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% [CloseInd,Neighbours] = nonlocalTV_weight_GPU(Im0, Rpatch, Rwin, Nclose, sigma)
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% FUNCTION
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% find close indices for the nonlocalTV_GPU method , similar to the nonlocal means method
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% Inputs:
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% Im0 - volume to be regularized
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% Rpatch - radius of the patch used to ocompare similarities
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% Rwin - radius of the window used to find similar regions
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% Nclose - number of most similar regions searched
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% sigma - similarity threshold, (tunning constant, value < 1)
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% Outputs:
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% CloseInd - close indices generated by nonlocalTV_weight code
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% Neighbours - list of neighboring pixels used for calculation and excluded from CloseInd
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% RECOMPILE COMMAND
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% mexcuda -output +regularization/private/nonlocalTV_weight_tex +regularization/private/TV_cuda_texture.cu +regularization/private/nonlocalTV_mex_weight.cpp
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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 [CloseInd,Neighbours] = nonlocalTV_weight_GPU(Im0, Rpatch, Rwin, Nclose, sigma)
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%% nonlocal TV
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% mexcuda -output nonlocalTV_weight_tex TV_cuda_texture.cu nonlocalTV_mex_weight.cpp
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Nwin= 2*Rwin+1;
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Nclose_min=2;
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Nclose_max = 256;
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if Nclose > Nclose_max
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error('Nclose is more than Nclose_max')
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end
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if ismatrix(Im0)
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assert(Nwin^2 < Nclose_max, 'Too large Nwin')
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% Neighbours=uint8(sub2ind([Nwin,Nwin],...
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% Rwin+1+[0,-1,1,0,0],Rwin+1+[0,0,0,-1,1]));
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Neighbours=uint8(sub2ind([Nwin,Nwin],...
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Rwin+1,Rwin+1));
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else
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assert(Nwin^3 < Nclose_max, 'Too large Nwin')
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% include all neighbors
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% Neighbours=uint8(sub2ind([Nwin,Nwin,Nwin],...
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% Rwin+1+[0,-1,1,0,0,0,0], ...
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% Rwin+1+[0,0,0,-1,1,0,0], ...
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% Rwin+1+[0,0,0,0,0,-1,1]));
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% only the central point !!
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Neighbours=uint8(sub2ind([Nwin,Nwin,Nwin],...
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Rwin+1, Rwin+1,Rwin+1));
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end
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% keyboard
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[Nx, Ny, Nz] = size(Im0);
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MAX_SIZE = 512; %% TESTED FOR TITAN X 12GB !!!
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% MAX_SIZE = 320; %% roughly for Quadro K4200
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split = ceil([Nx, Ny, Nz]/MAX_SIZE);
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if prod(split) == 1
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CloseInd = nonlocalTV_weight_GPU_partial(Im0, Rpatch, Rwin, Nclose,Nclose_min,sigma, Neighbours);
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else %% in case of too large datasets
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warning('Volume is too large, it will be sliced')
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CloseInd = zeros(Nx, Ny,Nz,Nclose, 'uint8');
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ind = {':',':',':'};
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for i = 1:split(1)
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ind{1} = (1+(i-1)*ceil(Nx/split(1))):min(Nx,i*ceil(Nx/split(1)));
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for j = 1:split(2)
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ind{2} = (1+(j-1)*ceil(Ny/split(2))):min(Ny,j*ceil(Ny/split(2)));
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for k = 1:split(3)
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ind{3} = (1+(k-1)*ceil(Nz/split(3))):min(Nz,j*ceil(Nz/split(3)));
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CloseInd(ind{:},:) = gather(nonlocalTV_weight_GPU_partial(Im0(ind{:}), Rpatch, Rwin, Nclose,Nclose_min, sigma, Neighbours));
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utils.progressbar(k + (j-1)*split(2)+(i-1)*split(1)*split(2), prod(split))
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end
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end
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end
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end
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end
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function CloseInd = nonlocalTV_weight_GPU_partial(Im0, Rpatch, Rwin, Nclose, Nclose_min, sigma, Neighbours)
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Im0_gpu = gpuArray(single(Im0));
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Npatch= 2*Rpatch+1;
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%% get simple estimate of the average gradients
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if ismatrix(Im0_gpu)
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dx = diff(Im0_gpu,1,1);
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dx = dx(:,2:end).^2;
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dy = diff(Im0_gpu,1,2);
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dy = dy(2:end,:).^2;
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ker = ones(Npatch, 'single');
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threshold = mean2(sqrt(conv2( (dx + dy)/2,ker, 'same')));
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elseif ndims(Im0_gpu) == 3
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dx = diff(Im0_gpu,1,1);
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dx = dx(:,2:end,2:end).^2;
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dy = diff(Im0_gpu,1,2);
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dy = dy(2:end,:,2:end).^2;
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dz = diff(Im0_gpu,1,3);
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dz = dz(2:end,2:end,:).^2;
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ker = ones([Npatch,Npatch,Npatch], 'single');
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threshold = mean2(sqrt(convn( (dx + dy + dz)/3,ker, 'same')));
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end
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% sigma is changing the threshold level
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%% patched more different than threshold will be rejected !!!
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threshold = gather(threshold ) * sigma;
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clear dx dy dz
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% tic
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CloseInd = nonlocalTV_weight_tex(Im0_gpu,Neighbours,Nclose,Nclose_min,Rwin,Rpatch,threshold);
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% toc
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end
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