matRad_calcWaterEqD

 matRad function to calculate the equivalent densities from a dicom ct 
 that originally uses intensity values

 call
   ct = matRad_calcWaterEqD(ct, pln)

 input
   ct: unprocessed dicom ct data which are stored as intensity values (IV)

       HU = IV * slope + intercept

   pln: matRad plan struct

 output
   ct: ct struct with cube with relative _electron_ densities

 References
   -

 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

 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.

 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

0001 function ct = matRad_calcWaterEqD(ct, pln)
0002 % matRad function to calculate the equivalent densities from a dicom ct
0003 % that originally uses intensity values
0004 %
0005 % call
0006 %   ct = matRad_calcWaterEqD(ct, pln)
0007 %
0008 % input
0009 %   ct: unprocessed dicom ct data which are stored as intensity values (IV)
0010 %
0011 %       HU = IV * slope + intercept
0012 %
0013 %   pln: matRad plan struct
0014 %
0015 % output
0016 %   ct: ct struct with cube with relative _electron_ densities
0017 %
0018 % References
0019 %   -
0020 %
0021 % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0022 %
0023 % Copyright 2018 the matRad development team.
0024 %
0025 % This file is part of the matRad project. It is subject to the license
0026 % terms in the LICENSE file found in the top-level directory of this
0027 % distribution and at https://github.com/e0404/matRad/LICENSES.txt. No part
0028 % of the matRad project, including this file, may be copied, modified,
0029 % propagated, or distributed except according to the terms contained in the
0030 % LICENSE file.
0031 %
0032 % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0033 
0034 % load hlut
0035 hlut = matRad_loadHLUT(ct, pln);
0036     
0037 for i = 1:ct.numOfCtScen
0038 
0039     % Manual adjustments if ct data is corrupt. If some values are out of range
0040     % of the LUT, then these values are adjusted.
0041     if max(ct.cubeHU{i}(:)) > max(hlut(:,1))
0042         warning('projecting out of range HU values');
0043         ct.cubeHU{i}(ct.cubeHU{i} > max(hlut(:,1))) = max(hlut(:,1));
0044     end
0045     if min(ct.cubeHU{i}(:)) < min(hlut(:,1))
0046         warning('projecting out of range HU values');
0047         ct.cubeHU{i}(ct.cubeHU{i} < min(hlut(:,1))) = min(hlut(:,1));
0048     end
0049 
0050     % interpolate HU to relative electron density or relative stopping power based on lookup table
0051     ct.cube{i} = reshape(matRad_interp1(hlut(:,1),hlut(:,2),double(ct.cubeHU{i}(:))),ct.cubeDim);
0052 
0053 end
0054 
0055 % save hlut
0056 ct.hlut = hlut;
0057 
0058 end