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80 lines
4.2 KiB
Matlab
80 lines
4.2 KiB
Matlab
% nonrigid_registration - recovered DVF for given full reconstruction and
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% subreconstructions using optical flow method
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%
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%[shift_3D_total, vol_err, img_deform] = nonrigid_registration(volume_deform, volume_reference, weight, par, smooth, Niter, shift_3D_total)
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%
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% Inputs:
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% **volume_deform low quality deformed volume to be matched with reference
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% **volume_reference reference volume used for alignment
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% **weight importance weights for the 3D volumes
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% **par tomography parameter structure
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% **smooth constant to smooth the recovered DVF
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% **Niter number of iterations for the optical flow method
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% **shift_3D_total initial deformation field (zeros)
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% Outputs:
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% ++shift_3D_all recovered deformation for given full reconstruction and subreconstructions
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% ++vol_err error between volume and subvolumes
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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 [shift_3D_total, vol_err] = nonrigid_registration(volume_deform, volume_reference, weight, par, smooth, Niter, shift_3D_total)
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% estimate deformation fields to match two 3D volumes
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Npix = size(volume_deform);
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if ~exist('shift_3D_total', 'var')
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for ii = 1:3
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shift_3D_total{ii}= gpuArray.zeros( ceil(Npix/par.downsample_DVF) , 'single');
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end
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end
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img_deform = utils.interp3_gpu(volume_deform, shift_3D_total{:});
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for iter = 1:Niter
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% core : estimate of the deformation field
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[shift_3D,vol_err(iter)] = nonrigid.find_shift_3D_nonrigid(img_deform,volume_reference, weight, par.downsample_DVF, smooth, par.regular);
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for ii = 1:3
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shift_3D_total{ii} = shift_3D_total{ii}+ par.relax_pos_corr*shift_3D{ii};
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end
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% apply inverse deformations on the deformated object
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img_deform = utils.interp3_gpu(volume_deform, -shift_3D_total{1}, -shift_3D_total{2}, -shift_3D_total{3} );
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if iter > 1 && vol_err(end) > vol_err(end-1)
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break
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end
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end
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end |