initial commit

+utils/imgaussfilt3_fft.m

@@ -0,0 +1,101 @@
+% IMGAUSSFILT3_FFT apply isotropic gaussian smoothing along all three 
+% dimensions, faster than matlab alternative
+%
+%  A = imgaussfilt3_fft(A,sigma, split)
+%
+% Inputs: 
+%   **A         3D volume to be smoothed 
+%   **sigma     gaussian smoothing constant 
+%   **split     3x1 int vector to split the volume and save memory 
+% *returns*: 
+%   ++A         filtered volume 
+
+    
+%*-----------------------------------------------------------------------*
+%|                                                                       |
+%|  Except where otherwise noted, this work is licensed under a          |
+%|  Creative Commons Attribution-NonCommercial-ShareAlike 4.0            |
+%|  International (CC BY-NC-SA 4.0) license.                             |
+%|                                                                       |
+%|  Copyright (c) 2017 by Paul Scherrer Institute (http://www.psi.ch)    |
+%|                                                                       |
+%|       Author: CXS group, PSI                                          |
+%*-----------------------------------------------------------------------*
+% You may use this code with the following provisions:
+%
+% If the code is fully or partially redistributed, or rewritten in another
+%   computing language this notice should be included in the redistribution.
+%
+% If this code, or subfunctions or parts of it, is used for research in a 
+%   publication or if it is fully or partially rewritten for another 
+%   computing language the authors and institution should be acknowledged 
+%   in written form in the publication: “Data processing was carried out 
+%   using the “cSAXS matlab package” developed by the CXS group,
+%   Paul Scherrer Institut, Switzerland.” 
+%   Variations on the latter text can be incorporated upon discussion with 
+%   the CXS group if needed to more specifically reflect the use of the package 
+%   for the published work.
+%
+% A publication that focuses on describing features, or parameters, that
+%    are already existing in the code should be first discussed with the
+%    authors.
+%   
+% This code and subroutines are part of a continuous development, they 
+%    are provided “as they are” without guarantees or liability on part
+%    of PSI or the authors. It is the user responsibility to ensure its 
+%    proper use and the correctness of the results.
+
+function A = imgaussfilt3_fft(A,sigma, split)
+    % gaussian blurring in 3D 
+    import math.*
+
+    if sigma == 0
+        return
+    end
+    if nargin < 3
+        split = 1; 
+    end
+
+    Npx = size(A);
+    isReal = isreal(A);
+    
+    A = fftn_partial(A, split);
+
+    for dim=1:3
+        grid = single((-Npx(dim)/2:Npx(dim)/2-1));
+        ker = exp(-grid.^2/ sigma^2)';
+        ker = ker / sum(ker);
+        ker = fft(ker,[],1);
+
+        ker_shape = ones(1,3);
+        ker_shape(dim) = Npx(dim);
+        B{dim} = reshape(ker,ker_shape);
+    end
+    if isa(A, 'gpuArray')
+        A = arrayfun(@prod3,A,B{:});
+    else
+        A = prod3(A,B{:});
+    end
+
+    
+    A = ifftn_partial(A, split);
+    if isReal
+        A = real(A);
+    end
+    
+    % Im not sure why, but the output needs to be fftshifted
+
+    for dim = 1:3
+        m = size(A, dim);
+        p = ceil(m/2);
+        idx{dim} = [p+1:m 1:p];
+    end
+
+    % Use comma-separated list syntax for N-D indexing.
+    A = A(idx{:});
+
+end
+
+function A = prod3(A,k1,k2,k3)
+    A = A .* k1 .* k2 .* k3;
+end