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