose = 1 - verbose = 0 : quiet, verbose : standard info , verbose = 2: debug
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% ** relax = 0 - relaxation constant, shorter steps , 1 == no relaxation
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% ** constraint= [] - constraint function that will be applied after every step
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%
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% *returns*
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% ++rec reconstruction
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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) 2017 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, err] = SART(rec, sinogram, cfg,vectors,cache,varargin)
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import tomo.*
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import utils.*
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import astra.*
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G = cfg.Grouping;
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cfg.iProjAngles = size(vectors,1);
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Nsets = ceil(cfg.iProjAngles/G);
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% try to optimize the group sizes
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G = ceil(cfg.iProjAngles / Nsets);
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Nsets = ceil(cfg.iProjAngles/G);
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par = inputParser;
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par.addOptional('split', 1)
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par.addParameter('valid_angles', [])
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par.addParameter('deformation_fields', cell(Nsets,1) ) % cell 3x1 of deformation arrays
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par.addParameter('inv_deformation_fields', cell(Nsets,1) ) % cell 3x1 of deformation arrays
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par.addParameter('GPU', []) % list of GPUs to be used in reconstruction
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par.addParameter('split_sub', 1) % splitting of the sub block on smaller tasks in the Atx_partial method , 1 == no splitting
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par.addParameter('verbose', 1) % verbose = 0 : quiet, verbose : standard info , verbose = 2: debug
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par.addParameter('relax', 0, @(x)(x < 1 && x >= -1)) % relaxation constant, shorter steps , 1 == no relaxation
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par.addParameter('constraint', []) % constraint function that will be applied after every step
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par.addParameter('keep_on_GPU', true) % constraint function that will be applied after every step
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par.parse(varargin{:})
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res = par.Results;
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if ~isempty(res.valid_angles)
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sinogram = sinogram(:,:,res.valid_angles);
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vectors = vectors(res.valid_angles,:);
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cache.R = cache.R(:,:,res.valid_angles);
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try cfg.lamino_angle = cfg.lamino_angle(res.valid_angles); end
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end
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if islogical(res.valid_angles); res.valid_angles = find(res.valid_angles); end
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err = nan(Nsets,1);
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rng('default')
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if isempty(res.deformation_fields) && isempty(res.inv_deformation_fields)
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indices = randperm(cfg.iProjAngles);
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for i=randperm(Nsets)
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ind{i} = indices((1+(i-1)*G):min(cfg.iProjAngles,i*G));
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end
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else
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% for deformation tomography keep the blocks corresponding to the
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% subtomograms
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for i=1:Nsets
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ind{i} = (1+(i-1)*G):min(cfg.iProjAngles,i*G);
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end
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end
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if ~isempty(res.valid_angles)
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for i=1:Nsets
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ind{i} = intersect(ind{i}, res.valid_angles);
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end
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end
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for i = 1:Nsets
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if res.verbose > 0
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utils.progressbar(i, Nsets);
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end
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cfg.iProjAngles = length(ind{i});
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data = sinogram(:,:,ind{i});
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R = cache.R(:,:,ind{i});
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if ~isempty(res.deformation_fields)
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R = R .* tukeywin(cfg.iProjV, 0.2); % avoid amplification of edge regions where deformation may be wrong
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end
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if res.keep_on_GPU
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data = gpuArray(data);
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end
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if ~isa(data, 'gpuArray') && (isempty(res.deformation_fields) || isempty(res.deformation_fields{i}))
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proj = Ax_sup_partial(rec, cfg, vectors(ind{i},:), res.split, 'GPU', res.GPU, 'split_sub', res.split_sub, 'verbose',0, 'deformation_fields',res.deformation_fields{i});
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else
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proj = Ax_partial(rec, cfg, vectors(ind{i},:), res.split_sub, 'verbose',0, 'deformation_fields', res.deformation_fields{i} );
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end
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D = data - proj;
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D = D .* R;
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if nargout > 1
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%% get error before update
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err(ind{i}) = gather(sqrt(mean(mean(D.^2))));
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end
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if ~isa(D, 'gpuArray') && (isempty(res.deformation_fields) || isempty(res.deformation_fields{i}))
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rec_upd = Atx_sup_partial(D, cfg, vectors(ind{i},:), res.split, 'GPU', res.GPU, 'split_sub', res.split_sub, 'verbose', res.verbose, 'deformation_fields', res.inv_deformation_fields{i} );
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else
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rec_upd = Atx_partial(D, cfg, vectors(ind{i},:), 1, 'verbose', res.verbose, 'deformation_fields', res.inv_deformation_fields{i} );
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end
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rec_upd = ((1-res.relax)/cfg.iProjAngles)*rec_upd;
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if ~isa(rec,'gpuArray')
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rec_upd = gather(rec_upd);
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end
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rec = rec + rec_upd;
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% apply constraints
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if ~isempty(res.constraint)
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rec = res.constraint(rec);
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end
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end
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if ~isempty(res.constraint)
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rec = res.constraint(rec);
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end
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end
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