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77 lines
3.3 KiB
Matlab
77 lines
3.3 KiB
Matlab
% IMGAUSSFILT3_CONV apply gaussian smoothing along all three dimensions using convolution,
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% faster than matlab alternative
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%
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%
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% A = imgaussfilt3_conv(A,sigma)
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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, scalar or use vector for anizotropic kernel smoothing
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% returns:
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% ++A smoothed 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 X = imgaussfilt3_conv(X, filter_size)
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%% faster equivalent to the imgaussfilt3 in matlab
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shape_0 = {[], 1,1};
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for ax = 1:3
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if filter_size(min(end,ax)) == 0
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continue
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end
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if ax == 1 || filter_size(min(end,ax-1)) ~= filter_size(min(end,ax))
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ker = get_kernel(filter_size(min(end,ax)) , class(X));
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end
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shape = circshift(shape_0, ax-1);
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X = convn(X, reshape(ker,shape{:}), 'same');
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end
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end
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function ker = get_kernel(filter_size, class)
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grid = (-ceil(2*filter_size):ceil(2*filter_size)) / filter_size;
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ker = exp(-grid.^2);
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ker = ker / sum(ker);
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if isa(class, 'gpuArray')
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ker = gpuArray(single(ker));
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end
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end
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