Merge pull request #410 from e0404/prepareBlaise

Preparations for the Release of "Blaise". Force merged now because review was already performed and approved by markbangert.

Author: wahln

.gitignore

@@ -0,0 +1 @@
+MCsquare/bin/Materials/

AUTHORS.txt

@@ -5,6 +5,7 @@ List of all matRad developers that contributed code (alphabetical)
 * Lucas Burigo
 * Gonzalo Cabal
 * Eduadro Cisternas
+* Edgardo Doerner
 * Louis Charton
 * Eric Christiansen
 * Hubert Gabrys
@@ -17,6 +18,7 @@ List of all matRad developers that contributed code (alphabetical)
 * Lucas-Raphael M�ller
 * Ahmad Neishabouri
 * Giuseppe Pezzano
+* Daniel Ramirez
 * Carsten Scholz
 * Alexander Stadler
 * Niklas Wahl

ChangeLog.txt

@@ -0,0 +1,39 @@
+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:
+	- integration tests using TravisCI (with Octave, so no GUI functionalities are tested)
+	- matRad_rc script to configure matRad paths
+    - matRad version can now be printed with matRad_version, version correctly shown in GUI and when using matRad_rc
+	- Seven new Matlab exmaple scripts to demonstrate use of matRad 
+	- added basic interfaces to the open-source photon/proton MC engines ompMC/MCsquare
+	- Overhaul of the optimization interface using OOP and integration of the fmincon optimizer from Mathworks' MATLAB Optimization toolbox
+	- Changes to the cst variable (new script to convert old to new cst structures in tools folder)
+	- separation of ct/optimization/dose calculation grids to allow different resolutions
+	- The graphical user interface can now be started in developer mode (more error information) and a simplified educational mode (some functionalities disabled, less buttons)
+	- base data and default phantoms now organized in subfolders
+	- DICOM export added (only script, dicomImport folder renamed to dicom)
+	- DICOM import GUI
+	- binary import and export functionalities (script & GUI)
+	- overhauled the standalone project file
+	- standalone toolbox file for matRad
+	- Dose calculation now uses generalized initialization scripts
+	- matRad_compareDose tool to compare two dose distributions with difference and gamma analysis
+	- more tools for visualisation and data analysis in the tools folder
+	- Possibility to define range shifter
+	- Quality indicator & DVH display wrapper scripts
+	- wrapper to allow 3D conformal planning using dij collapsing
+	- new colormap handling to allow integration of custom colormaps
+	- modularization of slice display by dedicated functions in plotting folder including generation of 3D views
+    - New global configuration object (matRad_cfg <- MatRad_Config.m) to store default values and with logging interface
+	- many bug fixes and many new bugs..	
+Version 2.1 "Alan"
+	First official relase of matRad including
+	- new optimizer IPOPT for constrained optimization
+	- validated ray tracing
+	- validated pencil beam particle dose calcualtion
+	- validated singular value decomposed pencil beam photon dose calculation
+	- DICOM import including dose and particle pencil beam scanning plan objects
+	- matRad standalone version
+	- improved GUI workflow
+	- many bug fixes and many new bugs...

IO/matRad_writeCube.m

@@ -12,7 +12,6 @@
 %   meta:                       meta-information in struct. 
 %                               Necessary fieldnames are:
 %                               - resolution: [x y z]
-%                               - datatype: numeric MATLAB-Datatype
 %                               Optional:
 %                               - axisPermutation (matRad default [2 1 3])
 %                               - coordinateSystem (matRad default 'LPS')

IO/matRad_writeMHA.m

@@ -76,6 +76,7 @@ function matRad_writeMHA(filepath,cube,metadata)
 fprintf(fid, 'ElementType = %s\n',matlabTypeToMHAtype(metadata.datatype));
 fprintf(fid, 'ElementDataFile = LOCAL\n');
 fwrite(fid,cube,metadata.datatype,'b');
+fclose(fid);
 
 end
 

Jenkinsfile

@@ -0,0 +1,60 @@
+node {
+    def osName
+    stage('Set Environment') {
+        echo 'Setting the environment..'
+		checkout scm
+        if (isUnix()) {
+            def uname = sh script: 'uname', returnStdout: true
+            if (uname.startsWith("Darwin")) {
+                osName= "Macos"
+				sh label: '', script: 'chmod +x ./submodules/MCsquare/MCsquare_mac'
+                sh label: '', script: 'chmod +x runtests.sh'
+            }
+            else {
+                osName= "Linux"
+                sh label: '', script: 'chmod +x ./submodules/MCsquare/MCsquare_linux'
+                sh label: '', script: 'chmod +x runtests.sh'
+            }
+        }
+        else {
+            osName= "Windows"
+        }
+
+    }
+    stage('Test with MATLAB') 
+	{
+        echo 'Testing on MATLAB..'
+        echo 'Make sure you can run matlab script from the command line'
+        if (osName == "Windows") {
+            bat label: '', script: 'matlab -noFigureWindow -nosplash -minimize -wait -r "cd unitTest; matRad_runTests"'
+        }
+        else {
+            sh label: '', script: 'matlab -nodisplay -r "cd unitTest; matRad_runTests"'
+        } 
+    }
+	
+	stage('Test with Octave') 
+	{
+		echo 'Testing on Octave..'
+        if (osName == "Windows") {
+            bat label: '', script: './runtests.sh octave-cli'
+        }
+        else {
+            sh label: '', script: './runtests.sh octave-cli'
+        } 
+	}
+	
+    stage('Build') {
+        echo 'Building....'
+        if (osName == "Windows") {
+            bat label: '', script: 'matlab -nodisplay -r "matRad_compileStandalone"'
+        }
+        else {
+            sh label: '', script: 'matlab -nodisplay -r "matRad_compileStandalone"'
+        } 
+    }
+    stage('Archive') {
+        echo 'Archiving....'
+        archiveArtifacts artifacts: 'standalone/for_redistribution/matRad_installer*', onlyIfSuccessful: true
+    }
+}

LICENSES.txt renamed to LICENSE.md

@@ -1,6 +1,7 @@
-matRad Ipopt
+matRad 
+with Ipopt MCsquare ompMC
 
-This is a compilation of matRad and Ipopt as separate and independent works (or 
+This matRad as a compilation with Ipopt, MCsquare and ompMC as separate and independent works (or 
 modules, components, programs). 
 
 It is the intention of the copyright owners of matRad and Ipopt that matRad and Ipopt 
@@ -35,7 +36,7 @@ http://e0404.github.io/matRad/;
 a wiki documentation is under constant development at 
 https://github.com/e0404/matRad/wiki.
 
-Copyright (C) 2015 by the contributors and German Cancer Research Center
+Copyright (C) 2020 by the contributors and German Cancer Research Center
 
 This program is free software: you can redistribute it and/or modify
 it under the terms of the GNU General Public License as published by
@@ -57,8 +58,8 @@ Ipopt (or a modified version of that library), containing parts covered
 by the terms of Eclipse Public License, Version 1.0 (EPL-1.0), the licensors of this 
 Program grant you additional permission to run, use and convey the resulting work. 
 
-Contact: Mark Bangert, E040 Research group Optimization Algorithms
-e-mail: [email protected]
+Contact: Niklas Wahl, E040 Research Group Radiotherapy Optimization
+e-mail: [email protected]
 address: 
 Division of Medical Physics in Radiation Oncology
 German Cancer Research Center
@@ -976,4 +977,27 @@ Agreement will bring a legal action under this Agreement more than one year
 after the cause of action arose. Each party waives its rights to a jury trial 
 in any resulting litigation.
 
+* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+
+ompMC
+
+Information and source code of ompMC is available on https://github.com/edoerner/ompMC
+Precompiled binaries and reference data of ompMC are used within matRad. 
+The source code itself is referenced as a git submodule. Contents of the ompMC subfolder 
+and the submodule are licensed under GNU GPL v3.0 as stated in the respective LICENSE 
+files located in these folders.
+
+* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+
+MCsquare
+
+MCsquare is an open-source software developed/maintained at UC Louvain, Belgium.
+Information and source code of MCsquare is available on http://openmcsquare.org and 
+https://https://gitlab.com/openmcsquare/MCsquare
+Precompiled binaries and reference data of MCsquare are used within and distributed with 
+matRad. 
+The source code itself is referenced as a git submodule. Contents of the MCsquare/bin 
+subfolder and the submodule are licensed under the Apache-2.0 license as stated in the 
+respective LICENSE files located in these folders.
+
 * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *

MCsquare/bin/BDL/BDL_default_DN.txt

@@ -0,0 +1,42 @@
+--UPenn beam model (double gaussian)--
+# Beam data library (IBA dedicated nozzle - P2)
+
+Nozzle exit to Isocenter distance
+410.0
+
+SMX to Isocenter distance
+2234.8
+
+SMY to Isocenter distance
+1859.1
+
+Beam parameters
+26 energies
+
+NominalEnergy 	 MeanEnergy 	 EnergySpread 	 ProtonsMU 	 Weight1 	 SpotSize1x 	 Divergence1x 	 Correlation1x 	 SpotSize1y 	 Divergence1y 	 Correlation1y 	 Weight2 	 SpotSize2x 	 Divergence2x 	 Correlation2x 	 SpotSize2y 	 Divergence2y 	 Correlation2y
+100.000 	 100.305 	 0.665290 	 86703300.0 	 0.948000 	 3.985307 	 0.006356 	 0.072822 	 5.586431 	 0.006545 	 -0.266240 	 0.052000 	 38.949745 	 0.045088 	 -0.125083 22.339186 	 0.036249 	 -0.222186 
+105.000 	 105.422 	 0.666242 	 89871181.4 	 0.949500 	 3.833945 	 0.006042 	 0.073534 	 5.367650 	 0.006287 	 -0.274306 	 0.050500 	 36.982519 	 0.044140 	 -0.137515 21.012691 	 0.034217 	 -0.218228 
+110.000 	 110.467 	 0.685850 	 93251731.2 	 0.951000 	 3.681490 	 0.005728 	 0.074736 	 5.147248 	 0.006029 	 -0.282458 	 0.049000 	 35.026632 	 0.043192 	 -0.151587 19.694115 	 0.032185 	 -0.214273 
+115.000 	 115.556 	 0.625346 	 94578587.1 	 0.953000 	 3.497435 	 0.005755 	 0.069735 	 4.968569 	 0.005852 	 -0.285047 	 0.047000 	 33.523035 	 0.042600 	 -0.193003 19.076456 	 0.030397 	 -0.204120 
+120.000 	 120.650 	 0.637829 	 98511877.6 	 0.954000 	 3.487801 	 0.005363 	 0.057775 	 4.776565 	 0.005600 	 -0.286595 	 0.046000 	 31.397749 	 0.044289 	 -0.195394 18.361173 	 0.029910 	 -0.209811 
+125.000 	 125.579 	 0.653920 	 101505000.0 	 0.955000 	 3.406551 	 0.005222 	 0.037192 	 4.649421 	 0.005597 	 -0.303451 	 0.045000 	 29.864739 	 0.041281 	 -0.153880 17.440032 	 0.026862 	 -0.156490 
+130.000 	 130.656 	 0.644983 	 105630000.0 	 0.956000 	 3.323215 	 0.005081 	 0.016711 	 4.523329 	 0.005595 	 -0.320989 	 0.044000 	 28.395821 	 0.038274 	 -0.109282 16.581150 	 0.023815 	 -0.097645 
+135.000 	 135.571 	 0.621086 	 106742000.0 	 0.956750 	 3.305639 	 0.004969 	 -0.016027 	 4.232780 	 0.005284 	 -0.287037 	 0.043250 	 27.087089 	 0.042076 	 -0.208666 15.791805 	 0.025198 	 -0.163535 
+140.000 	 140.496 	 0.636823 	 109872000.0 	 0.957500 	 3.284013 	 0.004857 	 -0.047616 	 3.949676 	 0.004974 	 -0.251242 	 0.042500 	 26.059423 	 0.045877 	 -0.313754 15.083101 	 0.026580 	 -0.235456 
+145.000 	 145.404 	 0.610956 	 113008000.0 	 0.958250 	 3.180466 	 0.004679 	 -0.043499 	 3.912240 	 0.004771 	 -0.261328 	 0.041750 	 24.263559 	 0.042630 	 -0.296853 14.519874 	 0.025190 	 -0.215696 
+150.000 	 150.559 	 0.626557 	 115140000.0 	 0.959000 	 3.077055 	 0.004502 	 -0.039148 	 3.871036 	 0.004567 	 -0.270952 	 0.041000 	 22.496600 	 0.039382 	 -0.278384 13.965773 	 0.023799 	 -0.194537 
+155.000 	 155.445 	 0.589504 	 118316250.0 	 0.960000 	 2.977594 	 0.004522 	 -0.058541 	 3.754582 	 0.004511 	 -0.282809 	 0.040000 	 20.815900 	 0.037870 	 -0.314509 13.320911 	 0.023652 	 -0.218842 
+160.000 	 160.429 	 0.600311 	 120487500.0 	 0.961000 	 2.879674 	 0.004542 	 -0.079435 	 3.638438 	 0.004455 	 -0.295247 	 0.039000 	 19.162852 	 0.036358 	 -0.355983 12.690601 	 0.023506 	 -0.245978 
+165.000 	 165.530 	 0.584234 	 123677500.0 	 0.962000 	 2.755333 	 0.004306 	 -0.044188 	 3.537004 	 0.004338 	 -0.301278 	 0.038000 	 17.529102 	 0.031529 	 -0.281662 12.186412 	 0.021208 	 -0.196310 
+170.000 	 170.502 	 0.569782 	 126875000.0 	 0.963000 	 2.635201 	 0.004070 	 -0.006930 	 3.435107 	 0.004220 	 -0.307402 	 0.037000 	 16.040880 	 0.026699 	 -0.192572 11.715631 	 0.018911 	 -0.141841 
+175.000 	 175.464 	 0.550193 	 129063750.0 	 0.964000 	 2.529284 	 0.003964 	 0.009452 	 3.347097 	 0.004192 	 -0.316191 	 0.036000 	 15.150856 	 0.023970 	 -0.152680 11.338980 	 0.017710 	 -0.128027 
+180.000 	 180.458 	 0.546055 	 132275000.0 	 0.965000 	 2.424619 	 0.003858 	 0.026109 	 3.259540 	 0.004164 	 -0.325502 	 0.035000 	 14.290621 	 0.021241 	 -0.107808 10.960669 	 0.016509 	 -0.112793 
+185.000 	 185.393 	 0.526841 	 133456250.0 	 0.965250 	 2.344716 	 0.003829 	 0.018276 	 3.149883 	 0.003814 	 -0.299819 	 0.034750 	 13.833703 	 0.019720 	 -0.103672 10.651510 	 0.014879 	 -0.080749 
+190.000 	 190.579 	 0.529259 	 136680000.0 	 0.965500 	 2.265417 	 0.003799 	 0.009508 	 3.042401 	 0.003464 	 -0.271910 	 0.034500 	 13.361031 	 0.018198 	 -0.097930 10.348118 	 0.013248 	 -0.046014 
+195.000 	 195.562 	 0.470476 	 139060000.0 	 0.965750 	 2.179563 	 0.003720 	 0.018909 	 2.967881 	 0.003233 	 -0.269937 	 0.034250 	 12.920569 	 0.018366 	 -0.091326 10.136295 	 0.013213 	 -0.048919 
+200.000 	 200.484 	 0.441133 	 141450000.0 	 0.966000 	 2.094484 	 0.003642 	 0.028193 	 2.891102 	 0.003001 	 -0.267050 	 0.034000 	 12.478472 	 0.018534 	 -0.085365 9.925279 	 0.013177 	 -0.052148 
+205.000 	 205.420 	 0.420131 	 142822500.0 	 0.966250 	 1.990941 	 0.003639 	 0.064952 	 2.866584 	 0.002748 	 -0.264913 	 0.033750 	 11.160975 	 0.012439 	 0.362073 9.672448 	 0.010983 	 0.079347 
+210.000 	 210.472 	 0.400878 	 145230000.0 	 0.966500 	 1.885162 	 0.003636 	 0.104236 	 2.838630 	 0.002494 	 -0.262297 	 0.033500 	 11.508698 	 0.006344 	 0.788183 9.573300 	 0.008789 	 0.213919 
+215.000 	 215.436 	 0.344861 	 147766666.7 	 0.966750 	 1.846725 	 0.003638 	 0.232336 	 2.882585 	 0.002114 	 -0.194544 	 0.033250 	 11.127675 	 0.008806 	 0.602110 9.711900 	 0.009239 	 0.193964 
+220.000 	 220.476 	 0.327202 	 150316666.7 	 0.967000 	 1.802803 	 0.003639 	 0.374296 	 2.939637 	 0.001735 	 -0.127838 	 0.033000 	 11.075270 	 0.011268 	 0.391640 9.854619 	 0.009689 	 0.174312 
+225.000 	 225.217 	 0.268174 	 152880000.0 	 0.968000 	 2.024567 	 0.003920 	 0.449243 	 3.223547 	 0.002592 	 -0.246340 	 0.032000 	 11.631725 	 0.009600 	 0.565136 10.688153 	 0.009301 	 0.145048