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102 lines
3.6 KiB
Matlab
102 lines
3.6 KiB
Matlab
% IMGAUSSFILT3_FFT apply isotropic gaussian smoothing along all three
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% dimensions, faster than matlab alternative
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%
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% A = imgaussfilt3_fft(A,sigma, split)
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%
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% Inputs:
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% **A 3D volume to be smoothed
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% **sigma gaussian smoothing constant
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% **split 3x1 int vector to split the volume and save memory
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% *returns*:
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% ++A filtered volume
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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 A = imgaussfilt3_fft(A,sigma, split)
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% gaussian blurring in 3D
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import math.*
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if sigma == 0
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return
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end
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if nargin < 3
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split = 1;
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end
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Npx = size(A);
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isReal = isreal(A);
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A = fftn_partial(A, split);
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for dim=1:3
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grid = single((-Npx(dim)/2:Npx(dim)/2-1));
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ker = exp(-grid.^2/ sigma^2)';
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ker = ker / sum(ker);
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ker = fft(ker,[],1);
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ker_shape = ones(1,3);
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ker_shape(dim) = Npx(dim);
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B{dim} = reshape(ker,ker_shape);
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end
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if isa(A, 'gpuArray')
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A = arrayfun(@prod3,A,B{:});
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else
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A = prod3(A,B{:});
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end
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A = ifftn_partial(A, split);
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if isReal
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A = real(A);
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end
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% Im not sure why, but the output needs to be fftshifted
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for dim = 1:3
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m = size(A, dim);
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p = ceil(m/2);
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idx{dim} = [p+1:m 1:p];
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end
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% Use comma-separated list syntax for N-D indexing.
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A = A(idx{:});
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end
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function A = prod3(A,k1,k2,k3)
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A = A .* k1 .* k2 .* k3;
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end
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