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116 lines
5.3 KiB
Matlab
116 lines
5.3 KiB
Matlab
% get_deformation_fields - calculate the DVF from the observed deformation
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% field arrays bu deconvolution
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%
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% [deform_tensors_linear, inv_deform_tensors_linear] = ...
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% get_deformation_fields(shift_tensors, regularize_lambda, Npix_vol)
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%
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% Inputs:
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% **shift_tensors observed deformation
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% **regularize_lambda regularization constant for the deconvolution
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% **Npix_vol size of the reconstructed volume
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% Outputs:
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% ++deform_tensors_linear calculate forward DVF
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% ++inv_deform_tensors_linear calculate inverse DVF
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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 [deform_tensors_linear, inv_deform_tensors_linear] = ...
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get_deformation_fields(shift_tensors, regularize_lambda, Npix_vol)
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% simple deconvolution of the recovered shift arrays to the object
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% defomration arrays for linear deformation model
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Nblocks = length(shift_tensors);
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if Nblocks == 1
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error('Number of blocks (subtomos) has to be > 1')
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end
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if Nblocks > 1
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conv_mat = spdiags(ones(Nblocks,1),0,Nblocks, Nblocks+1) + spdiags(ones(Nblocks,1),1,Nblocks, Nblocks+1);
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conv_mat = conv_mat ./ sum(conv_mat,2);
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regul_mat = spdiags(2*ones(Nblocks,1), 0, Nblocks, Nblocks+1) - spdiags(ones(Nblocks,1), 1, Nblocks, Nblocks+1)-spdiags(ones(Nblocks,1), -1, Nblocks, Nblocks+1);
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regul_mat(1,1:2) = 0;
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deform_mat = [];
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for block = 1:Nblocks
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for ax = 1:3
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deform_mat(:,:,:,ax,block) = gather(shift_tensors{block}{ax});
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end
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end
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size_deform_mat = size(deform_mat);
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deform_mat = reshape(deform_mat, [], Nblocks);
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%% perform Tikhonov based deconvolution
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% N = 50;
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% lams = logspace(-5,1,N);
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% for i = 1:N
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deconv_def_mat = ((conv_mat'*conv_mat + regularize_lambda*regul_mat'*regul_mat)\(conv_mat'*deform_mat'))';
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% enforce zero for the first deformation
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deconv_def_mat = deconv_def_mat - deconv_def_mat(:,1);
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% err(i) = math.mean2((conv_mat*deconv_def_mat' - deform_mat').^2);
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% end
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deconv_def_mat = reshape(deconv_def_mat,[size_deform_mat(1:4), Nblocks+1] );
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for block = 1:Nblocks+1
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for ax = 1:3
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deform_tensors{block}{ax} = single(deconv_def_mat(:,:,:,ax,block));
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end
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end
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else
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deform_tensors = shift_tensors;
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end
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[deform_tensors,inv_deform_tensors] = nonrigid.invert_DVF(deform_tensors, Npix_vol) ;
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% join blocks to keep initial and final deform for each block together
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% -> linear deformation evolution is assumed in between
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if Nblocks > 1
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for block = 1:Nblocks
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deform_tensors_linear{block} = [deform_tensors{block}; deform_tensors{block+1}];
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inv_deform_tensors_linear{block} = [inv_deform_tensors{block}; inv_deform_tensors{block+1}];
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end
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else % just assume one single deformation
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deform_tensors_linear = deform_tensors;
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inv_deform_tensors_linear = inv_deform_tensors;
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end
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end
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