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% GET_FROM_3D_PROJECTION add one small 3D block into large 3D array
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%
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% small_array = get_from_3D_projection(small_array,full_array, positions_offset, indices)
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%
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% Inputs:
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% **full_array - array from which the small_array will loaded
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% **small_array - empty array for storing the data
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% **positions_offset - [Nangles x 2] offset from (1,1) coordinate in pixels
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% for each slice , if provide only [1x2] vector, assume the same
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% offset for each slice
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% **indices - add only to selected sliced of the full_array
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% *optional*
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% **use_MEX - (use_MEX==true) use fast mex code
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% *returns*
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% ++small_array or none, results were writted !directly! to the input
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% array small_array, there is not need to take any output if MEX
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% function add_to_3D_projection was used
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%
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% Compilation from Matlab:
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% mex -R2018a 'CFLAGS="\$CFLAGS -fopenmp"' LDFLAGS="\$LDFLAGS -fopenmp" get_from_3D_projection_mex.cpp
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% Usage from Matlab:
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%
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% full_array = (randn(1000, 1000, 1, 'single'));
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% small_array = (ones(500, 500, 100, 'single'));
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%
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% positions_offset = int32([1:100; 1:100])';
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% indices = int32([1:100]); % indices are starting from 1 !!
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% tic; get_from_3D_projection_mex(small_array,full_array,positions_offset,indices); 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) 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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%
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function small_array = get_from_3D_projection(small_array, full_array, positions_offset, indices, use_MEX)
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Np_f = size(full_array);
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Np_s = size(small_array);
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if nargin < 4
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indices = 1:Np_f(3);
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end
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if nargin < 5
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use_MEX = true;
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end
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if size(positions_offset,1)==1
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positions_offset = repmat(positions_offset, size(small_array,3), 1);
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end
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positions_offset = int32(positions_offset);
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indices= int32(indices);
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if use_MEX && ~isa(full_array, 'gpuArray') && ~verLessThan('matlab', '9.4') && ~islogical(small_array) % logical arrays not yet implemented
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%% run fast MEX-based code if possible
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try
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get_from_3D_projection_mex(small_array,full_array, positions_offset, indices)
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catch err
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% recompile the scripts if needed
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if any(strcmp(err.identifier, { 'MATLAB:UndefinedFunction','MATLAB:mex:ErrInvalidMEXFile'}))
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utils.verbose(0, 'Recompilation of MEX functions ... ')
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path = replace(mfilename('fullpath'), mfilename, '');
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mex('-R2018a','-O', 'CFLAGS="\$CFLAGS -fopenmp"', '-O','LDFLAGS="\$LDFLAGS -fopenmp"',[path,'private/get_from_3D_projection_mex.cpp'], '-output', [path, 'private/get_from_3D_projection_mex'])
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get_from_3D_projection_mex(small_array,full_array, positions_offset, indices)
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else
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rethrow(err)
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end
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end
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return
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end
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%% simple matlab based version that may be too slow
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for ii = 1:size(positions_offset,1)
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jj = min(indices(ii),size(full_array,3));
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for i = 1:2
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% limit to the region inside full_array
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ind_f{i} = positions_offset(ii,i)+int32(1:Np_s(i));
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ind_f{i} = max(1,1+positions_offset(ii,i)):min(positions_offset(ii,i)+Np_s(i),Np_f(i));
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% adjust size of the small matrix to correspond
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ind_s{i} = ((ind_f{i}(1)-positions_offset(ii,i))):(ind_f{i}(end)-positions_offset(ii,i));
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end
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small_array(ind_s{:},ii) = full_array(ind_f{:},jj) ;
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end
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end
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