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tomo/+nonrigid/get_mask.m

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+% get_mask - estimate support mask for the provided reconstructed volume 
+%
+% [mask, W_rec] = get_mask(rec_0, mask_threshold, mask_dilate, show_mask)
+%
+% Inputs:
+%    **rec_0                reconstruction  volume 
+%    **mask_threshold       relative threshold with respect to the maximum 
+%    **mask_dilate          mask dilatation in pixels 
+%    **show_mask            true / false if you want to plot the mask 
+% Outputs: 
+%    ++mask             binary mask 
+%    ++W_rec            importance weights for the reconstructioin 
+
+%*-----------------------------------------------------------------------*
+%|                                                                       |
+%|  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) 2018 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 [mask, W_rec] = get_mask(rec_0, mask_threshold, mask_dilate, show_mask)
+    
+    if nargin < 4
+        show_mask = false; 
+    end
+
+    %% get mask 
+    
+    Nlayers = size(rec_0,3); 
+    Npix = size(rec_0,1);
+    mask_dilate = ceil(mask_dilate); 
+    
+    mask = rec_0 > mask_threshold * quantile(rec_0(:), 0.99); 
+    mask = convn(single(mask), ones(mask_dilate,mask_dilate,mask_dilate, 'single'), 'same') > 1e-3*mask_dilate^3;
+    
+
+    %% get importance weighting for difference regions 
+    % importance weighting 
+    W_rec = gpuArray(single(tukeywin(Npix, 0.2)  .*  tukeywin(Npix, 0.2)' .* reshape(tukeywin(Nlayers, 0.2)',1,1,[])  ));  % avoid edge issues
+    W_rec = W_rec .* mask; 
+    W_rec = utils.imgaussfilt3_fft(W_rec,mask_dilate/2);
+    W_rec = gather(W_rec);
+
+    if show_mask
+
+        plotting.smart_figure(212)
+        plotting.imagesc_tomo(mask)
+        suptitle('Estimated mask')
+        drawnow 
+
+        %% show mask 
+        plotting.smart_figure(46)
+        subplot(1,2,1)
+        plotting.imagesc3D(rec_0.* ~mask, 'init_frame', Nlayers/2)
+        colorbar
+        axis off image 
+        colormap bone 
+        title('Example of residuum after applied mask')
+        subplot(1,2,2)
+        hist(rec_0(1:100:end), 100)
+        axis tight 
+        drawnow 
+    end
+
+end