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tomo/utils/get_ROI.m

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+% GET_ROI find optimal rectange containing the region given by a binary mask 
+%
+%  [ROI] = get_ROI(mask, extent, multiply_of)
+%
+% Inputs: 
+%   **mask      - binary mask, true for valid region 
+%   **extent    - extra region around the mask calculated as extent*[W,H], default == 0
+%   **multiply_of - make the selected ROI dividable by this number, default = 1
+% *returns*: 
+%   ++ROI       - 2x1 cell containing indices of the selected region 
+
+
+%*-----------------------------------------------------------------------*
+%|                                                                       |
+%|  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 [ROI] = get_ROI(mask, extent, multiply_of)
+
+
+    if all(mask(:) == 0)
+        error('Empty mask')
+    end
+
+    if nargin < 3
+        multiply_of = 1;
+    end
+    if nargin < 2
+       extent = 0;
+    end
+    
+    if ~islogical(mask)
+       error('Not implemented')
+    end
+
+    x = any(mask,2);
+    y = any(mask,1);
+    coord = gather([find(x, 1,'first'), find(x, 1,'last'), find(y, 1,'first'), find(y, 1,'last')]);
+
+    w = (coord(2) - coord(1));
+    h = (coord(4) - coord(3));
+    Cx = (coord(2) +coord(1))/2;
+    Cy = (coord(4) + coord(3))/2;
+
+    %YJ: HAS BUG - WRONG INDEX FOR ENTIRE FOV. 
+    %CHEAP FIX: USE A SMALL NEGATIVE EXTENT
+    
+    %why only use extent for horitonal direction? 
+    coord(1) =  floor(Cx  - ceil( (0.5 + extent) *w ));
+    coord(2) =  ceil(Cx  + ceil((0.5 + extent) * w ));
+    %% added by YJ to apply extend to vertical direction
+    coord(3) =  floor(Cy  - ceil( (0.5 + extent) *h ));
+    coord(4) =  ceil(Cy  + ceil((0.5 + extent) * h )) ;
+    %%
+    w = floor((coord(2) - coord(1))/multiply_of)*multiply_of;
+    h = floor((coord(4) - coord(3))/multiply_of)*multiply_of;
+    
+    coord(2) = coord(1)+w-1;
+    coord(4) = coord(3)+h-1;
+
+    coord([1,3]) = max(1,coord([1,3]));
+    coord([2,4]) = min(size(mask),coord([2,4]));
+
+    ROI = {coord(1):coord(2), coord(3):coord(4)};
+
+end