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Merge dev_varRBErobOpt into research/heterogeneityCorrection
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commit 7cd7879
Merge: 37d4129 cb6b04a
Author: Niklas Wahl <niklaswahl2011@gmail.com>
Date:   Tue Nov 29 20:32:15 2022 +0100

    Merge branch 'master' into dev_varRBErobOpt

    # Conflicts:
    #	README.md

commit cb6b04a
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Tue Nov 29 20:26:59 2022 +0100

    Update README.md

    Update Cancer Aid Funding

commit 538f08b
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Tue Nov 29 20:23:17 2022 +0100

    Update README.md

    Add funding information

commit 37d4129
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Nov 11 18:05:52 2022 +0100

    add some compatibility functions to scenarioModel

commit 2c576ab
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Nov 11 18:04:35 2022 +0100

    spare resampling step if grids are the same

commit 05db32a
Merge: d34b182 9a431cd
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Oct 14 20:35:57 2022 +0200

    Merge branch 'dev_varRBErobOpt' of https://github.com/e0404/matRad into dev_varRBErobOpt

    # Conflicts:
    #	dicom/hlutLibrary/matRad_default.hlut
    #	matRad_calcDoseInitBeam.m
    #	matRad_calcParticleDose.m
    #	matRad_calcPhotonDose.m
    #	matRad_fluenceOptimization.m

commit 1b13404
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Sat Sep 24 00:39:04 2022 +0200

    Update tests.yml

commit d24dc5f
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Sat Sep 24 00:14:14 2022 +0200

    Update README.md

commit 942ea44
Merge: 75201fa f69a007
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Sat Sep 17 01:33:39 2022 +0200

    Merge pull request e0404#579 from wahln/master

    Create CITATION.cff

commit f69a007
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Sat Sep 17 01:28:31 2022 +0200

    Create CITATION.cff

commit 9a431cd
Merge: 3ae8fc1 54a6dfc
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Sep 16 18:23:49 2022 +0200

    Merge pull request e0404#537 from HomolkaN/dev_varRBErobOpt_ToolUpdate

    Tool update

commit 54a6dfc
Merge: 25ad484 3ae8fc1
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Sep 16 16:54:25 2022 +0200

    Merge remote-tracking branch 'origin/dev_varRBErobOpt' into pr/537

commit 3ae8fc1
Merge: 65b314f d5ae6e2
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Sep 16 16:13:41 2022 +0200

    Merge pull request e0404#572 from wahln/dev_varRBErobOpt_scen

    Object-oriented scenario implementation to replace matRad_multScen

commit d5ae6e2
Merge: 0a69b21 65b314f
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Sep 16 14:39:46 2022 +0200

    Merge branch 'dev_varRBErobOpt' of https://github.com/e0404/matRad into dev_varRBErobOpt_scen

    # Conflicts:
    #	matRad_fluenceOptimization.m

commit 65b314f
Merge: f5ec748 fea82a8
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Sep 16 14:33:14 2022 +0200

    Merge branch 'dev' into dev_varRBErobOpt

    # Conflicts:
    #	MatRad_Config.m
    #	matRad_calcParticleDose.m
    #	matRad_fluenceOptimization.m
    #	optimization/@matRad_OptimizationProblem/matRad_OptimizationProblem.m
    #	optimization/@matRad_OptimizationProblem/matRad_constraintJacobian.m

commit 0a69b21
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Sep 16 13:50:42 2022 +0200

    Extend Octave compatibility fix

commit 555d3ce
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Sep 16 13:39:30 2022 +0200

    fix missing return value in NominalScenario

commit 940d403
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Sep 16 13:39:10 2022 +0200

    Octave compatibility fix

commit beaa7ac
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Sep 16 11:51:16 2022 +0200

    a little bit and documentation and removal of unfinished functions

commit 09a6b8f
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Sep 16 11:44:24 2022 +0200

    Increase reusability of scenario code

commit 7a47f0b
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Sep 16 11:00:31 2022 +0200

    enable full combation of all grid scenarios

commit fea82a8
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Mon Sep 5 14:30:31 2022 +0200

    add some display reconfigurations for octave in matRad config

commit 75201fa
Merge: 3d29b76 e469b8f
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Mon Aug 22 15:37:07 2022 +0200

    Merge pull request e0404#574 from e0404/hotfix/dicomDoseImport

    Fix RTDose import when no RTPlan is imported

commit e469b8f
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Thu Aug 11 14:11:28 2022 +0200

    Fix RTDose import when no RTPlan is imported

commit 25ad484
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Mon Aug 8 14:30:00 2022 +0200

    Update matRad_getAlphaBetaCurves.m

    fixed error from recent octave compatibility patch

commit 2deb2c4
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Wed Aug 3 16:26:58 2022 +0200

    Replaced contains function by strfind for octave

    RIP contains, you were the love of my life.

commit d34b182
Merge: df91e40 f5ec748
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Wed Aug 3 14:34:17 2022 +0200

    Merge branch 'dev_varRBErobOpt' of https://github.com/e0404/matRad into dev_varRBErobOpt

commit ecf0d0b
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Tue Aug 2 11:45:32 2022 +0200

    Documentation update

commit 7a89042
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Tue Aug 2 11:44:02 2022 +0200

    remove temporary scripts

commit f370e84
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Jul 29 17:46:28 2022 +0200

    update to the IPOPT compilation script to use the active github links

commit be48e72
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Jul 29 17:45:33 2022 +0200

    documentation and compatibility fix

commit 95ab43a
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Jul 29 12:03:01 2022 +0200

    Octave compatability fix

commit 45d414f
Merge: ad2e93a f5ec748
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Jul 29 10:59:42 2022 +0200

    Merge branch 'dev_varRBErobOpt' into dev_varRBErobOpt_scen

    # Conflicts:
    #	MatRad_Config.m
    #	dicom/hlutLibrary/matRad_default.hlut
    #	examples/matRad_example6_protonsNoise.m
    #	matRad_calcDoseInitBeam.m
    #	matRad_calcParticleDose.m
    #	matRad_calcPhotonDose.m
    #	matRad_fluenceOptimization.m
    #	matRad_setOverlapPriorities.m

commit ad2e93a
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Jul 29 10:15:02 2022 +0200

    Include shift and range combinations

commit dba7cf4
Merge: f9f6ecc 6ef5d00
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Jul 29 10:01:07 2022 +0200

    Merge commit '6ef5d0020211c1dd4a74c9f8c30c0d543225b73b' into dev_varRBErobOpt_scen

commit f9f6ecc
Merge: 00d3176 0a624ce
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Jul 29 10:00:44 2022 +0200

    Merge commit '0a624cef39f7eed970e0bba58ec8a48df2c177a7' into dev_varRBErobOpt_scen

commit c0a9f08
Author: Niklas Wahl <niklaswahl2011@gmail.com>
Date:   Thu Jul 28 10:38:11 2022 +0200

    Remove old commented code

commit f5ec748
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Fri Jul 15 15:05:18 2022 +0200

    Update matRad_resizeCstToGrid.m

    This bug was fixed a while ago but not tracked on this branch.

commit 6ef5d00
Author: Niklas Wahl <niklaswahl2011@gmail.com>
Date:   Wed Jun 22 13:10:05 2022 +0200

    correctly set includeNominalScenario in WorstCase model

commit 0a624ce
Author: Niklas Wahl <niklaswahl2011@gmail.com>
Date:   Wed Jun 22 13:08:53 2022 +0200

    Add probability and weight to Nominal Scenario

commit 9a1e071
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Wed Jun 15 16:55:22 2022 +0200

    remove automatic clearing of matRad_cfg in matRad_rc and better handle calling matRad_rc from wrong folder

commit 2446784
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Wed Jun 15 16:54:13 2022 +0200

    fix error in dose calculation due to missing beam index

commit a886b04
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Wed Jun 15 14:02:13 2022 +0200

    First draft for added MU bounds in optimization

commit 4cd741c
Merge: d344dad 21f6ff8
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Tue Jun 14 13:30:00 2022 +0200

    Merge branch 'dev' of https://github.com/e0404/matRad into dev

commit 00d3176
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Jun 10 11:26:47 2022 +0200

    small update to matRadGUI

commit 99223dd
Merge: ecd4fd0 7b13c0e
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Mon May 30 16:48:39 2022 +0200

    Merge branch 'dev_varRBErobOpt_scen' of https://github.com/wahln/matRad into dev_varRBErobOpt_scen

commit ecd4fd0
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Mon May 30 16:48:11 2022 +0200

    implement new interface in matRad_sampling

commit 2f957c6
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Mon May 30 16:47:29 2022 +0200

    fix for downwards compatibility

commit 7b13c0e
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Tue May 24 18:20:13 2022 +0200

    Update tests.yml

    Change unitTest to test folder in Github workflow

commit b849675
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Tue May 24 17:56:39 2022 +0200

    deprecated properties in RandomScenarios class added

commit e1b9d5e
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Tue May 24 17:22:03 2022 +0200

    some more compatability and deprecation management for random scenario generation

commit 3e2865d
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri May 20 17:18:53 2022 +0200

    deprecation warning

commit af7719e
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri May 20 17:05:43 2022 +0200

    single scenario extractor

commit e18c7ec
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri May 20 16:58:25 2022 +0200

    New Scenario update with downwards compatability

commit b38936e
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Sun May 1 07:26:18 2022 +0200

    Update to spotRemoval

    - added spotRemovalDij class (removed outdated spotRemoval function, has been merged into class)
    - added example to spotRemoval

commit fbb07d5
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Sun May 1 07:24:50 2022 +0200

    Update matRad_getAlphaBetaCurves.m

commit d4c4223
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Apr 29 10:08:14 2022 +0200

    test scripts

commit df91e40
Merge: e0ffefe ea37a85
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Wed Apr 20 16:08:04 2022 +0200

    Merge branch 'dev_varRBErobOpt' of https://github.com/e0404/matRad into dev_varRBErobOpt

    # Conflicts:
    #	MatRad_Config.m
    #	dicom/hlutLibrary/matRad_default.hlut
    #	examples/matRad_example6_protonsNoise.m
    #	matRad_calcDoseInitBeam.m
    #	matRad_calcParticleDose.m
    #	matRad_calcPhotonDose.m
    #	matRad_fluenceOptimization.m
    #	matRad_setOverlapPriorities.m

commit 49ccff3
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Wed Apr 20 15:31:15 2022 +0200

    first draft of new scenario infrastructure

commit 21f6ff8
Author: Niklas Wahl <niklaswahl2011@gmail.com>
Date:   Fri Mar 25 15:04:03 2022 +0100

    faster initial intensity estimates by avoiding row-indexing in sparse dijs

commit 52e8ab7
Merge: 7ba093f ea37a85
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Tue Mar 15 17:04:13 2022 +0100

    Merge branch 'dev_varRBErobOpt' of https://github.com/e0404/matRad into pr/537

commit ea37a85
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Tue Mar 15 16:54:20 2022 +0100

    Update tests.yml

    correct for renaming of the test folder in github action

commit 7ba093f
Merge: c30930e 19ed7f6
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Tue Mar 15 16:49:52 2022 +0100

    Merge branch 'dev_varRBErobOpt' of https://github.com/e0404/matRad into pr/537

commit 19ed7f6
Merge: 2101d8f 4d28380
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Tue Mar 15 12:29:33 2022 +0100

    Merge remote-tracking branch 'origin/dev' into dev_varRBErobOpt

    # Conflicts:
    #	AUTHORS.txt
    #	MatRad_Config.m
    #	dicom/hlutLibrary/matRad_default.hlut
    #	dicom/matRad_convRtssContours2Indices.m
    #	examples/matRad_example6_protonsNoise.m
    #	matRad_calcDoseInitBeam.m
    #	matRad_calcParticleDose.m
    #	matRad_calcPhotonDose.m
    #	matRad_fluenceOptimization.m
    #	matRad_setOverlapPriorities.m

commit e0ffefe
Merge: c3844c3 c935518
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Wed Jan 19 14:29:48 2022 +0100

    Merge branch 'dev' of https://github.com/e0404/matRad into dev_varRBErobOpt

    # Conflicts:
    #	AUTHORS.txt
    #	MatRad_Config.m
    #	dicom/hlutLibrary/matRad_default.hlut
    #	examples/matRad_example6_protonsNoise.m
    #	matRad_calcDoseInitBeam.m
    #	matRad_calcParticleDose.m
    #	matRad_calcPhotonDose.m
    #	matRad_fluenceOptimization.m
    #	matRad_setOverlapPriorities.m

commit 4d28380
Author: Niklas Wahl <niklaswahl2011@gmail.com>
Date:   Thu Jan 20 16:46:44 2022 +0100

    Octave compatibility

commit c93f2c4
Author: Niklas Wahl <niklaswahl2011@gmail.com>
Date:   Thu Jan 20 15:42:18 2022 +0100

    matRad_importDicom does not any longer require interactive input to save the files, which is now handled from the GUI callback

commit 87891d5
Author: Niklas Wahl <niklaswahl2011@gmail.com>
Date:   Wed Jan 19 15:56:34 2022 +0100

    fine-sampling fix to always select correct number of sub-pencils

commit c3844c3
Merge: 42d4497 2101d8f
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Wed Jan 19 12:05:35 2022 +0100

    Merge branch 'dev_varRBErobOpt' of https://github.com/e0404/matRad into dev_varRBErobOpt

commit 42d4497
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Wed Jan 19 12:05:26 2022 +0100

    some fixes regarding x/y permutation in coordinates

commit 885aad5
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Wed Jan 19 12:04:49 2022 +0100

    fix when automatically setting the isocenter

commit 9cfba69
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Wed Jan 19 12:04:24 2022 +0100

    turn the biological model restrictions into a warning

commit 0c2c99d
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Wed Jan 19 12:03:37 2022 +0100

    helium adaptations

commit d5418d7
Author: Niklas Wahl <niklaswahl2011@gmail.com>
Date:   Fri Dec 17 14:12:22 2021 +0100

    make mean dose objective downwards compatible

commit 5d3b276
Author: Niklas Wahl <niklaswahl2011@gmail.com>
Date:   Fri Dec 17 13:20:34 2021 +0100

    better checking of DICOM RTstruct import problems

commit c30930e
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Tue Dec 7 04:56:13 2021 +0100

    Tool update:
    1. spotRemoval function which removes spots with weights under a certain threshold (especially useful for TOPAS)
    2. calculateAlphaBeta function to calculate proton alpha/beta dose curves for the baseData

commit 2101d8f
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Mon Dec 6 11:32:28 2021 +0100

    Update matRad_convRtssContours2Indices.m

    Add more sophisticated sanity checks during contour voxelization

commit 7c187f8
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Mon Dec 6 11:29:59 2021 +0100

    Update matRad_importDicom.m

    Structures that have errors during voxelization are skipped with a warning

commit c935518
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Dec 3 13:51:33 2021 +0100

    Update tests.yml

commit 82fac50
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Dec 3 13:36:28 2021 +0100

    Warning instead of error in case of objetive overlap

commit d639421
Merge: de4e6e1 dcded21
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Thu Dec 2 12:07:38 2021 +0100

    Merge pull request e0404#531 from wahln/dev_varRBErobOpt

    dev_varRBErobOpt MC update

commit dcded21
Merge: 02cfee9 14f585f
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Thu Dec 2 11:57:52 2021 +0100

    Merge branch 'dev_MonteCarlo' of https://github.com/e0404/matRad into dev_varRBErobOpt

    # Conflicts:
    #	MatRad_Config.m
    #	examples/matRad_example12_simpleParticleMonteCarlo.m
    #	matRad_calcParticleDoseMCsquare.m
    #	matRad_calcParticleDoseMCtopas.m

commit 02cfee9
Merge: 2b2cd50 de4e6e1
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Tue Nov 30 13:34:33 2021 +0100

    Merge branch 'dev_varRBErobOpt' of https://github.com/e0404/matRad into dev_varRBErobOpt

commit 50145f0
Author: Niklas Wahl <niklaswahl2011@gmail.com>
Date:   Fri Nov 19 16:22:50 2021 +0100

    fixing required transpose when calling interpn for octave in photon dose calculation

commit 8740668
Author: Niklas Wahl <niklaswahl2011@gmail.com>
Date:   Fri Nov 19 12:40:32 2021 +0100

    GUI now also works when cst has only 6 columns

commit d08fe1d
Merge: dbef217 f16fce3
Author: Niklas Wahl <niklaswahl2011@gmail.com>
Date:   Thu Nov 11 13:49:39 2021 +0100

    Merge branch 'dev_optimizer' into dev

commit f16fce3
Author: Niklas Wahl <niklaswahl2011@gmail.com>
Date:   Thu Nov 11 13:49:01 2021 +0100

    enable passing of initial fluence to fluence optimization

commit 97fcec6
Author: Niklas Wahl <niklaswahl2011@gmail.com>
Date:   Thu Nov 11 13:46:52 2021 +0100

    stricter IPOPT tolerances to avoid early stopping in constrained problems

commit d344dad
Merge: 041066f dbef217
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Thu Nov 4 16:46:45 2021 +0100

    Merge branch 'dev' of https://github.com/e0404/matRad into dev

    # Conflicts:
    #	MatRad_Config.m
    #	matRad_rc.m

commit dbef217
Author: Niklas Wahl <niklaswahl2011@gmail.com>
Date:   Fri Sep 17 17:15:53 2021 +0200

    issue with the finesampling query in doseinit resolved

commit 658b390
Author: Niklas Wahl <niklaswahl2011@gmail.com>
Date:   Fri Sep 17 17:15:30 2021 +0200

    fixing a problem with the constant matRadRoot property in the config class

commit a97b6be
Author: Niklas Wahl <niklaswahl2011@gmail.com>
Date:   Fri Sep 17 17:15:03 2021 +0200

    the mean dose objective has now the option to choose optimization of a linear or quadratic difference to a reference value

commit 1db68c1
Author: Niklas Wahl <niklaswahl2011@gmail.com>
Date:   Fri Sep 17 14:19:59 2021 +0200

    using interpn for octave in the photon dose calculation significantly boosts performance

commit 11759ed
Merge: 8d68676 3d29b76
Author: Niklas Wahl <niklaswahl2011@gmail.com>
Date:   Thu Sep 9 11:22:19 2021 +0200

    Merge branch 'master' of https://github.com/e0404/matRad into dev

    # Conflicts:
    #	AUTHORS.txt

commit de4e6e1
Merge: 03f6059 3ecd6dd
Author: Niklas Wahl <niklaswahl2011@gmail.com>
Date:   Fri Sep 3 14:19:36 2021 +0200

    Merge branch 'dev_varRBErobOpt' of https://github.com/e0404/matRad into becker89/dev_varRBErobOpt

commit 03f6059
Merge: 27b2fe4 d36d48f
Author: Niklas Wahl <niklaswahl2011@gmail.com>
Date:   Fri Sep 3 13:32:07 2021 +0200

    Merge branch 'dev_varRBErobOpt' into becker89/dev_varRBErobOpt

    # Conflicts:
    #	optimization/@matRad_OptimizationProblem/matRad_constraintFunctions.m
    #	optimization/@matRad_OptimizationProblem/matRad_objectiveFunction.m
    #	optimization/@matRad_OptimizationProblem/matRad_objectiveGradient.m

commit 3ecd6dd
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Thu Aug 5 10:55:46 2021 +0200

    Update matRad_OptimizationProblem.m

    Added references to the logsumexp & pNorm implementation

commit 3d29b76
Merge: b478ede be8b2bf
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Jul 9 12:57:49 2021 +0200

    Merge pull request e0404#506 from e0404/hotfixes/daoWithConstraints

    Fix Direct Aperture Optimization with Constraints

commit be8b2bf
Merge: 62c825e b478ede
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Jul 9 12:05:22 2021 +0200

    Merge branch 'master' into hotfixes/daoWithConstraints

commit b478ede
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Jul 9 12:05:06 2021 +0200

    Migrate from TravisCI to GitHub actions (e0404#514)

    * create github action for testing

    * Update tests.yml

    * change permissions for linux MCsquare within git directly

    * Update tests.yml

    Add Octave Testing

    * Update tests.yml

    Headless tests with respective GitHub Action

    * Update tests.yml

    Some streamlining and Artifact Upload on failure for Octave tests

commit 2b2cd50
Merge: 205735a d36d48f
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Tue Jun 8 15:18:01 2021 +0200

    Merge branch 'dev_varRBErobOpt' of https://github.com/e0404/matRad into dev_varRBErobOpt

commit 8d68676
Merge: f127db4 677dd90
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Mon Jun 7 10:57:42 2021 +0200

    Merge pull request e0404#509 from NathanKunz/dev_refactorDosisCalc

    Fix for issue e0404#503 in dicom import and small change in the liver.mat file for e0404#501

commit d36d48f
Author: Niklas Wahl <niklaswahl2011@gmail.com>
Date:   Fri May 21 15:00:12 2021 +0200

    fixed and cleaned up logsumexp gradients and added the possibility to use the pNorm instead in matRad_OptimizationProblem

commit f127db4
Merge: 27a1aef 223fbc9
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Mon May 17 09:32:31 2021 +0200

    Merge pull request e0404#511 from NathanKunz/dev_exportDij_new

    Dev export dij new, second pull request

commit 223fbc9
Author: NathanKunz <nathan9kunz@gmail.com>
Date:   Fri May 14 16:45:04 2021 +0200

    Added parent folder to export and fixed exception handling in octave

commit d73e58b
Author: NathanKunz <nathan9kunz@gmail.com>
Date:   Fri May 14 10:43:49 2021 +0200

    Update matRad_exportDij fix Octave string concat problem

    Fix for Octave compatibility by changing the string concatenation in matRad_exportDij.
    Possible fix for the not successful check in PR e0404#407

commit d14b334
Merge: 6fad1b8 9cd1602
Author: NathanKunz <nathan9kunz@gmail.com>
Date:   Wed May 12 16:04:13 2021 +0200

    Merge branch 'dev_exportDij_new' of https://github.com/acsevillam/matRad into dev_exportDij_new
    Bug fix for dij export

commit 677dd90
Author: NathanKunz <nathan9kunz@gmail.com>
Date:   Wed May 5 16:55:09 2021 +0200

    Second fix e0404#503

    Made it so the interpolation is essential when a grid is present.

commit 6ce1e78
Author: NathanKunz <nathan9kunz@gmail.com>
Date:   Tue May 4 14:40:44 2021 +0200

    Removed forgotten test code

commit 7112876
Author: NathanKunz <nathan9kunz@gmail.com>
Date:   Mon May 3 16:28:43 2021 +0200

    First fix for e0404#503 (without any GUI changes)

    Possible fix for issue e0404#503, by skipping the interpolation, if the given resolution and the original resolution are the same (considering an acceptance of 1e^-6).

    Possible still existing problem in matRad_interpDicomCube() with the permutation of the ct cube.

    Also fix for the rounding issue in the scan Dicom import.

commit 62c825e
Merge: fe1d7e7 8669892
Author: Niklas Wahl <niklaswahl2011@gmail.com>
Date:   Mon May 3 14:32:16 2021 +0200

    Merge branch 'hotfixes/daoWithConstraints' of https://github.com/e0404/matRad into hotfixes/daoWithConstraints

commit fe1d7e7
Author: Niklas Wahl <niklaswahl2011@gmail.com>
Date:   Mon May 3 14:31:06 2021 +0200

    improve performance by only converting shape info when necessary

commit 8669892
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Apr 30 18:06:15 2021 +0200

    explicit counter setting for better readability

commit 6763859
Author: Niklas Wahl <niklaswahl2011@gmail.com>
Date:   Fri Apr 30 16:54:47 2021 +0200

    Fix correct jacobian structure computation for DAO with constraints
    Fix dosimetric constraint function computation

commit ca94c5b
Author: NathanKunz <nathan9kunz@gmail.com>
Date:   Thu Apr 29 12:08:21 2021 +0200

    Update LIVER.mat for issue e0404#501

commit 27a1aef
Merge: f40c903 b1816ea
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Wed Apr 21 10:50:49 2021 +0200

    Merge pull request e0404#498 from NathanKunz/dev_refactorDosisCalc

    Fix for MatRad_Config downwards compatibility issue

commit 0efba94
Merge: d0b59e6 972b6d5
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Wed Apr 21 10:48:56 2021 +0200

    Merge pull request e0404#504 from naninano1/patch-1

    Update AUTHORS.txt

commit 972b6d5
Merge: fd13c0f d0b59e6
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Tue Apr 20 21:22:34 2021 +0200

    Merge branch 'master' into patch-1

commit d0b59e6
Merge: d10fb18 4e33ec1
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Tue Apr 20 21:21:37 2021 +0200

    Merge pull request e0404#505 from naninano1/patch-2

    Update matRad_MeanDose.m

commit 4e33ec1
Author: Navid Khaledi <77858420+naninano1@users.noreply.github.com>
Date:   Tue Apr 20 20:33:21 2021 +0430

    Update matRad_MeanDose.m

    Oh, so sorry. I thought you applied the change.
    Thank you.

commit fd13c0f
Author: Navid Khaledi <77858420+naninano1@users.noreply.github.com>
Date:   Tue Apr 20 19:10:43 2021 +0430

    Update AUTHORS.txt

commit b1816ea
Author: NathanKunz <nathan9kunz@gmail.com>
Date:   Thu Apr 1 18:28:19 2021 +0200

    Added my name to the authors list

commit d10fb18
Merge: 6fad1b8 803d0de
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Thu Apr 1 17:15:01 2021 +0200

    Merge pull request e0404#492 from e0404/master_hotfixEffectiveCutoff

    Fix issue with effective lateral cutoff for large photon fields

commit 8fbf0c0
Author: NathanKunz <nathan9kunz@gmail.com>
Date:   Thu Apr 1 14:04:03 2021 +0200

    Fix in MatRad_Config for Octave compatibility

commit c4c9416
Author: NathanKunz <nathan9kunz@gmail.com>
Date:   Tue Mar 30 15:52:07 2021 +0200

    Typo fix

commit c4954c3
Author: NathanKunz <nathan9kunz@gmail.com>
Date:   Fri Mar 26 12:07:16 2021 +0100

    Overload loadobj function of MatRad_Config for issue e0404#496

commit e07b2a2
Author: Niklas Wahl <niklaswahl2011@gmail.com>
Date:   Fri Mar 19 15:00:29 2021 +0100

    fix bug in LET reshaping due to reshape not supporting sparse arrays

commit 430462e
Author: Niklas Wahl <niklaswahl2011@gmail.com>
Date:   Fri Mar 19 13:59:06 2021 +0100

    more accurate gradients in robust optimization using logSumExp approximations for minimax optimization

commit 803d0de
Author: Niklas Wahl <niklaswahl2011@gmail.com>
Date:   Fri Mar 19 10:36:00 2021 +0100

    separate kernel cutoff from geometric lateral cutoff for large field accuracy

commit 14f585f
Author: Niklas Wahl <niklaswahl2011@gmail.com>
Date:   Thu Mar 11 12:23:42 2021 +0100

    add configuration possibilities. Add Material Conversions HUSchneider & HUSchneiderDensity

commit 7c6f3c2
Author: Niklas Wahl <niklaswahl2011@gmail.com>
Date:   Wed Mar 10 18:25:20 2021 +0100

    commit allow range shifters within topas

commit c51cd4b
Author: Niklas Wahl <niklaswahl2011@gmail.com>
Date:   Wed Mar 10 18:21:56 2021 +0100

    replace readHLUT with loadHLUT for automatic HLUT detection

commit f40c903
Merge: 0bc706d 863e5c2
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Feb 26 16:09:55 2021 +0100

    Merge pull request e0404#466 from pamede/dev_fineSamplingNoHistory

    Fine sampling via russo and fitted splitting

commit 863e5c2
Author: pamede <p.meder@protonmail.com>
Date:   Fri Feb 26 11:02:45 2021 +0100

    moved initial sigma calculation, restructured LET if statement

commit 93999fc
Merge: d735566 2317d73
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Thu Feb 25 23:44:50 2021 +0100

    Merge pull request e0404#494 from pamede/dev_MCtmp

    fixed typo in MC example

commit 2317d73
Author: pamede <p.meder@protonmail.com>
Date:   Tue Feb 23 10:41:14 2021 +0100

    fixed typo in MC example

commit ad3f94e
Author: pamede <p.meder@protonmail.com>
Date:   Mon Feb 22 11:21:01 2021 +0100

    added documentaiton errors and implemented slightly faster calGeoDist calculation

commit 9dc5973
Author: Niklas Wahl <niklaswahl2011@gmail.com>
Date:   Mon Feb 22 00:18:09 2021 +0100

    fix in photon dose calculation to consider quadratic field shape in effictive cutoff computation (and some comment spelling errors fixed)

commit 0bc706d
Author: Niklas Wahl <niklaswahl2011@gmail.com>
Date:   Fri Feb 19 11:08:26 2021 +0100

    Fix the SFUD optimization wrapper function for new pln and cst format.

commit dcda4f7
Author: pamede <p.meder@protonmail.com>
Date:   Thu Feb 18 12:02:54 2021 +0100

    implemented requested changes, now using matRad_calcSigmaIni in particle dose calculation

commit f0ad671
Merge: 16af573 34e0608
Author: Niklas Wahl <niklaswahl2011@gmail.com>
Date:   Wed Feb 17 15:04:48 2021 +0100

    Merge branch 'dev_varRBErobOpt' of https://github.com/e0404/matRad into dev_varRBErobOpt

    # Conflicts:
    #	phantoms/ALDERSON.mat

commit d735566
Merge: 3eec663 d9a1199
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Mon Feb 8 14:38:28 2021 +0100

    Merge pull request e0404#485 from burigolucas/dev_MonteCarlo

    Refactor HU to material conversion

commit 5af6d5b
Author: pamede <p.meder@protonmail.com>
Date:   Wed Feb 3 14:23:00 2021 +0100

    fixed error in initial sigma calculation with octave, updated example 6 to include direct particle dose calculation via fine sampling

commit 00124b5
Author: pamede <p.meder@protonmail.com>
Date:   Mon Feb 1 19:05:12 2021 +0100

    deleted fine sampling example script 8

commit 4fa2394
Author: pamede <p.meder@protonmail.com>
Date:   Mon Feb 1 18:48:36 2021 +0100

    implemented most requested changes, restructured example to be included in example proton noise

commit d9a1199
Author: Lucas Norberto Burigo <burigolucas@gmail.com>
Date:   Sat Jan 30 03:24:09 2021 +0100

    Add option for TOPAS RSP conversion method

commit dc86a85
Author: Lucas Norberto Burigo <burigolucas@gmail.com>
Date:   Sat Jan 30 03:22:39 2021 +0100

    Refactor HU to RSP conversion for TOPAS

commit e72651c
Author: Lucas Norberto Burigo <burigolucas@gmail.com>
Date:   Fri Jan 29 23:46:45 2021 +0100

    Redefine default matRad scanner for MCsquare

commit 36604cb
Author: Lucas Norberto Burigo <burigolucas@gmail.com>
Date:   Fri Jan 29 23:35:28 2021 +0100

    Redifine HU to SPR conversion for MCsquare

commit 449a49f
Merge: b2f2c4c 3eec663
Author: Lucas Norberto Burigo <burigolucas@gmail.com>
Date:   Fri Jan 29 09:44:44 2021 +0100

    Merge remote-tracking branch 'upstream/dev_MonteCarlo' into dev_MonteCarlo

commit 3eec663
Merge: b2f2c4c 734c16c
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Mon Jan 25 14:02:26 2021 +0100

    Merge pull request e0404#483 from AdmiralHomes/dev_MonteCarlo_Master

    TOPAS: added error message for insufficient number of histories

commit 734c16c
Author: homolka <n.homolka@dkfz.de>
Date:   Mon Jan 25 13:30:07 2021 +0100

    TOPAS: added error message for insufficient number of histories, where the code was stuck in a while loop.

commit 34e0608
Merge: afed8b6 98a640e
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Wed Jan 20 17:51:20 2021 +0100

    Merge pull request e0404#480 from pamede/dev_varRBErobOptUpdate

    Merge master into dev_MonteCarlo into dev_varRBErobOpt

commit b2f2c4c
Merge: 93098f2 492888e
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Wed Jan 20 17:49:58 2021 +0100

    Merge pull request e0404#479 from pamede/dev_MonteCarloUpdate

    Merged master into dev_MonteCarlo and updated submodule

commit 98a640e
Merge: afed8b6 492888e
Author: pamede <p.meder@protonmail.com>
Date:   Wed Jan 20 17:34:44 2021 +0100

    Merge branch 'master' into 'dev_MonteCarlo' into dev_varRBErobOpt  # Conflicts: phantoms/ALDERSON.mat

commit 492888e
Merge: 93098f2 6fad1b8
Author: pamede <p.meder@protonmail.com>
Date:   Wed Jan 20 17:15:08 2021 +0100

    Merge branch 'master' of https://github.com/e0404/matRad into dev_MonteCarlo

commit afed8b6
Merge: c722e12 84fb247
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Mon Jan 11 11:33:34 2021 +0100

    Merge pull request e0404#425 from amitantony/dev_varRBErobOpt

    reshape LET cube to dose grid Correction in CalcCubes

commit 6fad1b8
Merge: d930c3e 5a0db2c
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Mon Dec 28 15:02:49 2020 +0100

    Merge pull request e0404#467 from e0404/dev_siggelRef

    include a download link to martin siggels thesis

commit 27b2fe4
Author: Hans-Peter Wieser <h.wieser@dkfz-heidelberg.de>
Date:   Fri Dec 18 08:16:33 2020 +0100

    added helium base data set

commit 0c6106b
Merge: 3ab98e2 c722e12
Author: Hans-Peter Wieser <h.wieser@dkfz-heidelberg.de>
Date:   Fri Dec 18 08:12:47 2020 +0100

    Merge commit 'c722e1243453b2fbf1e2faeffdf3dc03e2e64c27' into dev_varRBErobOpt

commit 16af573
Merge: c722e12 d930c3e
Author: Niklas Wahl <niklaswahl2011@gmail.com>
Date:   Fri Dec 11 18:12:30 2020 +0100

    Merge branch 'master' of https://github.com/e0404/matRad into dev_varRBErobOpt

    # Conflicts:
    #	phantoms/ALDERSON.mat

commit c722e12
Author: Niklas Wahl <niklaswahl2011@gmail.com>
Date:   Thu Dec 10 00:38:19 2020 +0100

    fix scenForProb in scenario permuted combiantion

commit f9d4786
Author: Niklas Wahl <niklaswahl2011@gmail.com>
Date:   Thu Dec 10 00:29:42 2020 +0100

    fixes sorting error in multScen.scenForProb

commit 3ab98e2
Author: Hans-Peter Wieser <h.wieser@dkfz-heidelberg.de>
Date:   Fri Dec 4 09:38:19 2020 +0100

    modified robust example

    beam doses should only be calcualted for the nominal scenario

commit ce6c954
Author: Hans-Peter Wieser <h.wieser@dkfz-heidelberg.de>
Date:   Fri Dec 4 08:55:04 2020 +0100

    continued on robust optimization techquines
    Still to be done:
    check PROB optimizaiton
    check OWC optimization
    check constraint implementaion

commit 76a2215
Author: pamede <p.meder@protonmail.com>
Date:   Thu Dec 3 22:02:11 2020 +0100

    reset unwanted changes in proton Monte Carlo dose calculation

commit 5a0db2c
Author: TURING\localbangertm <markbangert@gmail.com>
Date:   Thu Dec 3 20:48:15 2020 +0100

    include a download link to martin siggels thesis

commit 4de3ae1
Author: pamede <p.meder@protonmail.com>
Date:   Thu Dec 3 19:25:09 2020 +0100

    implemented fine sampling via russo and fitted splitting

commit 4c987aa
Merge: 52e1d08 1d2bc93
Author: Hans-Peter Wieser <h.wieser@dkfz-heidelberg.de>
Date:   Thu Dec 3 15:12:53 2020 +0100

    Merge commit  dev into dev_varRBErobOpt

commit 93098f2
Merge: 00f9a6c f11c42f
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Mon Nov 23 16:01:49 2020 +0100

    Merge pull request e0404#465 from pamede/dev_MonteCarlo

    Machine saving error

commit f11c42f
Author: pamede <p.meder@protonmail.com>
Date:   Mon Nov 23 15:28:49 2020 +0100

    fixed error of missing bioParam field in matRad_compareDose

commit 29e1f86
Author: pamede <p.meder@protonmail.com>
Date:   Mon Nov 23 15:23:43 2020 +0100

    Revert "automatic figure naming in matRad_compareDose"

    This reverts commit 8c3cf71.

commit 946c025
Author: pamede <p.meder@protonmail.com>
Date:   Mon Nov 23 13:55:21 2020 +0100

    fixed error in saving of matRad machine that contains Monte Carlo data, added name in AUTHORS

commit d930c3e
Merge: e3126c5 1d2bc93
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Nov 20 13:40:06 2020 +0100

    Merge pull request e0404#461 from e0404/rc/v2.10.1

    1st Patch Release for Blaise - v2.10.1

commit 1d2bc93
Author: Niklas Wahl <niklaswahl2011@gmail.com>
Date:   Fri Nov 20 11:27:45 2020 +0100

    update icons

commit c925765
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Thu Nov 19 16:29:19 2020 +0100

    fix in standalone computation

commit 641fc81
Merge: 8c3cf71 00f9a6c
Author: pamede <p.meder@protonmail.com>
Date:   Thu Nov 19 12:32:17 2020 +0100

    Merge branch 'dev_MonteCarlo' of https://github.com/e0404/matRad into dev_MonteCarlo

commit 205735a
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Tue Nov 17 14:24:10 2020 +0100

    small typo in VWWC objective

commit 3051d07
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Tue Nov 17 14:23:34 2020 +0100

    fix multScen when using zero set-up uncertainty

commit adb1c66
Author: Niklas Wahl <niklaswahl2011@gmail.com>
Date:   Wed Nov 11 14:21:51 2020 +0100

    fix str2double in string parsing in GUI

commit 52e1d08
Author: Niklas Wahl <niklaswahl2011@gmail.com>
Date:   Wed Nov 11 12:51:55 2020 +0100

    fix issue in dij filling

commit cda4ac1
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Tue Nov 10 17:05:12 2020 +0100

    update standalone compilation

commit 8667d30
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Tue Nov 10 16:30:43 2020 +0100

    Configuration update

commit 42ae9e4
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Tue Nov 10 16:30:08 2020 +0100

    Update of standalone prj file.

commit ac6eda2
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Tue Nov 10 16:27:10 2020 +0100

    remove ALDERSON phantom

commit 5636d92
Author: Niklas Wahl <niklaswahl2011@gmail.com>
Date:   Mon Nov 9 16:19:21 2020 +0100

    Better checking of weight vectors when triggering recalc from GUI (fixes e0404#381)

commit 2ff35f9
Author: Niklas Wahl <niklaswahl2011@gmail.com>
Date:   Mon Nov 9 15:32:21 2020 +0100

    fixing issues with setting "field" for bixel Width in GUI (Github Issue e0404#369)

commit cacbada
Merge: b13b4e1 55c0ba5
Author: Niklas Wahl <niklaswahl2011@gmail.com>
Date:   Mon Nov 9 10:34:42 2020 +0100

    Merge branch 'dev' into rc/v2.10.1

commit 55c0ba5
Author: Niklas Wahl <niklaswahl2011@gmail.com>
Date:   Mon Nov 9 10:34:08 2020 +0100

    fix indicator interface

commit b13b4e1
Author: Niklas Wahl <niklaswahl2011@gmail.com>
Date:   Thu Nov 5 16:44:07 2020 +0100

    Change version number

commit bd891b6
Author: Niklas Wahl <niklaswahl2011@gmail.com>
Date:   Thu Nov 5 14:26:34 2020 +0100

    update readme (Zenodo DOIs) [skip ci]

commit 8910424
Author: Niklas Wahl <niklaswahl2011@gmail.com>
Date:   Thu Nov 5 13:03:02 2020 +0100

    Update Readme

commit 1f32d39
Author: Niklas Wahl <niklaswahl2011@gmail.com>
Date:   Thu Nov 5 12:35:58 2020 +0100

    update to changelog and fix documentation in compareDose

commit 8c11f04
Merge: e01a5dc df2da63
Author: Niklas Wahl <niklaswahl2011@gmail.com>
Date:   Thu Nov 5 12:13:46 2020 +0100

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

commit 041066f
Merge: 3164533 a0564e7
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Tue Nov 3 11:21:19 2020 +0100

    Merge branch 'dev' of https://github.com/e0404/matRad into dev

    # Conflicts:
    #	MatRad_Config.m

commit e01a5dc
Merge: 81aec44 fa0cf44
Author: Niklas Wahl <niklaswahl2011@gmail.com>
Date:   Wed Oct 28 11:57:29 2020 +0100

    Merge branch 'dev' into rc/v2.10.1

commit 81aec44
Merge: 4460ef2 6fff2cb
Author: Niklas Wahl <niklaswahl2011@gmail.com>
Date:   Fri Oct 23 15:05:13 2020 +0200

    Merge branch 'dev' into rc/v2.10.1

commit 4460ef2
Merge: 480e148 99ffcc9
Author: Niklas Wahl <niklaswahl2011@gmail.com>
Date:   Tue Oct 20 19:11:22 2020 +0200

    Merge branch 'dev' into rc/v2.10.1

commit 480e148
Merge: 522aa4f 2ac0946
Author: Niklas Wahl <niklaswahl2011@gmail.com>
Date:   Tue Oct 20 14:45:10 2020 +0200

    Merge branch 'dev' into rc/v2.10.1

commit 522aa4f
Merge: b6d7714 0505046
Author: Niklas Wahl <niklaswahl2011@gmail.com>
Date:   Fri Oct 16 10:43:51 2020 +0200

    Merge branch 'dev' into rc/v2.10.1

commit b6d7714
Merge: 95b7324 04b0875
Author: Niklas Wahl <niklaswahl2011@gmail.com>
Date:   Thu Oct 15 19:50:41 2020 +0200

    Merge branch 'dev' into rc/v2.10.1

commit 95b7324
Merge: 1cda2d7 6880d54
Author: Niklas Wahl <niklaswahl2011@gmail.com>
Date:   Fri Oct 9 19:40:59 2020 +0200

    Merge branch 'dev' into rc/v2.10.1

commit 1cda2d7
Merge: 6872f05 65fcdd4
Author: Niklas Wahl <niklaswahl2011@gmail.com>
Date:   Fri Oct 9 18:04:24 2020 +0200

    Merge branch 'dev' into rc/v2.10.1

commit 6872f05
Author: Niklas Wahl <niklaswahl2011@gmail.com>
Date:   Fri Sep 25 17:28:45 2020 +0200

    update changelog

commit 3164533
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Wed Aug 26 14:35:24 2020 +0200

    reduce possibility of conflict between multiple matRad instances

commit 8c3cf71
Author: nhomolka <n.homolka@dkfz.de>
Date:   Thu Jul 16 16:00:31 2020 +0200

    automatic figure naming in matRad_compareDose

commit 84fb247
Author: abennan <a.bennan@dkfz-heidelberg.de>
Date:   Thu Jun 25 15:52:48 2020 +0200

    reshape LET cube to dose grid Correction in CalcCubes

commit 9cd1602
Author: Camilo Sevilla <acsevillam@unal.edu.co>
Date:   Fri Mar 13 10:21:05 2020 -0300

    Include export dij function in example1

commit 548aa97
Author: Camilo Sevilla <acsevillam@unal.edu.co>
Date:   Thu Mar 12 21:24:06 2020 -0300

    added export dij function
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40 changes: 40 additions & 0 deletions .github/workflows/tests.yml
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@@ -0,0 +1,40 @@
# This is a basic workflow to help you get started with Actions
name: Tests
# Controls when the action will run.
on: [push, pull_request, workflow_dispatch]
jobs:
test-matlab: #Matlab test Job
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2 # Checks-out repository under $GITHUB_WORKSPACE
# Install MATLAB
- name: Install MATLAB
uses: matlab-actions/setup-matlab@v1
# Runs test command
- name: Run Tests
uses: matlab-actions/run-command@v1
with:
command: cd test; matRad_runTests
test-octave: #Octave test Job
runs-on: ubuntu-20.04 # We use Ubuntu-20.04 because it has Octave 5.2
steps:
- uses: actions/checkout@v2 # 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
if: failure()
with:
name: Test Log
path: runtests.log

5 changes: 5 additions & 0 deletions AUTHORS.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -14,15 +14,20 @@ List of all matRad developers that contributed code (alphabetical)
* Cindy Hermann
* Noa Homolka
* Fabian Jäger
* Navid Khaledi
* Thomas Klinge
* Jeremias Kunz
* Paul Anton Meder
* Henning Mescher
* Lucas-Raphael Müller
* Ahmad Neishabouri
* Martina Palkowitsch
* Giuseppe Pezzano
* Daniel Ramirez
* Carsten Scholz
* Camilo Sevilla
* Alexander Stadler
* Uwe Titt
* Niklas Wahl
* Jona Welsch
* Hans-Peter Wieser
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123 changes: 123 additions & 0 deletions CITATION.cff
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cff-version: 1.2.0
message: "If you use matRad, consider citing it and the corresponding research paper"
authors:
- family-names: "Ackermann"
given-names: "Benjamin"
- family-names: "Bangert"
given-names: "Mark"
- family-names: "Bennan"
given-names: "Amit Ben Antony"
- family-names: "Burigo"
given-names: "Lucas"
- family-names: "Cabal"
given-names: "Gonzalo"
- family-names: "Cisternas"
given-names: "Eduardo"
- family-names: "Charton"
given-names: "Louis"
- family-names: "Christiansen"
given-names: "Eric"
- family-names: "Ecker"
given-names: "Swantje"
- family-names: "Ellerbrock"
given-names: "Malte"
- family-names: "Gabryś"
given-names: "Hubert"
- family-names: "Handrack"
given-names: "Josefine"
- family-names: "Heath"
given-names: "Emily"
- family-names: "Hermann"
given-names: "Cindy"
- family-names: "Homolka"
given-names: "Noa"
- family-names: "Jäkel"
given-names: "Oliver"
- family-names: "Klinge"
given-names: "Thomas"
- family-names: "Mairani"
given-names: "Andrea"
- family-names: "Mescher"
given-names: "Hennig"
- family-names: "Müller"
given-names: "Lucas-Raphael"
- family-names: "Neishabouri"
given-names: "Ahmad"
- family-names: "Palkowitsch"
given-names: "Martina"
- family-names: "Parodi"
given-names: "Katia"
- family-names: "Pezzano"
given-names: "Giuseppe"
- family-names: "Ramirez"
given-names: "Daniel"
- family-names: "Stadler"
given-names: "Alexander"
- family-names: "Ulrich"
given-names: "Silke"
- family-names: "Wahl"
given-names: "Niklas"
orcid: "https://orcid.org/0000-0002-1451-223X"
- family-names: "Welsch"
given-names: "Jona"
- family-names: "Wieser"
given-names: "Hans-Peter"
- family-names: "Winter"
given-names: "Johanna"
- family-names: "Xu"
given-names: "Tong"

title: "matRad"
version: 2.10.1
doi: 10.5281/zenodo.3879616
date-released: 2020-06-05
url: "http://www.matRad.org"
location: "Heidelberg"
organization: "Deutsches Krebsforschungszentrum"
preferred-citation:
type: article
authors:
- family-names: "Wieser"
given-names: "Hans-Peter"
- family-names: "Cisternas"
given-names: "Eduardo"
- family-names: "Wahl"
given-names: "Niklas"
orcid: "https://orcid.org/0000-0002-1451-223X"
- family-names: "Ulrich"
given-names: "Silke"
- family-names: "Stadler"
given-names: "Alexander"
- family-names: "Mescher"
given-names: "Hennig"
- family-names: "Müller"
given-names: "Lucas-Raphael"
- family-names: "Klinge"
given-names: "Thomas"
- family-names: "Gabryś"
given-names: "Hubert"
- family-names: "Burigo"
given-names: "Lucas"
- family-names: "Mairani"
given-names: "Andrea"
- family-names: "Ecker"
given-names: "Swantje"
- family-names: "Ackermann"
given-names: "Benjamin"
- family-names: "Ellerbrock"
given-names: "Malte"
- family-names: "Parodi"
given-names: "Katia"
- family-names: "Jäkel"
given-names: "Oliver"
- family-names: "Bangert"
given-names: "Mark"

doi: 10.1002/mp.12251
journal: "Medical Physics"
start: 2556
end: 2568
title: "Development of the open-source dose calculation and optimization toolkit matRad"
issue: 6
volume: 46
year: 2017
23 changes: 22 additions & 1 deletion ChangeLog.txt
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Version 2.10.0 "Blaise"
Development Changes
- Bugfixes:
- Fix SFUD wrapper for new pln & cst format

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:
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