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%% simple script to test performace of the MEX accelerated functions
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% utils.get_from_3D_projection and utils.add_to_3D_projection
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% the MEX functions use OpenMP to accelerate memory transfer from
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% large array into small sub array and back
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%
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% Matlab equivalent is :
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% small_array = full_array(1:Npix_small(1),1:Npix_small(2),1:Npix_small(3));
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% full_array(1:Npix_small(1),1:Npix_small(2),1:Npix_small(3)) = full_array(1:Npix_small(1),1:Npix_small(2),1:Npix_small(3)) + small_array;
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cd(fullfile( fileparts(mfilename('fullpath')), '..'))
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addpath('tests')
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addpath('utils')
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addpath('./')
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addpath(find_base_package)
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utils.verbose(0)
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%% if needed, recompile the mex functions manually
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% cd cSAXS_matlab_base/+utils/private
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% if verLessThan('matlab', '9.4')
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% mex -largeArrayDims 'CFLAGS="\$CFLAGS -fopenmp"' LDFLAGS="\$LDFLAGS -fopenmp" get_from_3D_projection.cpp
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% mex -largeArrayDims 'CFLAGS="\$CFLAGS -fopenmp"' LDFLAGS="\$LDFLAGS -fopenmp" add_to_3D_projection.cpp
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% else
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% mex -R2018a 'CFLAGS="\$CFLAGS -fopenmp"' LDFLAGS="\$LDFLAGS -fopenmp" get_from_3D_projection_mex.cpp
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% mex -R2018a 'CFLAGS="\$CFLAGS -fopenmp"' LDFLAGS="\$LDFLAGS -fopenmp" add_to_3D_projection_mex.cpp
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% end
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Npix_full = [600,600,600];
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Npix_small = [400,400,400];
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utils.verbose(0,'--- get_from_3D_projection')
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full_array = randn(Npix_full, 'single')+1i;
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small_array = ones(Npix_small, 'like', single(1i));
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positions = (10*rand(Npix_small(3),2));
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indices = ([1:Npix_small(3)]); % indices start from 1
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%% get 3D stack array "small_array" from 3D stack array "full_array" given the offsets "positions" and layers "indices"
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utils.verbose(0,'Speed test MEX')
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for ii = 1:3
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tic; utils.get_from_3D_projection(small_array,full_array,positions,indices); toc
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end
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assert(norm(small_array(:)-reshape(utils.get_from_3D_projection(small_array,full_array,positions,indices, false),[],1))==0, 'get_from_3D_projection MEX function does not provide exact results')
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utils.verbose(0,'Speed test Matlab')
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for ii = 1:3
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tic; small_array = full_array(1:Npix_small(1),1:Npix_small(2),1:Npix_small(3)); toc
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end
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%% add 3D stack array "small_array" into 3D stack array "full_array" given the offsets "positions" and layers "indices"
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utils.verbose(0,'--- add_to_3D_projection')
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full_array = zeros(Npix_full, 'like', single(1i));
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small_array = ones(Npix_small, 'like', single(1i));
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positions = (10*rand(Npix_small(3),2));
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indices = ([1:Npix_small(3)]); % indices are starting from 1 !!
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add_values = true;
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utils.verbose(0,'=== add values atomic')
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utils.verbose(0,'Speed test MEX')
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for ii = 1:3
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tic; utils.add_to_3D_projection(small_array,full_array,positions, indices,add_values, true);toc
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end
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assert(norm(full_array(:)-reshape(utils.add_to_3D_projection(3*small_array,zeros(Npix_full, 'like', single(1i)),positions, indices,add_values,true,false),[],1))==0, 'add_to_3D_projection MEX function does not provide exact results')
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utils.verbose(0,'Speed test Matlab')
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tic; full_array(1:Npix_small(1),1:Npix_small(2),1:Npix_small(3)) = full_array(1:Npix_small(1),1:Npix_small(2),1:Npix_small(3)) + small_array; toc
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%% set 3D stack array "small_array" into 3D stack array "full_array" given the offsets "positions" and layers "indices"
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utils.verbose(0,'=== add values nonatomic')
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add_values = true;
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utils.verbose(0,'Speed test MEX')
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full_array = zeros(Npix_full, 'like', single(1i));
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for ii = 1:3
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tic; utils.add_to_3D_projection(small_array,full_array,positions, indices,add_values, false);toc
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end
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assert(norm(full_array(:)-reshape(utils.add_to_3D_projection(3*small_array,zeros(Npix_full, 'like', single(1i)),positions, indices,add_values,false,false),[],1))==0, 'add_to_3D_projection MEX function does not provide exact results')
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utils.verbose(0,'Speed test Matlab')
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tic; full_array(1:Npix_small(1),1:Npix_small(2),1:Npix_small(3)) = full_array(1:Npix_small(1),1:Npix_small(2),1:Npix_small(3)) + small_array; toc
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%% set 3D stack array "small_array" into 3D stack array "full_array" given the offsets "positions" and layers "indices"
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utils.verbose(0,'=== set values')
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add_values = false;
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utils.verbose(0,'Speed test MEX')
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full_array = zeros(Npix_full, 'like', single(1i));
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for ii = 1:3
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tic; utils.add_to_3D_projection(small_array,full_array,positions, indices,add_values);toc
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end
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assert(norm(full_array(:)-reshape(utils.add_to_3D_projection(small_array,zeros(Npix_full, 'like', single(1i)),positions, indices,add_values,false,false),[],1))==0, 'add_to_3D_projection MEX function does not provide exact results')
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utils.verbose(0,'Speed test Matlab')
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tic; full_array(1:Npix_small(1),1:Npix_small(2),1:Npix_small(3)) = small_array; toc
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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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