generate body contour (#768)

* Function to generate body contour for imported patient cases thet do not have one

* Checking for image processing toolbox

* move body contour generation to util as it might be useful within matRad itself

* some reformatting to body contour generator

* test of body contour generator

---------

Co-authored-by: Niklas Wahl <[email protected]>

Author: amitantony

matRad/util/matRad_generateBodyContour.m

@@ -0,0 +1,67 @@
+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 2024 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/LICENSE.md. 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.
+%
+% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+matRad_cfg = MatRad_Config.instance();
+% dicom import needs image processing toolbox -> check if available
+available = matRad_checkEnvDicomRequirements(matRad_cfg.env);
+
+if ~available
+    matRad_cfg.dispError('Image processing toolbox / packages not available!');
+end
+
+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;
+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

test/util/test_generateBodyContour.m

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+function test_suite = test_generateBodyContour
+%The output should always be test_suite, and the function name the same as
+%your file name
+
+%% Header
+% The header is required to be in this format for automatic test collection
+% by MOxUnit
+
+%To collect all tests defined below, this is needed in newer Matlab
+%versions. test_functions will collect function handles to below test
+%functions
+test_functions=localfunctions(); 
+
+% This will initialize the test suite, i.e., take the functions from
+% test_functions, check if they contain "test", convert them into a MOxUnit
+% Test Case, and add them to the test-runner
+initTestSuite;
+
+%% Custom Tests
+% Tests use assert*-like Functions to check outputs etc:
+% assertTrue(a) - a is true
+% assertFalse(a) - a is false
+% assertEqual(a,b) - a and be are equal (isequal)
+% assertElementsAlmostEqual(a,b) - numerical test for all vector / matrix elements. Has Additional arguments for absolute / relative tolerance 
+% assertVectorsAlmostEqual(a,b) - numerical test using vector norm
+% assertExceptionThrown(f,id) - test if exception of id is thrown. Take care of Octave issues with exception id (or don't provide id)
+% Check MOxUnit for more information or look at other tests
+
+function test_boxphantom_contour
+    load BOXPHANTOM.mat
+    cstNew = matRad_generateBodyContour(ct,cst);
+    voxIxGenerated = cstNew{end,4}{1};
+    voxIxExisting = cstNew{1,4}{1};
+
+    assertEqual(numel(voxIxGenerated),numel(voxIxExisting));
+    assertEqual(sort(voxIxGenerated),sort(voxIxExisting));
+
+function test_boxphantom_contour_withThreshold
+    load BOXPHANTOM.mat
+    cstNew = matRad_generateBodyContour(ct,cst,10);
+    voxIxGenerated = cstNew{end,4}{1};
+    assertTrue(isempty(voxIxGenerated));
+
+