generate body contour

tools/matRad_generateBodyContour.m

@@ -0,0 +1,59 @@
+function cst = matRad_generateBodyContour(ct,cst,thresholdHU)
+% function to create a BODY contour for imported patient cases that do not have one
+% 
+% call
+%   cst = matRad_generateBodyContour(ct,cst,thresholdHU)
+%
+% input
+%   ct:             matrad ct structure
+%   cst:            matrad cst structure
+%   thresholdHU:    HU thresholding value (optional) default = -500 HU
+%                  
+%
+% output
+%   cst:        matRads cst struct  with inserted BODY contour
+%
+% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2018 the matRad development team.
+%
+% This file is part of the matRad project. It is subject to the license
+% terms in the LICENSE file found in the top-level directory of this
+% distribution and at https://github.com/e0404/matRad/LICENSES.txt. No part
+% of the matRad project, including this file, may be copied, modified,
+% propagated, or distributed except according to the terms contained in the
+% LICENSE file.
+%
+% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+if nargin<3
+    thresholdHU = -500;
+end
+% visualize Histogram
+% figure,
+% histogram(ct.cubeHU{1});
+% hold on
+% scatter(-500,100,'x')
+% hold off
+% xlabel('HU')
+% ylabel('#')
+
+% Thresholding on HU
+mask = zeros(ct.cubeDim);
+mask(ct.cubeHU{1}>thresholdHU) = 1;
+list = find(mask);
+filledIm= imfill(mask);
+
+% Write to cst
+pos = size(cst,1);
+cst{pos+1,1}    = pos;
+cst{pos+1,2}    = 'BODY';
+cst{pos+1,3}    = 'OAR';
+cst{pos+1,4}{1} = find(filledIm);
+cst{pos+1,5}.Priority    = 99;
+cst{pos+1,5}.alphaX     = 0.1;
+cst{pos+1,5}.betaX      = 0.05;
+cst{pos+1,5}.Visible    = 1;
+cst{pos+1,5}.visibleColor = [0.7,0.3,0.1];
+cst{pos+1,6}    = [];
+
+end