Adapt dose engine concept to dev_varRBErobOpt

.travis/before_install_linux.sh → .github/before_install_linux.sh

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-sudo chmod +x .travis/runtests.sh
+sudo chmod +x .github/runtests.sh
 sudo chmod +x MCsquare/bin/MCsquare_linux
 
 mv optimization/optimizer/ipopt.m optimization/optimizer/ipopt.m.bak

.travis/runtests.sh → .github/runtests.sh

@@ -4,7 +4,8 @@
 ## Make sure some failures are detected by the CI runners
 function exitIfError {
 	# pass "$?" as argument: i.e. the exit status of the last call
-	if [ "$1" -ne 0 ]; then
+	# currently octave 6 can finish with a segfault when the program is closed due to some bug, for now we try to ignore it
+	if [ "$1" -ne 0 ] && [ "$1" -ne 139 ]; then
 		exit $1;
 	fi
 }

.github/workflows/tests.yml

@@ -6,7 +6,7 @@ jobs:
   test-matlab: #Matlab test Job
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2 # Checks-out repository under $GITHUB_WORKSPACE
+      - uses: actions/checkout@v3 # Checks-out repository under $GITHUB_WORKSPACE
       # Install MATLAB
       - name: Install MATLAB
         uses: matlab-actions/setup-matlab@v1        
@@ -16,23 +16,24 @@ jobs:
         with:
           command: cd unitTest; matRad_runTests
   test-octave: #Octave test Job
-    runs-on: ubuntu-20.04 # We use Ubuntu-20.04 because it has Octave 5.2
+    runs-on: ubuntu-22.04 # We use Ubuntu-22.04 because it has Octave 6.4
     steps:
-      - uses: actions/checkout@v2 # Checks-out repository under $GITHUB_WORKSPACE
+      - uses: actions/checkout@v3 # Checks-out repository under $GITHUB_WORKSPACE
       - name: Install OCTAVE
         run: |
           sudo apt-get update
           sudo apt-get install -y gdb gfortran fonts-freefont-otf gnuplot-x11 libgdcm-dev octave liboctave-dev
       - name: Prepare Test Environment
         run: |
-          sudo chmod +x .travis/before_install_linux.sh
-          sudo .travis/before_install_linux.sh
-      - name: Run Tests
-        uses: GabrielBB/xvfb-action@v1 #For Headless tests
-        with:
-          run: .travis/runtests.sh octave-cli
-      - name: Upload Logs if failure
-        uses: actions/upload-artifact@v2
+          sudo chmod +x .github/before_install_linux.sh
+          sudo .github/before_install_linux.sh
+      - name: Run Tests 
+        run: xvfb-run -a .github/runtests.sh octave-cli
+        # uses: GabrielBB/xvfb-action@v1 #For Headless tests
+        # with:
+        #   run: .github/runtests.sh octave-cli
+      - name: Upload logs if test fails
+        uses: actions/upload-artifact@v3
         if: failure()
         with:
           name: Test Log

AUTHORS.txt

@@ -33,4 +33,4 @@ List of all matRad developers that contributed code (alphabetical)
 * Jona Welsch
 * Hans-Peter Wieser
 * Johanna Winter
-* Tong Xu
+* Tong Xu

MCsquare/matRad_compileMCsquareSparseReader.m

@@ -43,7 +43,7 @@ function matRad_compileMCsquareSparseReader(dest,sourceFolder)
 end
 
 if exist ('OCTAVE_VERSION', 'builtin')
-    ccName = eval('mkoctfile -p CXX');
+    ccName = evalc('mkoctfile -p CXX');
 else
     myCCompiler = mex.getCompilerConfigurations('C','Selected');
     ccName = myCCompiler.ShortName;

MatRad_Config.m

@@ -22,10 +22,10 @@
     properties
 
         %Logging
-        logLevel = 3; %1 = only Errors, 2 = with Warnings, 3 = Info output, 4 = deprecation warnings, 5 = debug information
+        logLevel = 4; %1 = only Errors, 2 = with Warnings, 3 = Info output, 4 = deprecation warnings, 5 = debug information
         keepLog = false; %Stores the full log in memory
         writeLog = false; %Writes the log to a file on-the-fly
-
+                
         %Default Properties
         propDoseCalc;
         propOpt;
@@ -34,6 +34,7 @@
 
         %Disable GUI
         disableGUI = false;
+
         devMode = false;
         eduMode = false;
 
@@ -50,10 +51,12 @@
         isOctave; %Helper bool to check for Octave
         isMatlab; %Helper bool to check for Matlab
         matRad_version; %MatRad version string
+
+        matRadRoot; %Path to matRadRoot
     end
 
     properties (SetAccess = private)
-        matRadRoot;
+
     end
 
     methods (Access = private)
@@ -63,7 +66,7 @@
             %  Therefore its constructor is private
             %  For instantiation, use the static MatRad_Config.instance();
 
-            obj.matRadRoot = fileparts(mfilename('fullpath'))
+            obj.matRadRoot = fileparts(mfilename('fullpath'));
             addpath(genpath(obj.matRadRoot));
 
             %Set Version
@@ -167,22 +170,30 @@ function setDefaultProperties(obj)
             obj.propStf.defaultAddMargin = true; %expand target for beamlet finding
             obj.propStf.defaultBixelWidth = 5;
 
+            %Dose Calculation Options
             obj.propDoseCalc.defaultResolution = struct('x',3,'y',3,'z',3); %[mm]
-            obj.propDoseCalc.defaultLateralCutOff = 0.995; %[rel.]
-            obj.propDoseCalc.defaultGeometricCutOff = 50; %[mm]
+            obj.propDoseCalc.defaultDosimetricLateralCutOff = 0.995; %[rel.]
+            obj.propDoseCalc.defaultGeometricLateralCutOff = 50; %[mm]
             obj.propDoseCalc.defaultKernelCutOff = Inf; %[mm]
             obj.propDoseCalc.defaultSsdDensityThreshold = 0.05; %[rel.]
             obj.propDoseCalc.defaultUseGivenEqDensityCube = false; %Use the given density cube ct.cube and omit conversion from cubeHU.
             obj.propDoseCalc.defaultIgnoreOutsideDensities = true; %Ignore densities outside of cst contours
             obj.propDoseCalc.defaultUseCustomPrimaryPhotonFluence = false; %Use a custom primary photon fluence
-
+            obj.propDoseCalc.defaultDoseEngines = {'SVD Pencil Beam','Particle Pencil-Beam'}; %Names for default engines used when no other is given
+
             % default properties for fine sampling calculation
             obj.propDoseCalc.defaultFineSamplingProperties.sigmaSub = 1;
             obj.propDoseCalc.defaultFineSamplingProperties.N = 21;
             obj.propDoseCalc.defaultFineSamplingProperties.method = 'russo';
-
+
+            %Monte Carlo options
+            obj.propDoseCalc.defaultNumHistoriesPerBeamlet = 2e4;
+            obj.propDoseCalc.defaultNumHistoriesDirect = 1e6;
+            obj.propDoseCalc.defaultOutputMCvariance = true;
+
             obj.propOpt.defaultMaxIter = 500;
 
+            %deprecated monte carlo options
             obj.propMC.ompMC_defaultHistories = 1e6;
             obj.propMC.ompMC_defaultOutputVariance = false;
             obj.propMC.MCsquare_defaultHistories = 1e6;
@@ -206,21 +217,28 @@ function setDefaultPropertiesForTesting(obj)
             obj.propStf.defaultBixelWidth = 20;
 
             obj.propDoseCalc.defaultResolution = struct('x',5,'y',6,'z',7); %[mm]
-            obj.propDoseCalc.defaultGeometricCutOff = 20;
-            obj.propDoseCalc.defaultLateralCutOff = 0.8;
+            obj.propDoseCalc.defaultGeometricLateralCutOff = 20;
+            obj.propDoseCalc.defaultDosimetricLateralCutOff = 0.8;
             obj.propDoseCalc.defaultKernelCutOff = 20; %[mm]
             obj.propDoseCalc.defaultSsdDensityThreshold = 0.05;
             obj.propDoseCalc.defaultUseGivenEqDensityCube = false; %Use the given density cube ct.cube and omit conversion from cubeHU.
             obj.propDoseCalc.defaultIgnoreOutsideDensities = true;
             obj.propDoseCalc.defaultUseCustomPrimaryPhotonFluence = false; %Use a custom primary photon fluence
+            obj.propDoseCalc.defaultDoseEngines = {'SVD Pencil Beam','Particle Pencil-Beam'}; %Names for default engines used when no other is given
 
             % default properties for fine sampling calculation
             obj.propDoseCalc.defaultFineSamplingProperties.sigmaSub = 2;
             obj.propDoseCalc.defaultFineSamplingProperties.N = 5;
             obj.propDoseCalc.defaultFineSamplingProperties.method = 'russo';
 
+            %Monte Carlo options
+            obj.propDoseCalc.defaultNumHistoriesPerBeamlet = 100;
+            obj.propDoseCalc.defaultNumHistoriesDirect = 100;
+            obj.propDoseCalc.defaultOutputMCvariance = true;
+
             obj.propOpt.defaultMaxIter = 10;
 
+            %Deprecated Monte Carlo options
             obj.propMC.ompMC_defaultHistories = 100;
             obj.propMC.ompMC_defaultOutputVariance = true;
             obj.propMC.MCsquare_defaultHistories = 100;

basedata/matRad_loadMachine.m

@@ -0,0 +1,55 @@
+function machine = matRad_loadMachine(pln,filepath)
+% matRad_loadMachine load a machine base data file from pln struct
+%
+% call
+%   machine = matRad_loadMachine(pln,filepath)
+%   machine = matRad_loadMachine(pln)
+%
+% input
+%   pln:            matRad plan meta information struct
+%   filepath:       (optional) filepath where to look for machine. default
+%                   is basedata in the matRad root folder 
+%
+% output
+%   machine:        matRad machine struct
+%
+% References
+%
+%
+% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2022 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();
+if isfield(pln, 'radiationMode')
+    if isfield(pln, 'machine')
+        fileName = [pln.radiationMode '_' pln.machine];
+    else
+        fileName = [pln.radiationMode '_Generic'];
+        matRad_cfg.dispWarning('No machine name given, loading generic machine');
+    end
+else
+    matRad_cfg.dispError('No radiation mode given in pln');
+end
+
+if ~exist('filepath','var')
+    filepath = [matRad_cfg.matRadRoot filesep 'basedata' filesep fileName];
+end
+
+try
+    m = load(filepath, 'machine');
+    machine = m.machine; % strip first layer of loaded struct for convenience
+catch
+    matRad_cfg.dispError('Could not find the following machine file: %s\n',fileName);
+end
+end
+

dicom/matRad_calcWaterEqD.m

@@ -1,19 +1,18 @@
-function ct = matRad_calcWaterEqD(ct, pln)
+function ct = matRad_calcWaterEqD(ct, radiationMode)
 % matRad function to calculate the equivalent densities from a dicom ct 
 % that originally uses intensity values
 %
 % call
-%   ct = matRad_calcWaterEqD(ct, pln)
+%   ct = matRad_calcWaterEqD(ct, radiationMode)
 %
 % input
-%   ct: unprocessed dicom ct data which are stored as intensity values (IV)
-%
-%       HU = IV * slope + intercept
-%
-%   pln: matRad plan struct
+%   ct:             ct containing a cubeHU to compute rED/rSP values from
+%   radiationMode:  radiationMode as character array (e.g. 'photons') since matRad 3.
+%                   Can also be a pln-struct for downwards compatibility
 %
 % output
-%   ct: ct struct with cube with relative _electron_ densities
+%   ct: ct struct with cube with relative _electron_ densities stored in
+%   ct.cube
 %
 % References
 %   -
@@ -32,7 +31,7 @@
 % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 % load hlut
-hlut = matRad_loadHLUT(ct, pln);
+hlut = matRad_loadHLUT(ct, radiationMode);
 
 for i = 1:ct.numOfCtScen
 

dicom/matRad_loadHLUT.m

@@ -1,12 +1,13 @@
-function hlut = matRad_loadHLUT(ct, pln)
+function hlut = matRad_loadHLUT(ct, radiationMode)
 % matRad function to load HLUT file based on the provided ct
 %
 % call
 %   hlut = matRad_loadHLUT(ct, pln)
 %
 % input
-%   ct:   unprocessed dicom ct data 
-%   pln:  matRad pln struct
+%   ct:             ct with dicom information
+%   radiationMode:  radiationMode as character array (e.g. 'photons') since matRad 3.
+%                   Can also be a pln-struct for downwards compatibility
 %
 % output
 %   hlut: lookup table
@@ -36,11 +37,20 @@
     hlutDir = [];
 end
 
+%Old version - takes radiation mode from pln
+if isstruct(radiationMode) && isfield(radiationMode,'radiationMode')
+    particle = radiationMode.radiationMode;
+elseif ischar(radiationMode)
+    particle = radiationMode;
+else
+    matRad_cfg.dispError('Invalid radiation mode!');
+end
+
+
 % if possible -> file standard out of dicom tags
 try
 
     hlutFileName = '';
-    particle     = pln.radiationMode;
     manufacturer = ct.dicomInfo.Manufacturer;
     model        = ct.dicomInfo.ManufacturerModelName;
     convKernel   = ct.dicomInfo.ConvolutionKernel;