1st Patch Release for Blaise - v2.10.1

.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.
+

.travis.yml

@@ -1,65 +1,102 @@
-language: cpp
-group: travis_latest
-
-matrix:
+jobs:
   include:
     # works on Precise and Trusty
-    - os: linux
+    - name: "Ubuntu Octave"
+      os: linux
+      language: cpp
+      dist: focal # 20.04 -> Octave 5.2
+      services: 
+        - xvfb
       addons:
         apt:
-          sources:
-            - ubuntu-toolchain-r-test
+          update: true
           packages:
-            - g++-7
-      env:
-        - MATRIX_EVAL="CC=gcc-7 && CXX=g++-7"
-    - os: osx
-    - os: windows
+            - gdb
+            - gfortran
+            - fonts-freefont-otf
+            - gnuplot-x11
+            - libgdcm-dev
+            - octave
+            - liboctave-dev      
+    - name: "Ubuntu Matlab"
+      os: linux
+      language: matlab
+      dist: focal
+    - name: "OSX Octave"
+      os: osx
+      language: cpp
+      addons:
+        homebrew:
+          update: true
+          packages: 
+            - llvm
+            - libomp
+            - gdcm
+            - octave
+      cache:
+        directories:
+          - $HOME/Library/Caches/Homebrew
+    - name: "Windows Octave"
+      os: windows
+      language: cpp
+      cache:
+        directories:
+          - $HOME/AppData/Local/Temp/chocolatey
+          - /C/ProgramData/chocolatey/
   allow_failures:
     - os: windows
     - os: osx
 
 before_install:
   # Linux setup
-  - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then echo "Testing matRad on linux..." ; fi
-  - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then eval "${MATRIX_EVAL}" ; fi
-  - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then sudo chmod +x before_install_linux.sh ; fi
-  - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then sudo ./before_install_linux.sh; fi
+  - if [[ "$TRAVIS_JOB_NAME" == "Ubuntu Octave" ]]; then echo "Testing matRad on linux with Octave..." ; fi
+  - if [[ "$TRAVIS_JOB_NAME" == "Ubuntu Octave" ]]; then sudo chmod +x .travis/before_install_linux.sh ; fi
+  - if [[ "$TRAVIS_JOB_NAME" == "Ubuntu Octave" ]]; then sudo .travis/before_install_linux.sh; fi
+
+  # Linux Matlab Setup
+  - if [[ "$TRAVIS_JOB_NAME" == "Ubuntu Matlab" ]]; then echo "Testing matRad on linux with Matlab..." ; fi
+  - if [[ "$TRAVIS_JOB_NAME" == "Ubuntu Matlab" ]]; then sudo chmod +x .travis/runtests.sh ; fi
+  - if [[ "$TRAVIS_JOB_NAME" == "Ubuntu Matlab" ]]; then sudo chmod +x MCsquare/bin/MCsquare_linux ; fi
 
   # OSX setup
-  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then echo "Testing matRad on Mac OSX..." ; fi
-  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew install octave  > /dev/null ; fi
-  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew install llvm > /dev/null ; fi
-  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew install libomp > /dev/null ; fi
-  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then sudo chmod +x before_install_osx.sh ; fi
-  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then sudo ./before_install_osx.sh; fi
+  - if [[ "$TRAVIS_JOB_NAME" == "OSX Octave" ]]; then echo "Testing matRad on Mac OSX..." ; fi
+  - if [[ "$TRAVIS_JOB_NAME" == "OSX Octave" ]]; then sudo chmod +x .travis/before_install_osx.sh ; fi
+  - if [[ "$TRAVIS_JOB_NAME" == "OSX Octave" ]]; then sudo .travis/before_install_osx.sh; fi
 
   # Windows Setup
-  - if [[ "$TRAVIS_OS_NAME" == "windows" ]]; then echo "Testing matRad on Windows..." ; fi
-  - if [[ "$TRAVIS_OS_NAME" == "windows" ]]; then choco install octave.portable ; fi  
-  - if [[ "$TRAVIS_OS_NAME" == "windows" ]]; then choco install cmake --installargs 'ADD_CMAKE_TO_PATH=System' ; fi
-  - if [[ "$TRAVIS_OS_NAME" == "windows" ]]; then bash ./before_install_win_gitbash.sh ; fi
+  - 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 .travis/before_install_win_gitbash.sh ; fi
 
 
 before_script:
-  - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then ulimit -c unlimited -S ; fi
+  - if [[ "$TRAVIS_JOB_NAME" == "Ubuntu Octave" ]]; then ulimit -c unlimited -S ; fi
 
 
 after_failure:
   ## Linux stack trace
   # find core file
-  - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then COREFILE=$(find . -maxdepth 1 -name "core*" | head -n 1) ; fi 
+  - if [[ "$TRAVIS_JOB_NAME" == "Ubuntu Octave" ]]; then COREFILE=$(find . -maxdepth 1 -name "core*" | head -n 1) ; fi 
   # print stack trace
-  - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then gdb -c "$COREFILE" -ex "thread apply all bt" -ex "set pagination 0" -batch /usr/bin/octave-cli ; fi
-  - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then tail runtests.log ; fi
+  - if [[ "$TRAVIS_JOB_NAME" == "Ubuntu Octave" ]]; then gdb -c "$COREFILE" -ex "thread apply all bt" -ex "set pagination 0" -batch /usr/bin/octave-cli ; fi
+  - if [[ "$TRAVIS_JOB_NAME" == "Ubuntu Octave" ]]; then tail runtests.log ; fi
 
 script:
-  # Linux script
-  - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then travis_wait 45 ./runtests.sh octave-cli ; fi
+  # Linux Octave script
+  - if [[ "$TRAVIS_JOB_NAME" == "Ubuntu Octave" ]]; then travis_wait 45 .travis/runtests.sh octave-cli ; fi
+  # Linux Matlab script
+  - if [[ "$TRAVIS_JOB_NAME" == "Ubuntu Matlab" ]]; then travis_wait 45 .travis/runtests.sh matlab; fi
   # OSX script
-  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then travis_wait 45 ./runtests.sh octave-cli ; fi
+  - if [[ "$TRAVIS_JOB_NAME" == "OSX Octave" ]]; then travis_wait 45 .travis/runtests.sh octave-cli ; fi
   # Windows script
-  - if [[ "$TRAVIS_OS_NAME" == "windows" ]]; then travis_wait 45 ./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_linux.sh

@@ -0,0 +1,9 @@
+#!/usr/bin/env bash
+
+sudo chmod +x .travis/runtests.sh
+sudo chmod +x MCsquare/bin/MCsquare_linux
+
+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"

.travis/before_install_osx.sh

@@ -0,0 +1,9 @@
+#!/usr/bin/env bash
+
+sudo chmod +x .travis/runtests.sh
+sudo chmod +x MCsquare/bin/MCsquare_mac
+
+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"

.travis/before_install_win_gitbash.sh

@@ -0,0 +1,11 @@
+#!/usr/bin/env bash
+
+sudo chmod +x .travis/runtests.sh
+#sudo chmod +x MCsquare/MCsquare_windows.exe
+
+#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"
+
+cmd.exe //C RefreshEnv.cmd

runtests.sh → .travis/runtests.sh

@@ -18,7 +18,7 @@ fi
 if [ -z "$Switches" ] ; then
 	case "$Runner" in
 		*matlab* )
-			Switches="-nodesktop -r"
+			Switches="-batch"
 			;;
 
 		*octave* )

AUTHORS.txt

@@ -17,6 +17,7 @@ List of all matRad developers that contributed code (alphabetical)
 * Henning Mescher
 * Lucas-Raphael M�ller
 * Ahmad Neishabouri
+* Martina Palkowitsch
 * Giuseppe Pezzano
 * Daniel Ramirez
 * Carsten Scholz

ChangeLog.txt

@@ -1,4 +1,21 @@
-Version 2.10.0 "Blaise"
+Version 2.10.1 - Patch release for "Blaise" 
+	Release with small updates, clean-ups and bugfixes    
+    - Bugfix in 3D view due to inconsistent angles in pln & stf
+    - Bugfix for using incorrect dicom UID's and wrong writing order in the dicom export
+    - Bugfix for weird colormap issue in plotting
+    - New handling of environment checking with matRad_cfg (old function is still working)
+    - Code documentation update
+    - Remove hardcoded penumbra width in photon dose calculation -> can now be stored in machine file (machine.data.penumbraFWHMatIso)
+    - Update to ompMC to use virtual Gaussian source (uses measured penumbra value) incld precompiled mex files
+    - remove useless global statements before matRad_cfg
+    - add blue/white/red difference map to colormaps (in the correct way)
+    - Updated TravisCI testing (Sped up by using pre-compiled mex interfaces and including testing with Matlab (on Ubuntu), Azure DevOps as fallback
+    - Github gimmicks added: Stalebot, Issue & PR Templates
+	- code optimization for jacobian evaluation (x10-100 speedup)
+	- New option pln.propDoseCalc.useGivenEqDensityCube (default false) to directly use the literal values from ct.cube and omit HU to WEQ conversion from ct.cubeHU
+	- New option pln.propDoseCalc.ignoreOutsideDensities (default true) to disable/enable inclusion of WEPL outside the patient contour in ray-tracing
+
+Version 2.10.0 - "Blaise"
 	Second Release of matRad. Note that despite major incompatibilities with "Alan" we still chose major version number "2" to have a consistent versioning in the future.
 	we want to thank all new contributing authors (see AUTHORS.txt)
 	The new release contains:

IO/matRad_importPatient.m

@@ -3,14 +3,15 @@
 % 
 % call
 %   [ct,cst] = matRad_importPatient(cubeFile,maskFiles)
+%   [ct,cst] = matRad_importPatient(cubeFile,maskFiles, hlutFilename)
 %
 % input
 %   ctFile:     path to CT file. If HLUT is not set, values are interpreted
 %               as HU and interpolated to ED. 
 %   maskFiles:  cell array with filenames to the masks
 %               if maskFiels contains a folder, all contained and
 %               recognized data files are treated as masks
-%   HLUT:       optional HLUT, (n,2) array. if set to 'default', we will
+%   hlutFilname:(optional) HLUT, (n,2) array. if set to 'default', we will
 %               use a default HLUT
 % output
 %   ct          ct struct for use with matlab

IO/matRad_readHLUT.m

@@ -1,30 +1,30 @@
 function hlut = matRad_readHLUT(filename)
-  % matRad function to read HLUT from filename
-  %
-  % call
-  %   hlut = matRad_readHLUT(filename)
-  %
-  % input
-  %   filename:   hlut filename
-  %
-  % output
-  %   hlut: lookup table
-  %
-  % 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.
-  %
-  % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% matRad function to read HLUT from filename
+%
+% call
+%   hlut = matRad_readHLUT(filename)
+%
+% input
+%   filename: hlut filename
+%
+% output
+%   hlut:     lookup table
+%
+% 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.
+%
+% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
   % Check the extension
   [~,~,ext] = fileparts(filename);

IO/matRad_readNRRD.m

@@ -2,7 +2,7 @@
 % matRad NRRD reader
 % 
 % call
-%   matRad_readNRRD(filename)
+%   [cube, metadata] = matRad_readNRRD(filename)
 %
 % input
 %   filename:   full path to nrrd file

IO/matRad_writeCube.m

@@ -2,14 +2,14 @@
 % matRad wrapper for Cube export
 % 
 % call
-%   matRad_writeCube(filepath,cube,meta)
+%   [saved_metadata] = matRad_writeCube(filepath,cube,meta)
 %
 % input
 %   filepath:                   full output path. needs the right extension
 %                               to choose the appropriate writer
 %   cube:                       cube that is to be written
 %   datatype:                   MATLAB numeric datatype
-%   meta:                       meta-information in struct. 
+%   metadata:                   meta-information in struct. 
 %                               Necessary fieldnames are:
 %                               - resolution: [x y z]
 %                               Optional:

IO/matRad_writeMHA.m

@@ -2,7 +2,7 @@ function matRad_writeMHA(filepath,cube,metadata)
 % matRad function to write mha files
 % 
 % call
-%   matRad_writeMHA(cube,metadata,filename)
+%   matRad_writeMHA(filepath,cube,metadata)
 %
 % input
 %   filepath:   full filename (with extension)

IO/matRad_writeVTK.m

@@ -2,7 +2,7 @@ function matRad_writeVTK(filepath,cube,metadata)
 % matRad function to write vtk cubes
 % 
 % call
-%   matRad_writeVTK(cube,metadata,filename)
+%   matRad_writeVTK(filepath,cube,metadata)
 %
 % input
 %   filepath:   full filename (with extension)

MCsquare/matRad_compileMCsquareSparseReader.m

@@ -1,16 +1,16 @@
 function matRad_compileMCsquareSparseReader(dest,sourceFolder)
-% Compiles the sparse mcsquare reader as mex interface for the current
-% platform
+% Compiles the sparse mcsquare reader as mex interface 
+% for the current platform
 %
 % call
 %   matRad_compileMCsquareSparseReader()
 %   matRad_compileMCsquareSparseReader(dest)
 %   matRad_compileMCsquareSparseReader(dest,sourceFolder)
 %
 % input:
-%   dest:           destination for mex file. Default: location of this
+%   dest:           (optional) destination for mex file. Default: location of this
 %                   file
-%   sourceFolder:   path to folder (optional). Default: location of this
+%   sourceFolder:   (optional) path to folder. Default: location of this
 %                   file
 %
 % References
@@ -31,7 +31,7 @@ function matRad_compileMCsquareSparseReader(dest,sourceFolder)
 %
 % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
-global matRad_cfg; 
+
 matRad_cfg = MatRad_Config.instance();
 
 if nargin < 1