Merge remote-tracking branch 'origin/dev' into rc/v2.10.1

.github/PULL_REQUEST_TEMPLATE/bugfix_pull_request.md

@@ -0,0 +1,15 @@
+### Bug description
+Either describe the bug and how to reproduce it (see the corresponding issue template) or reference the respective issue.
+
+### Approach
+Describe why your approach fixes the described bug
+
+### Open Questions and/or Concerns
+Use a github checklists to adress any concerns like. e.g.
+- [ ] I wasn't sure about this or that variable and if I did the correct thing with it
+- [ ] I am not sure if this is compatible with the latest Matlab version
+- [ ] etc.
+This checklist then has to be checked before merge
+
+### References
+Any helpful external information (e.g. links to stackoverflow question, blogposts, etc.)

.github/PULL_REQUEST_TEMPLATE/feature_pull_request.md

@@ -0,0 +1,18 @@
+### Bug description
+Describe the new feature you want to contribute and reference respective issues if this specific enhancement was asked for.
+
+### Approach
+Describe how you implemented the feature:
+- How does my feature change matRad code?
+- Are there any new parameters associated with the feature that need to be documented? (maybe think about providing defaults in MatRad_Config)
+- Are there external dependencies (toolboxes, mex files, etc.)?
+
+### Open Questions and/or Concerns
+Use a github checklists to adress any concerns like. e.g.
+- [ ] I wasn't sure about this or that variable and if I did the correct thing with it
+- [ ] I am not sure if this is compatible with the latest Matlab version
+- [ ] etc.
+This self-defined checklist then has to be checked before merge by reviewers and yourself.
+
+### References
+Any helpful external information (e.g. links to stackoverflow question, blogposts, external software websites, etc.)

.github/PULL_REQUEST_TEMPLATE/release_checklist_pull_request.md

@@ -0,0 +1,17 @@
+### Release Version
+Version of new Release and Type (new major release, minor release, patch release)
+
+### Release Checklist
+
+- [ ] Version number changed in matRad_getVersion
+- [ ] Adapted Changelog.txt
+- [ ] All required mex files compiled
+- [ ] Third Party libraries / scripts up to date
+- [ ] Standalone(s) generated and tested
+- [ ] Wiki adapted
+- [ ] Optional changes to README.md
+- [ ] Check license information
+
+### References
+Any references regarding new functionality etc.
+

.github/stale.yml

@@ -0,0 +1,26 @@
+# Number of days of inactivity before an issue becomes stale
+daysUntilStale: 14
+# Number of days of inactivity before a stale issue is closed
+daysUntilClose: 28
+# Issues with these labels will never be considered stale
+exemptLabels:
+  - Hotfix needed
+  - bug
+  - enhancement
+  - help wanted
+# Label to use when marking an issue as stale
+staleLabel: stale
+# Comment to post when marking an issue as stale. Set to `false` to disable
+markComment: >
+  This issue has been automatically marked as stale because it has not had
+  recent activity. It will be closed if no further activity occurs. Thank you
+  for your contributions. 
+# Comment to post when closing a stale issue. Set to `false` to disable
+closeComment: >
+  This issue has been automatically closed because it has not seen any 
+  activity in four weeks. This happens usually when the issue has already
+  been solved or it is no longer relevant. If that's not the case,
+  feel free to reopen the issue.
+
+#Only use on issues for now
+only: issues

.travis.yml

@@ -29,9 +29,10 @@ jobs:
         homebrew:
           update: true
           packages: 
-            - octave
             - llvm
             - libomp
+            - gdcm
+            - octave
       cache:
         directories:
           - $HOME/Library/Caches/Homebrew
@@ -65,7 +66,7 @@ before_install:
   # Windows Setup
   - if [[ "$TRAVIS_JOB_NAME" == "Windows Octave" ]]; then echo "Testing matRad on Windows..." ; fi
   - if [[ "$TRAVIS_JOB_NAME" == "Windows Octave" ]]; then choco install octave.portable ; fi  
-  # - if [[ "$TRAVIS_JOB_NAME" == "Windows Octave" ]]; then bash ./before_install_win_gitbash.sh ; fi
+  - if [[ "$TRAVIS_JOB_NAME" == "Windows Octave" ]]; then bash .travis/before_install_win_gitbash.sh ; fi
 
 
 before_script:
@@ -88,10 +89,14 @@ script:
   # OSX script
   - if [[ "$TRAVIS_JOB_NAME" == "OSX Octave" ]]; then travis_wait 45 .travis/runtests.sh octave-cli ; fi
   # Windows script
-  - if [[ "$TRAVIS_JOB_NAME" == "Windows Octave" ]]; then travis_wait 45 .travis/runtests.sh octave-cli ; fi
+  - if [[ "$TRAVIS_JOB_NAME" == "Windows Octave" ]]; then travis_wait 45 "cmd.exe //C RefreshEnv.cmd & .travis/runtests.sh octave-cli" ; fi
 
 before_cache:
   - if [[ "$TRAVIS_JOB_NAME" == "OSX Octave" ]]; then brew cleanup; fi
 
 notifications:
-    slack: e0404:u5tBXbO6D1mEwzJuFZV0MmqJ
+  slack: 
+    if: repo = e0404/matRad 
+    rooms:
+      - e0404:u5tBXbO6D1mEwzJuFZV0MmqJ
+

.travis/before_install_win_gitbash.sh

@@ -1,9 +1,11 @@
 #!/usr/bin/env bash
 
 sudo chmod +x .travis/runtests.sh
-sudo chmod +x submodules/MCsquare/MCsquare_linux
+#sudo chmod +x MCsquare/MCsquare_windows.exe
 
-mv optimization/optimizer/ipopt.m optimization/optimizer/ipopt.m.bak
+#mv optimization/optimizer/ipopt.m optimization/optimizer/ipopt.m.bak
 
-octave --no-gui --eval "pkg install -forge dicom"
-octave --no-gui --eval "pkg install -forge nan"
+#octave --no-gui --eval "pkg install -forge dicom"
+#octave --no-gui --eval "pkg install -forge nan"
+
+cmd.exe //C RefreshEnv.cmd

matRadGUI.m

@@ -1355,15 +1355,33 @@ function Update3DView(handles)
         Result = evalin('base','resultGUI');
     end
 
+    ct  = evalin('base','ct');
+    cst = evalin('base','cst');
+    pln = evalin('base','pln');
+
     if  ismember('stf',AllVarNames)
         stf = evalin('base','stf');
+
+        %validate stf with current pln settings
+        validStf = true;
+        gantryAngles = [stf.gantryAngle];
+        validStf = isequal(gantryAngles,pln.propStf.gantryAngles) & validStf;
+        couchAngles = [stf.couchAngle];
+        validStf = isequal(couchAngles,pln.propStf.couchAngles) & validStf;
+        isoCenter = vertcat(stf.isoCenter);
+        validStf = isequal(isoCenter,pln.propStf.isoCenter) & validStf;
+
+        if ~validStf
+            matRad_cfg = MatRad_Config.instance();
+            matRad_cfg.dispWarning('stf and pln are not consistent, using pln for geometry display!');
+            stf = [];
+        end
+
     else
         stf = [];
     end
 
-    ct  = evalin('base','ct');
-    cst = evalin('base','cst');
-    pln = evalin('base','pln');
+
 end
 
 oldView = get(axesFig3D,'View');

matRad_calcPhotonDoseMC.m

@@ -57,6 +57,17 @@
 
 matRad_calcDoseInit;
 
+% gaussian filter to model penumbra from (measured) machine output / see diploma thesis siggel 4.1.2
+if isfield(machine.data,'penumbraFWHMatIso')
+    penumbraFWHM = machine.data.penumbraFWHMatIso;
+else
+    penumbraFWHM = 5;
+    matRad_cfg.dispWarning('photon machine file does not contain measured penumbra width in machine.data.penumbraFWHMatIso. Assuming 5 mm.');
+end
+
+sourceFWHM = penumbraFWHM * machine.meta.SCD/(machine.meta.SAD - machine.meta.SCD);
+sigmaGauss = sourceFWHM / sqrt(8*log(2)); % [mm] 
+
 % set up arrays for book keeping
 dij.bixelNum = NaN*ones(dij.totalNumOfBixels,1);
 dij.rayNum   = NaN*ones(dij.totalNumOfBixels,1);
@@ -79,9 +90,11 @@
 ompMCoptions.randomSeeds = [97 33];
 
 %start source definition      
-ompMCoptions.spectrumFile = [omcFolder filesep 'spectra' filesep 'mohan6.spectrum'];
-ompMCoptions.monoEnergy   = 0.1; 
-ompMCoptions.charge       = 0;
+ompMCoptions.spectrumFile       = [omcFolder filesep 'spectra' filesep 'mohan6.spectrum'];
+ompMCoptions.monoEnergy         = 0.1; 
+ompMCoptions.charge             = 0;
+ompMCoptions.sourceGeometry     = 'gaussian';
+ompMCoptions.sourceGaussianWidth = 0.1*sigmaGauss;
 
 % start MC transport
 ompMCoptions.dataFolder   = [omcFolder filesep 'data' filesep];
@@ -193,7 +206,7 @@
 end
 
 %% Create beamlet source
-useCornersSCD = false; %false -> use ISO corners
+useCornersSCD = true; %false -> use ISO corners
 
 numOfBixels = [stf(:).numOfRays];
 beamSource = zeros(dij.numOfBeams, 3);
@@ -305,7 +318,7 @@
         end
     catch ME
         errorString = [ME.message '\nThis error was thrown by the MEX-interface of ompMC.\nMex interfaces can raise compatability issues which may be resolved by compiling them by hand directly on your particular system.'];
-        matRad_cfg.dispError(ME.identifier,errorString);
+        matRad_cfg.dispError(errorString);
     end
 
     %Calibrate the dose with above factor