Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Fix RTDose import when no RTPlan is imported #574

Merged
merged 1 commit into from
Aug 22, 2022
Merged

Fix RTDose import when no RTPlan is imported #574

merged 1 commit into from
Aug 22, 2022

Conversation

wahln
Copy link
Contributor

@wahln wahln commented Aug 11, 2022

This is a hotfix directly on the master branch. It fixes a bug in the DICOM import (brought up in #558) that, when wanting to import RTDose without an RTPlan, skipped the dose import such that the dose was never imported.

The fix is fairly simple, so I will directly merge this as soon as the checks pass.

@wahln wahln mentioned this pull request Aug 11, 2022
Open
@wahln wahln merged commit 75201fa into master Aug 22, 2022
HomolkaN pushed a commit to HomolkaN/matRad that referenced this pull request Oct 12, 2022
Merge dev_VARBE_MC_Update into dev_VARBE_MC_experimental
da02eae 
commit 3610bf5
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Wed Oct 12 13:57:57 2022 +0200

    Update TopasConfig

    - added output of numOfBixels that did not meet the minimum numOfParticles required
    - removed unnecessary statement regarding alpha beta parameters
    - added comment to externalCalculation

commit 834bb1f
Merge: 19e22df 1b13404
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Wed Oct 5 17:21:33 2022 +0200

    Merge branch 'master' into pr/536

    # Conflicts:
    #	README.md

commit 19e22df
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Wed Oct 5 16:36:42 2022 +0200

    reset to old bixelwidth-dependent dij sampling

commit 1ee132d
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Tue Oct 4 20:31:30 2022 +0200

    Merge dev_varRBErobOpt_experimental

     Important branch Bug Fix:

        - fixed 2 major bugs in matRad_calcCubes!
        - fixed bug in TopasConfig, where the empty preallocated dij field was used to calculate tallies instead of the actual dose
        - made beamSetup more concise with shorter spaces between numbers
        - added fix for selection of focusIndex for generated phaseSpace data
        - changed handling of 0 fields
        - use isprop instead of isfield now that the class system is used
        - removed several statements that are no longer used or required

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 4a3e73a
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Thu Sep 22 21:35:00 2022 +0200

    Update to emittanceBaseData energyspread handling

commit 87bf5fe
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Sep 23 15:25:24 2022 +0200

    Fix indent

commit 37d3c58
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Thu Sep 22 20:53:11 2022 +0200

    Update to matRad_calcCubes.m

    - removed section that added "non-processed MC tallies", not needed anymore
    - removed 2 lines from MCsquare calculation that still referenced the outdated MC_tallies system

commit dc9552e
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Thu Sep 22 13:45:13 2022 +0200

    MC dij update calcDoseDirect

    - renamed topasCubes variable into dij to make it clearer (used to be a relict from deprecated workflow)
    - Brought dij generation of MCsquare and TOPAS in line for calcDoseDirect (all beam/ray/bixel fields are 1)

commit be032cc
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Thu Sep 22 13:42:04 2022 +0200

    bug fix for recent resampling update

    - fixed resampleCTtoGrid function being called incorrectly
    - fixed input

commit 45b6517
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Wed Sep 21 16:44:07 2022 +0200

    Merge dev_varRBErobOpt_experimental -> dev_varRBErobOpt_Update

    Update PR:
    - removed TOPAS scripts
    - added compatibility patch
    - Added patch for fluence Optimization and input of precalculated weigths
    - Added input of LET into calcLQParameter function
    - Moved resampling function from TOPASconfig in general tools
    - made externalCalculation parameter clearer to use and saved folder is output to the console
    -

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 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
HomolkaN pushed a commit to HomolkaN/matRad that referenced this pull request Nov 24, 2022
Merge dev_varRBErobOpt_Update into dev_varRBErobOpt_experimental
4db836f 
commit f1e446a
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Wed Nov 23 18:28:10 2022 +0100

    minor MC workflow fixes

commit 63bb149
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Tue Nov 22 17:02:52 2022 +0100

    small fix wenn getting number of emittance gaussians from the weight array

commit 348ba2f
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Tue Nov 22 16:48:04 2022 +0100

    remove weird slab file in scenarios folder

commit d81012d
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Tue Nov 22 13:43:40 2022 +0100

    make mex file compilation a static function

commit 20626d1
Merge: fcc026f 37d4129
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Tue Nov 22 13:39:35 2022 +0100

    Merge branch 'dev_varRBErobOpt' of https://github.com/e0404/matRad into pr/536

commit fcc026f
Merge: 051dfdb 93571e6
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Tue Nov 22 13:38:33 2022 +0100

    Merge branch 'dev_varRBErobOpt_Update' of https://github.com/HomolkaN/matRad into pr/536

commit 051dfdb
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Tue Nov 22 13:35:52 2022 +0100

    add different SADs for x and y to the base data class

commit 93571e6
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Fri Nov 18 18:00:07 2022 +0100

    Update MatRad_TopasConfig.m

    minor compatibility changes for TOPAS

commit 3355d05
Merge: b6188d1 c8fd302
Author: Hardt <jennifer.hardt@dkfz-heidelberg.de>
Date:   Fri Nov 18 16:45:13 2022 +0100

    Merge branch 'dev_varRBErobOpt_Update' of https://github.com/HomolkaN/matRad into dev_varRBErobOpt_Update

commit b6188d1
Author: Hardt <jennifer.hardt@dkfz-heidelberg.de>
Date:   Fri Nov 18 16:44:30 2022 +0100

    SAD and wsl fix

    SAD was wrong given in cm in header file, and phase space file location is given as a relative path, wsl dosent like the direct path

commit 277fef5
Author: Hardt <jennifer.hardt@dkfz-heidelberg.de>
Date:   Fri Nov 18 16:42:07 2022 +0100

    Phase space file starts at end of colimator

commit 16c9610
Author: Hardt <jennifer.hardt@dkfz-heidelberg.de>
Date:   Fri Nov 18 16:41:46 2022 +0100

    otherwise out and log file are the same file

commit c8fd302
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Fri Nov 18 16:06:14 2022 +0100

    Update matRad_calcPhotonDoseOmpMC.m

    Typo

commit 704d2c0
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Fri Nov 18 14:59:51 2022 +0100

    introduce ompMC class

    This change was done primarily to increase compatibility with the other MonteCarlo changes that have been done, mainly how the MC classes are currently structured and loaded.

commit 926d700
Author: Hardt <jennifer.hardt@dkfz-heidelberg.de>
Date:   Fri Nov 18 10:32:02 2022 +0100

    Update .gitignore

commit 147f058
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Fri Nov 18 10:10:18 2022 +0100

    Update matRad_runTests.m

    added small fix for runTests that couldn't find testing scripts

commit d6fd9f2
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Thu Nov 17 11:55:28 2022 +0100

    Update matRad_runTests.m

    Make sure a failing script does not get stuck in a directory

commit bb40eca
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Mon Nov 14 20:14:14 2022 +0100

    Update MatRad_TopasConfig.m

    Some more octave changes

commit 2f0b541
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Mon Nov 14 17:42:32 2022 +0100

    potential fix for testing

    renamed topas beam setup files to lowercase

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 b08ddc4
Merge: d8588e1 d0e246c
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Oct 28 14:45:19 2022 +0200

    Merge branch 'dev_varRBErobOpt_Update' of https://github.com/HomolkaN/matRad into pr/536

commit d8588e1
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Oct 28 14:44:46 2022 +0200

    change how emittance and energy spectrum should be represented in base data

commit 9b5c17a
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Oct 28 14:43:47 2022 +0200

    some technical fixes

commit ee58c3d
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Oct 28 14:43:23 2022 +0200

    remove the MCsquare MU correction as it is no longer valid

commit d0e246c
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Wed Oct 26 16:59:52 2022 +0200

    adjusted topas calcDose functions

    - streamlined topas photon calcDose function to be in line with newer function for particles
    - orderfields probably does not accept empty variables in older versions of matlab

commit d1c34ab
Merge: fe9adb8 c9d190e
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Wed Oct 26 16:35:33 2022 +0200

    Merge branch 'dev_varRBErobOpt_Update' of https://github.com/HomolkaN/matRad into dev_varRBErobOpt_Update

commit fe9adb8
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Wed Oct 26 16:35:27 2022 +0200

    added default beamProfile for photons

    - default beamProfile for photons in matRad_cfg
    - removed hardcoded beamProfile and numOfRuns in photonDoseMCtopas
    - added check if beam profile is compatible with radiationMode

commit c9d190e
Merge: f328b96 05db32a
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Wed Oct 26 16:00:39 2022 +0200

    Merge branch 'dev_varRBErobOpt' of https://github.com/e0404/matRad into pr/536

    # Conflicts:
    #	matRad_fluenceOptimization.m

commit 0af8238
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Wed Oct 26 15:58:45 2022 +0200

    small update to photons phasespace

    - set phasespace file as changable in config to maybe be implemented as a variable.
    - check is performed to see if phaseSpaceFile is available
    - Info is output if externalCalculation is turned on (manually place phaseSpace file)

commit f328b96
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Wed Oct 26 15:53:20 2022 +0200

    fix props in MatRad_Config

commit 0c2094d
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Tue Oct 25 23:36:24 2022 +0200

    Update TOPAS_beamSetup_Phasespace.txt.in

    - Fix to phaseSpace beamsetup.
    - .pshp file is still missing in order to run this properly

commit 2f53358
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Tue Oct 25 01:58:09 2022 +0200

    Finished merge of TopasConfig_Photons

    - further progression on photons for TOPAS.
    - added phasespace data SIEMENS*.header which is read through beamSetup_phasespace. If the file can be found by TOPAS in the subfolder has to be checked.
    - time feature splitting for dij calculation is turned off for now, this has to be discussed further

commit 93233d1
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Mon Oct 24 22:05:25 2022 +0200

    Update MatRad_Config.m

    disabled ompMC for now and change default photon engine to TOPAS. This can be reverted at a later stage when this is properly implemented.

commit 4b59c62
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Mon Oct 24 18:03:04 2022 +0200

    Merge piastammer/dev_varRBErobOpt_photonsTopas into dev_varRBErobOpt_Update

    This is a preliminary implementation. Next, I will implement this properly into the updated TOPAS structure.

    commit 0b82924
    Author: pia.stammer <pia.stammer@kit.edu>
    Date:   Fri Oct 21 16:09:00 2022 +0200

        Added phase space source
        *need testing!*
        -load phase space from source file SIEMENS_PRIMUS_6.0_0.10_15.0x15.0 available at https://www-nds.iaea.org/phsp/photon/SIEMENS_Primus_6MV/
        -added beamProfile 'phasespace' and appropriate input file
        -no pencil beam scanning supported, only single angle/position atm
        ToDo: Check geometry, especially distances between nozzle, phase space, MLC and patient (surface/isocenter?)

    commit 5ee5467
    Author: Noa Homolka <n.homolka@dkfz.de>
    Date:   Fri Sep 16 17:19:28 2022 +0200

        PhotonTOPAS Update

        - export leafWidth from aperture2collimation
        - small bug with additional "end" fix in ParticleDoseMCtopas
        - added switch for uniform weights in case of ~calcDoseDirect
        - changed materialConversion to 'RSP'
        - renamed numOfLeaves and leafTimes parameters for easier understanding
        - Translated MLC so that the Nozzle lies at beginning of MLC, not centered

    commit d43b80c
    Author: pia.stammer <pia.stammer@kit.edu>
    Date:   Fri Sep 16 14:47:50 2022 +0200

        Reduced size of source, increased number of histories

    commit 9067aa9
    Author: pia.stammer <pia.stammer@kit.edu>
    Date:   Fri Sep 16 11:31:06 2022 +0200

        Add uniform source and rotate MLC

    commit e7031b1
    Author: Noa Homolka <n.homolka@dkfz.de>
    Date:   Fri Sep 16 10:30:36 2022 +0200

        disabled tracking of MCrun folder

    commit 23b517a
    Author: pia.stammer <pia.stammer@kit.edu>
    Date:   Fri Sep 16 09:57:44 2022 +0200

        Status 2nd Hackday: Some corrections, TOPAS runs through, results mediocre

    commit bd68b3b
    Author: pia.stammer <pia.stammer@kit.edu>
    Date:   Fri Jun 10 17:00:17 2022 +0200

        Initial commit: Added MLC shape capabilities for TOPAS
        - shapes generated by matRad_aperture2collimation are written into TOPAS config file
        - use class matRad_TopasConfigPhotons with "virtualGaussian" beam and "mlc" Multileaf collimator set-up if corresponding info exists
        - TOPAS config files for several beams, rays, leafs and shapes are created and run through
        !!Caution: Results not yet validated!!

    commit c6dd0cb
    Author: Niklas Wahl <n.wahl@dkfz.de>
    Date:   Fri Apr 29 09:49:26 2022 +0200

        added basic photon infrastructure

    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 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 3610bf5
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Wed Oct 12 13:57:57 2022 +0200

    Update TopasConfig

    - added output of numOfBixels that did not meet the minimum numOfParticles required
    - removed unnecessary statement regarding alpha beta parameters
    - added comment to externalCalculation

commit 834bb1f
Merge: 19e22df 1b13404
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Wed Oct 5 17:21:33 2022 +0200

    Merge branch 'master' into pr/536

    # Conflicts:
    #	README.md

commit 19e22df
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Wed Oct 5 16:36:42 2022 +0200

    reset to old bixelwidth-dependent dij sampling

commit 1ee132d
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Tue Oct 4 20:31:30 2022 +0200

    Merge dev_varRBErobOpt_experimental

     Important branch Bug Fix:

        - fixed 2 major bugs in matRad_calcCubes!
        - fixed bug in TopasConfig, where the empty preallocated dij field was used to calculate tallies instead of the actual dose
        - made beamSetup more concise with shorter spaces between numbers
        - added fix for selection of focusIndex for generated phaseSpace data
        - changed handling of 0 fields
        - use isprop instead of isfield now that the class system is used
        - removed several statements that are no longer used or required

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 4a3e73a
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Thu Sep 22 21:35:00 2022 +0200

    Update to emittanceBaseData energyspread handling

commit 87bf5fe
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Sep 23 15:25:24 2022 +0200

    Fix indent

commit 37d3c58
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Thu Sep 22 20:53:11 2022 +0200

    Update to matRad_calcCubes.m

    - removed section that added "non-processed MC tallies", not needed anymore
    - removed 2 lines from MCsquare calculation that still referenced the outdated MC_tallies system

commit dc9552e
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Thu Sep 22 13:45:13 2022 +0200

    MC dij update calcDoseDirect

    - renamed topasCubes variable into dij to make it clearer (used to be a relict from deprecated workflow)
    - Brought dij generation of MCsquare and TOPAS in line for calcDoseDirect (all beam/ray/bixel fields are 1)

commit be032cc
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Thu Sep 22 13:42:04 2022 +0200

    bug fix for recent resampling update

    - fixed resampleCTtoGrid function being called incorrectly
    - fixed input

commit 45b6517
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Wed Sep 21 16:44:07 2022 +0200

    Merge dev_varRBErobOpt_experimental -> dev_varRBErobOpt_Update

    Update PR:
    - removed TOPAS scripts
    - added compatibility patch
    - Added patch for fluence Optimization and input of precalculated weigths
    - Added input of LET into calcLQParameter function
    - Moved resampling function from TOPASconfig in general tools
    - made externalCalculation parameter clearer to use and saved folder is output to the console
    -

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 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 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 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
HomolkaN pushed a commit to HomolkaN/matRad that referenced this pull request Nov 24, 2022
Squashed commit of the following:
adf1aa8 
commit f1e446a
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Wed Nov 23 18:28:10 2022 +0100

    minor MC workflow fixes

commit 63bb149
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Tue Nov 22 17:02:52 2022 +0100

    small fix wenn getting number of emittance gaussians from the weight array

commit 348ba2f
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Tue Nov 22 16:48:04 2022 +0100

    remove weird slab file in scenarios folder

commit d81012d
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Tue Nov 22 13:43:40 2022 +0100

    make mex file compilation a static function

commit 20626d1
Merge: fcc026f 37d4129
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Tue Nov 22 13:39:35 2022 +0100

    Merge branch 'dev_varRBErobOpt' of https://github.com/e0404/matRad into pr/536

commit fcc026f
Merge: 051dfdb 93571e6
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Tue Nov 22 13:38:33 2022 +0100

    Merge branch 'dev_varRBErobOpt_Update' of https://github.com/HomolkaN/matRad into pr/536

commit 051dfdb
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Tue Nov 22 13:35:52 2022 +0100

    add different SADs for x and y to the base data class

commit 93571e6
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Fri Nov 18 18:00:07 2022 +0100

    Update MatRad_TopasConfig.m

    minor compatibility changes for TOPAS

commit 3355d05
Merge: b6188d1 c8fd302
Author: Hardt <jennifer.hardt@dkfz-heidelberg.de>
Date:   Fri Nov 18 16:45:13 2022 +0100

    Merge branch 'dev_varRBErobOpt_Update' of https://github.com/HomolkaN/matRad into dev_varRBErobOpt_Update

commit b6188d1
Author: Hardt <jennifer.hardt@dkfz-heidelberg.de>
Date:   Fri Nov 18 16:44:30 2022 +0100

    SAD and wsl fix

    SAD was wrong given in cm in header file, and phase space file location is given as a relative path, wsl dosent like the direct path

commit 277fef5
Author: Hardt <jennifer.hardt@dkfz-heidelberg.de>
Date:   Fri Nov 18 16:42:07 2022 +0100

    Phase space file starts at end of colimator

commit 16c9610
Author: Hardt <jennifer.hardt@dkfz-heidelberg.de>
Date:   Fri Nov 18 16:41:46 2022 +0100

    otherwise out and log file are the same file

commit c8fd302
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Fri Nov 18 16:06:14 2022 +0100

    Update matRad_calcPhotonDoseOmpMC.m

    Typo

commit 704d2c0
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Fri Nov 18 14:59:51 2022 +0100

    introduce ompMC class

    This change was done primarily to increase compatibility with the other MonteCarlo changes that have been done, mainly how the MC classes are currently structured and loaded.

commit 926d700
Author: Hardt <jennifer.hardt@dkfz-heidelberg.de>
Date:   Fri Nov 18 10:32:02 2022 +0100

    Update .gitignore

commit 147f058
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Fri Nov 18 10:10:18 2022 +0100

    Update matRad_runTests.m

    added small fix for runTests that couldn't find testing scripts

commit d6fd9f2
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Thu Nov 17 11:55:28 2022 +0100

    Update matRad_runTests.m

    Make sure a failing script does not get stuck in a directory

commit bb40eca
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Mon Nov 14 20:14:14 2022 +0100

    Update MatRad_TopasConfig.m

    Some more octave changes

commit 2f0b541
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Mon Nov 14 17:42:32 2022 +0100

    potential fix for testing

    renamed topas beam setup files to lowercase

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 b08ddc4
Merge: d8588e1 d0e246c
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Oct 28 14:45:19 2022 +0200

    Merge branch 'dev_varRBErobOpt_Update' of https://github.com/HomolkaN/matRad into pr/536

commit d8588e1
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Oct 28 14:44:46 2022 +0200

    change how emittance and energy spectrum should be represented in base data

commit 9b5c17a
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Oct 28 14:43:47 2022 +0200

    some technical fixes

commit ee58c3d
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Oct 28 14:43:23 2022 +0200

    remove the MCsquare MU correction as it is no longer valid

commit d0e246c
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Wed Oct 26 16:59:52 2022 +0200

    adjusted topas calcDose functions

    - streamlined topas photon calcDose function to be in line with newer function for particles
    - orderfields probably does not accept empty variables in older versions of matlab

commit d1c34ab
Merge: fe9adb8 c9d190e
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Wed Oct 26 16:35:33 2022 +0200

    Merge branch 'dev_varRBErobOpt_Update' of https://github.com/HomolkaN/matRad into dev_varRBErobOpt_Update

commit fe9adb8
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Wed Oct 26 16:35:27 2022 +0200

    added default beamProfile for photons

    - default beamProfile for photons in matRad_cfg
    - removed hardcoded beamProfile and numOfRuns in photonDoseMCtopas
    - added check if beam profile is compatible with radiationMode

commit c9d190e
Merge: f328b96 05db32a
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Wed Oct 26 16:00:39 2022 +0200

    Merge branch 'dev_varRBErobOpt' of https://github.com/e0404/matRad into pr/536

    # Conflicts:
    #	matRad_fluenceOptimization.m

commit 0af8238
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Wed Oct 26 15:58:45 2022 +0200

    small update to photons phasespace

    - set phasespace file as changable in config to maybe be implemented as a variable.
    - check is performed to see if phaseSpaceFile is available
    - Info is output if externalCalculation is turned on (manually place phaseSpace file)

commit f328b96
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Wed Oct 26 15:53:20 2022 +0200

    fix props in MatRad_Config

commit 0c2094d
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Tue Oct 25 23:36:24 2022 +0200

    Update TOPAS_beamSetup_Phasespace.txt.in

    - Fix to phaseSpace beamsetup.
    - .pshp file is still missing in order to run this properly

commit 2f53358
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Tue Oct 25 01:58:09 2022 +0200

    Finished merge of TopasConfig_Photons

    - further progression on photons for TOPAS.
    - added phasespace data SIEMENS*.header which is read through beamSetup_phasespace. If the file can be found by TOPAS in the subfolder has to be checked.
    - time feature splitting for dij calculation is turned off for now, this has to be discussed further

commit 93233d1
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Mon Oct 24 22:05:25 2022 +0200

    Update MatRad_Config.m

    disabled ompMC for now and change default photon engine to TOPAS. This can be reverted at a later stage when this is properly implemented.

commit 4b59c62
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Mon Oct 24 18:03:04 2022 +0200

    Merge piastammer/dev_varRBErobOpt_photonsTopas into dev_varRBErobOpt_Update

    This is a preliminary implementation. Next, I will implement this properly into the updated TOPAS structure.

    commit 0b82924
    Author: pia.stammer <pia.stammer@kit.edu>
    Date:   Fri Oct 21 16:09:00 2022 +0200

        Added phase space source
        *need testing!*
        -load phase space from source file SIEMENS_PRIMUS_6.0_0.10_15.0x15.0 available at https://www-nds.iaea.org/phsp/photon/SIEMENS_Primus_6MV/
        -added beamProfile 'phasespace' and appropriate input file
        -no pencil beam scanning supported, only single angle/position atm
        ToDo: Check geometry, especially distances between nozzle, phase space, MLC and patient (surface/isocenter?)

    commit 5ee5467
    Author: Noa Homolka <n.homolka@dkfz.de>
    Date:   Fri Sep 16 17:19:28 2022 +0200

        PhotonTOPAS Update

        - export leafWidth from aperture2collimation
        - small bug with additional "end" fix in ParticleDoseMCtopas
        - added switch for uniform weights in case of ~calcDoseDirect
        - changed materialConversion to 'RSP'
        - renamed numOfLeaves and leafTimes parameters for easier understanding
        - Translated MLC so that the Nozzle lies at beginning of MLC, not centered

    commit d43b80c
    Author: pia.stammer <pia.stammer@kit.edu>
    Date:   Fri Sep 16 14:47:50 2022 +0200

        Reduced size of source, increased number of histories

    commit 9067aa9
    Author: pia.stammer <pia.stammer@kit.edu>
    Date:   Fri Sep 16 11:31:06 2022 +0200

        Add uniform source and rotate MLC

    commit e7031b1
    Author: Noa Homolka <n.homolka@dkfz.de>
    Date:   Fri Sep 16 10:30:36 2022 +0200

        disabled tracking of MCrun folder

    commit 23b517a
    Author: pia.stammer <pia.stammer@kit.edu>
    Date:   Fri Sep 16 09:57:44 2022 +0200

        Status 2nd Hackday: Some corrections, TOPAS runs through, results mediocre

    commit bd68b3b
    Author: pia.stammer <pia.stammer@kit.edu>
    Date:   Fri Jun 10 17:00:17 2022 +0200

        Initial commit: Added MLC shape capabilities for TOPAS
        - shapes generated by matRad_aperture2collimation are written into TOPAS config file
        - use class matRad_TopasConfigPhotons with "virtualGaussian" beam and "mlc" Multileaf collimator set-up if corresponding info exists
        - TOPAS config files for several beams, rays, leafs and shapes are created and run through
        !!Caution: Results not yet validated!!

    commit c6dd0cb
    Author: Niklas Wahl <n.wahl@dkfz.de>
    Date:   Fri Apr 29 09:49:26 2022 +0200

        added basic photon infrastructure

    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 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 3610bf5
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Wed Oct 12 13:57:57 2022 +0200

    Update TopasConfig

    - added output of numOfBixels that did not meet the minimum numOfParticles required
    - removed unnecessary statement regarding alpha beta parameters
    - added comment to externalCalculation

commit 834bb1f
Merge: 19e22df 1b13404
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Wed Oct 5 17:21:33 2022 +0200

    Merge branch 'master' into pr/536

    # Conflicts:
    #	README.md

commit 19e22df
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Wed Oct 5 16:36:42 2022 +0200

    reset to old bixelwidth-dependent dij sampling

commit 1ee132d
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Tue Oct 4 20:31:30 2022 +0200

    Merge dev_varRBErobOpt_experimental

     Important branch Bug Fix:

        - fixed 2 major bugs in matRad_calcCubes!
        - fixed bug in TopasConfig, where the empty preallocated dij field was used to calculate tallies instead of the actual dose
        - made beamSetup more concise with shorter spaces between numbers
        - added fix for selection of focusIndex for generated phaseSpace data
        - changed handling of 0 fields
        - use isprop instead of isfield now that the class system is used
        - removed several statements that are no longer used or required

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 4a3e73a
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Thu Sep 22 21:35:00 2022 +0200

    Update to emittanceBaseData energyspread handling

commit 87bf5fe
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Sep 23 15:25:24 2022 +0200

    Fix indent

commit 37d3c58
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Thu Sep 22 20:53:11 2022 +0200

    Update to matRad_calcCubes.m

    - removed section that added "non-processed MC tallies", not needed anymore
    - removed 2 lines from MCsquare calculation that still referenced the outdated MC_tallies system

commit dc9552e
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Thu Sep 22 13:45:13 2022 +0200

    MC dij update calcDoseDirect

    - renamed topasCubes variable into dij to make it clearer (used to be a relict from deprecated workflow)
    - Brought dij generation of MCsquare and TOPAS in line for calcDoseDirect (all beam/ray/bixel fields are 1)

commit be032cc
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Thu Sep 22 13:42:04 2022 +0200

    bug fix for recent resampling update

    - fixed resampleCTtoGrid function being called incorrectly
    - fixed input

commit 45b6517
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Wed Sep 21 16:44:07 2022 +0200

    Merge dev_varRBErobOpt_experimental -> dev_varRBErobOpt_Update

    Update PR:
    - removed TOPAS scripts
    - added compatibility patch
    - Added patch for fluence Optimization and input of precalculated weigths
    - Added input of LET into calcLQParameter function
    - Moved resampling function from TOPASconfig in general tools
    - made externalCalculation parameter clearer to use and saved folder is output to the console
    -

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 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 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 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
HomolkaN pushed a commit to HomolkaN/matRad that referenced this pull request Nov 30, 2022
Merge dev_varRBErobOpt into research/heterogeneityCorrection
056c0c8 
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
HomolkaN pushed a commit to HomolkaN/matRad that referenced this pull request Nov 30, 2022
Merge dev_varRBErobOpt_Update
611e9ba 
commit f1e446a8d06eff73e8224a59498bbfde53bc4456
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Wed Nov 23 18:28:10 2022 +0100

    minor MC workflow fixes

commit 63bb149b191840e240e21e07f257f6172241f8f8
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Tue Nov 22 17:02:52 2022 +0100

    small fix wenn getting number of emittance gaussians from the weight array

commit 348ba2fee095ced97e2d957b674a24c9812310a8
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Tue Nov 22 16:48:04 2022 +0100

    remove weird slab file in scenarios folder

commit d81012dd18badb6fcb74dacf5518c9fd267ef99c
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Tue Nov 22 13:43:40 2022 +0100

    make mex file compilation a static function

commit 20626d1e4321e2b3d9e5887d4904c1f5c5f5f9b3
Merge: fcc026f0 37d41298
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Tue Nov 22 13:39:35 2022 +0100

    Merge branch 'dev_varRBErobOpt' of https://github.com/e0404/matRad into pr/536

commit fcc026f01709beef78f2ea861dceb6054af00d49
Merge: 051dfdbd 93571e61
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Tue Nov 22 13:38:33 2022 +0100

    Merge branch 'dev_varRBErobOpt_Update' of https://github.com/HomolkaN/matRad into pr/536

commit 051dfdbd9f8eb6bb60ecfbb258eef310115bd0a5
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Tue Nov 22 13:35:52 2022 +0100

    add different SADs for x and y to the base data class

commit 93571e61baa9a4d4a8b89b0883f92893b0ee84cf
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Fri Nov 18 18:00:07 2022 +0100

    Update MatRad_TopasConfig.m

    minor compatibility changes for TOPAS

commit 3355d0519af14942d4201ff4220c1fcaa19c5292
Merge: b6188d1f c8fd3029
Author: Hardt <jennifer.hardt@dkfz-heidelberg.de>
Date:   Fri Nov 18 16:45:13 2022 +0100

    Merge branch 'dev_varRBErobOpt_Update' of https://github.com/HomolkaN/matRad into dev_varRBErobOpt_Update

commit b6188d1f5c0df47a808392290feaf12705190989
Author: Hardt <jennifer.hardt@dkfz-heidelberg.de>
Date:   Fri Nov 18 16:44:30 2022 +0100

    SAD and wsl fix

    SAD was wrong given in cm in header file, and phase space file location is given as a relative path, wsl dosent like the direct path

commit 277fef513dbc2bb972b77521dcfd342cefaa576e
Author: Hardt <jennifer.hardt@dkfz-heidelberg.de>
Date:   Fri Nov 18 16:42:07 2022 +0100

    Phase space file starts at end of colimator

commit 16c9610a9b65ad45b1dabbea5ddd155e2019eb80
Author: Hardt <jennifer.hardt@dkfz-heidelberg.de>
Date:   Fri Nov 18 16:41:46 2022 +0100

    otherwise out and log file are the same file

commit c8fd30297275590ef6f390239267c1f49f10d4a5
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Fri Nov 18 16:06:14 2022 +0100

    Update matRad_calcPhotonDoseOmpMC.m

    Typo

commit 704d2c08ae503705d87dafc8af8a65f223754ec6
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Fri Nov 18 14:59:51 2022 +0100

    introduce ompMC class

    This change was done primarily to increase compatibility with the other MonteCarlo changes that have been done, mainly how the MC classes are currently structured and loaded.

commit 926d70097867a9bac85f1bb4f78684a4cfaaf503
Author: Hardt <jennifer.hardt@dkfz-heidelberg.de>
Date:   Fri Nov 18 10:32:02 2022 +0100

    Update .gitignore

commit 147f0582bfc487378ea651bce4d2ff1e185698bb
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Fri Nov 18 10:10:18 2022 +0100

    Update matRad_runTests.m

    added small fix for runTests that couldn't find testing scripts

commit d6fd9f2997881af72985c5df0a1562880e9eb48b
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Thu Nov 17 11:55:28 2022 +0100

    Update matRad_runTests.m

    Make sure a failing script does not get stuck in a directory

commit bb40ecab977e8992c17cbb093a726499328fb0f1
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Mon Nov 14 20:14:14 2022 +0100

    Update MatRad_TopasConfig.m

    Some more octave changes

commit 2f0b541a6791c340b316a7f5db275e8a1304f913
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Mon Nov 14 17:42:32 2022 +0100

    potential fix for testing

    renamed topas beam setup files to lowercase

commit 37d412983857db3c163b8b5a4b4719a55a989207
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Nov 11 18:05:52 2022 +0100

    add some compatibility functions to scenarioModel

commit 2c576ab155599f00650d408fe9089cae999bde21
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 b08ddc49c7f84cec4df56bc5213c4ef726609be3
Merge: d8588e13 d0e246c6
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Oct 28 14:45:19 2022 +0200

    Merge branch 'dev_varRBErobOpt_Update' of https://github.com/HomolkaN/matRad into pr/536

commit d8588e131751fdff71389f7cfab2f13b69ff1e9e
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Oct 28 14:44:46 2022 +0200

    change how emittance and energy spectrum should be represented in base data

commit 9b5c17af4cc000483a46989fc51d8609129412ea
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Oct 28 14:43:47 2022 +0200

    some technical fixes

commit ee58c3d155a7b33ac44c60753b35d48fcb409904
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Oct 28 14:43:23 2022 +0200

    remove the MCsquare MU correction as it is no longer valid

commit d0e246c6da2c53bfab2389cb4b7271b3fb9ce495
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Wed Oct 26 16:59:52 2022 +0200

    adjusted topas calcDose functions

    - streamlined topas photon calcDose function to be in line with newer function for particles
    - orderfields probably does not accept empty variables in older versions of matlab

commit d1c34aba8a11fdcb86c80e271c2e844d0c5fcba6
Merge: fe9adb80 c9d190e1
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Wed Oct 26 16:35:33 2022 +0200

    Merge branch 'dev_varRBErobOpt_Update' of https://github.com/HomolkaN/matRad into dev_varRBErobOpt_Update

commit fe9adb804144f5739ed541bdc290c9d9aa1961de
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Wed Oct 26 16:35:27 2022 +0200

    added default beamProfile for photons

    - default beamProfile for photons in matRad_cfg
    - removed hardcoded beamProfile and numOfRuns in photonDoseMCtopas
    - added check if beam profile is compatible with radiationMode

commit c9d190e16c784994989bcb1c1d69a311522ab61c
Merge: f328b964 05db32a3
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Wed Oct 26 16:00:39 2022 +0200

    Merge branch 'dev_varRBErobOpt' of https://github.com/e0404/matRad into pr/536

    # Conflicts:
    #	matRad_fluenceOptimization.m

commit 0af8238dd63ad051b446253682dd30d96abad8ca
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Wed Oct 26 15:58:45 2022 +0200

    small update to photons phasespace

    - set phasespace file as changable in config to maybe be implemented as a variable.
    - check is performed to see if phaseSpaceFile is available
    - Info is output if externalCalculation is turned on (manually place phaseSpace file)

commit f328b96408e79750aea512e85d27344c0ec65fc2
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Wed Oct 26 15:53:20 2022 +0200

    fix props in MatRad_Config

commit 0c2094d33ba42566fb7a186b81975bdb93288105
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Tue Oct 25 23:36:24 2022 +0200

    Update TOPAS_beamSetup_Phasespace.txt.in

    - Fix to phaseSpace beamsetup.
    - .pshp file is still missing in order to run this properly

commit 2f53358537c4fb6e9d1c46c43649b739493338dc
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Tue Oct 25 01:58:09 2022 +0200

    Finished merge of TopasConfig_Photons

    - further progression on photons for TOPAS.
    - added phasespace data SIEMENS*.header which is read through beamSetup_phasespace. If the file can be found by TOPAS in the subfolder has to be checked.
    - time feature splitting for dij calculation is turned off for now, this has to be discussed further

commit 93233d1d4a7fa58c3bffdab8476d00fc2ea3d367
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Mon Oct 24 22:05:25 2022 +0200

    Update MatRad_Config.m

    disabled ompMC for now and change default photon engine to TOPAS. This can be reverted at a later stage when this is properly implemented.

commit 4b59c62b782844cfe98e4f335cffb1363a181bef
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Mon Oct 24 18:03:04 2022 +0200

    Merge piastammer/dev_varRBErobOpt_photonsTopas into dev_varRBErobOpt_Update

    This is a preliminary implementation. Next, I will implement this properly into the updated TOPAS structure.

    commit 0b82924cb06e43568801ae97cddc67bd7316f814
    Author: pia.stammer <pia.stammer@kit.edu>
    Date:   Fri Oct 21 16:09:00 2022 +0200

        Added phase space source
        *need testing!*
        -load phase space from source file SIEMENS_PRIMUS_6.0_0.10_15.0x15.0 available at https://www-nds.iaea.org/phsp/photon/SIEMENS_Primus_6MV/
        -added beamProfile 'phasespace' and appropriate input file
        -no pencil beam scanning supported, only single angle/position atm
        ToDo: Check geometry, especially distances between nozzle, phase space, MLC and patient (surface/isocenter?)

    commit 5ee546711c2bda90eec3fef84726eecbab61fd05
    Author: Noa Homolka <n.homolka@dkfz.de>
    Date:   Fri Sep 16 17:19:28 2022 +0200

        PhotonTOPAS Update

        - export leafWidth from aperture2collimation
        - small bug with additional "end" fix in ParticleDoseMCtopas
        - added switch for uniform weights in case of ~calcDoseDirect
        - changed materialConversion to 'RSP'
        - renamed numOfLeaves and leafTimes parameters for easier understanding
        - Translated MLC so that the Nozzle lies at beginning of MLC, not centered

    commit d43b80cc5f7a58dcd781d5d986aa4b7842bcb2e3
    Author: pia.stammer <pia.stammer@kit.edu>
    Date:   Fri Sep 16 14:47:50 2022 +0200

        Reduced size of source, increased number of histories

    commit 9067aa9c7ea33be6c219b98ca260a35e1f6357d6
    Author: pia.stammer <pia.stammer@kit.edu>
    Date:   Fri Sep 16 11:31:06 2022 +0200

        Add uniform source and rotate MLC

    commit e7031b191568979b54bdc2c89811d0248f59d5d2
    Author: Noa Homolka <n.homolka@dkfz.de>
    Date:   Fri Sep 16 10:30:36 2022 +0200

        disabled tracking of MCrun folder

    commit 23b517aa56a9cb88b1e65d12c91cff6cbf1fa056
    Author: pia.stammer <pia.stammer@kit.edu>
    Date:   Fri Sep 16 09:57:44 2022 +0200

        Status 2nd Hackday: Some corrections, TOPAS runs through, results mediocre

    commit bd68b3b70aa41321ec69248f748f1c8696b3811d
    Author: pia.stammer <pia.stammer@kit.edu>
    Date:   Fri Jun 10 17:00:17 2022 +0200

        Initial commit: Added MLC shape capabilities for TOPAS
        - shapes generated by matRad_aperture2collimation are written into TOPAS config file
        - use class matRad_TopasConfigPhotons with "virtualGaussian" beam and "mlc" Multileaf collimator set-up if corresponding info exists
        - TOPAS config files for several beams, rays, leafs and shapes are created and run through
        !!Caution: Results not yet validated!!

    commit c6dd0cb6ddbe9ee8ddb502c5db66b4dc4b87fa6c
    Author: Niklas Wahl <n.wahl@dkfz.de>
    Date:   Fri Apr 29 09:49:26 2022 +0200

        added basic photon infrastructure

    commit df91e40747d1e84ff8ef06e59513b7b6596d0340
    Merge: e0ffefeb ea37a851
    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 05db32a31303bb78c9f2cc70feab9ea0f1af31e3
Merge: d34b1826 9a431cdb
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 3610bf50d710d0370e6e306393ea6e2f11905372
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Wed Oct 12 13:57:57 2022 +0200

    Update TopasConfig

    - added output of numOfBixels that did not meet the minimum numOfParticles required
    - removed unnecessary statement regarding alpha beta parameters
    - added comment to externalCalculation

commit 834bb1f651137e8ff1c1ac3d441157bfd3dd7a76
Merge: 19e22df3 1b13404b
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Wed Oct 5 17:21:33 2022 +0200

    Merge branch 'master' into pr/536

    # Conflicts:
    #	README.md

commit 19e22df3ba1553adb14b516fbe4d674ebd221b64
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Wed Oct 5 16:36:42 2022 +0200

    reset to old bixelwidth-dependent dij sampling

commit 1ee132d5e2b85176681cdaf86ce06946164d0688
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Tue Oct 4 20:31:30 2022 +0200

    Merge dev_varRBErobOpt_experimental

     Important branch Bug Fix:

        - fixed 2 major bugs in matRad_calcCubes!
        - fixed bug in TopasConfig, where the empty preallocated dij field was used to calculate tallies instead of the actual dose
        - made beamSetup more concise with shorter spaces between numbers
        - added fix for selection of focusIndex for generated phaseSpace data
        - changed handling of 0 fields
        - use isprop instead of isfield now that the class system is used
        - removed several statements that are no longer used or required

commit 1b13404b357f07245869dfa2c815a016d0a5c84c
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Sat Sep 24 00:39:04 2022 +0200

    Update tests.yml

commit d24dc5faa966e63a93643c0aacdab98379bd0f84
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Sat Sep 24 00:14:14 2022 +0200

    Update README.md

commit 4a3e73a9cb4f825214478ebfc5ef43e60ca9cc42
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Thu Sep 22 21:35:00 2022 +0200

    Update to emittanceBaseData energyspread handling

commit 87bf5febf8bc02481a17c7c72de09ecafbb4622c
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Sep 23 15:25:24 2022 +0200

    Fix indent

commit 37d3c58f3ce42427ba3717002202b50cfa17335b
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Thu Sep 22 20:53:11 2022 +0200

    Update to matRad_calcCubes.m

    - removed section that added "non-processed MC tallies", not needed anymore
    - removed 2 lines from MCsquare calculation that still referenced the outdated MC_tallies system

commit dc9552e4b26a8645385ea4e369338dd6b4764045
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Thu Sep 22 13:45:13 2022 +0200

    MC dij update calcDoseDirect

    - renamed topasCubes variable into dij to make it clearer (used to be a relict from deprecated workflow)
    - Brought dij generation of MCsquare and TOPAS in line for calcDoseDirect (all beam/ray/bixel fields are 1)

commit be032ccbd9b3ef6568c37c81cf191af6392a6c8b
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Thu Sep 22 13:42:04 2022 +0200

    bug fix for recent resampling update

    - fixed resampleCTtoGrid function being called incorrectly
    - fixed input

commit 45b651788dbacf15b4fd09c60f7ebbeb3511fe5d
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Wed Sep 21 16:44:07 2022 +0200

    Merge dev_varRBErobOpt_experimental -> dev_varRBErobOpt_Update

    Update PR:
    - removed TOPAS scripts
    - added compatibility patch
    - Added patch for fluence Optimization and input of precalculated weigths
    - Added input of LET into calcLQParameter function
    - Moved resampling function from TOPASconfig in general tools
    - made externalCalculation parameter clearer to use and saved folder is output to the console
    -

commit d9e4b21f23d2a4f35f03f79dea933679d1ad2577
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Mon Sep 19 15:56:01 2022 +0200

    fix fprintf error in octave due to non-escaped percentage character

commit ddb0454da09507d6bd921cc902196a471699d8ac
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Mon Sep 19 15:07:33 2022 +0200

    fix compatibility issue in the MCemmittance class

commit 0bf81e2811de533a359023d9a5811786939716e7
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Mon Sep 19 14:00:16 2022 +0200

    fix wrong case in path

commit 2a80135091ec6a79a5645a1137e895ed1c94ab74
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Mon Sep 19 13:36:03 2022 +0200

    update direct dose calculation

commit 9b968e805d13f16d82668a4809684b1503d0c118
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Mon Sep 19 12:52:08 2022 +0200

    Update matRad_calcDoseDirectMC.m

    small bug fix that should also resolve this iteration of unit testing

commit 942ea448cc43dd4ac3c00d7760499d228f68efa7
Merge: 75201faa f69a0076
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Sat Sep 17 01:33:39 2022 +0200

    Merge pull request #579 from wahln/master

    Create CITATION.cff

commit f69a0076a11dfbcf4e3d642c8453f2ed94e2f553
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Sat Sep 17 01:28:31 2022 +0200

    Create CITATION.cff

commit 9a431cdb86096f4776135ad8591077d1fa49312b
Merge: 3ae8fc1e 54a6dfc6
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Sep 16 18:23:49 2022 +0200

    Merge pull request #537 from HomolkaN/dev_varRBErobOpt_ToolUpdate

    Tool update

commit 80d1396a79c9d2c97e94c6c40c0c3db54b33ebde
Merge: 3de7537f 3ae8fc1e
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Sep 16 17:23:00 2022 +0200

    Merge branch 'dev_varRBErobOpt' into pr/536

    # Conflicts:
    #	MatRad_Config.m
    #	matRad_calcCubes.m
    #	matRad_calcParticleDose.m
    #	matRad_fluenceOptimization.m
    #	matRad_generateStf.m

commit 54a6dfc6d4f9433af87f5825c801380089ab2557
Merge: 25ad484e 3ae8fc1e
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 3ae8fc1e56b7942108ae2f408f1dde58b1752fbf
Merge: 65b314f3 d5ae6e29
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Sep 16 16:13:41 2022 +0200

    Merge pull request #572 from wahln/dev_varRBErobOpt_scen

    Object-oriented scenario implementation to replace matRad_multScen

commit d5ae6e2951f1d9e72224b0753fb4f2f5b1337093
Merge: 0a69b216 65b314f3
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 65b314f3823bbe8f474c1009314f95a5aed4888b
Merge: f5ec748a fea82a8c
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 0a69b21633ad3460ef2d777456809d49caa9d1ac
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Sep 16 13:50:42 2022 +0200

    Extend Octave compatibility fix

commit 555d3ce9a1a4d623f66b19797f3177084e3a288b
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Sep 16 13:39:30 2022 +0200

    fix missing return value in NominalScenario

commit 940d403e718548513a42448849e6f2128c084fa1
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Sep 16 13:39:10 2022 +0200

    Octave compatibility fix

commit beaa7acfdafbe82e6c4e86eadfe7c53a999d60ec
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 09a6b8f7e24063fb18f6d97489deb52a8a16d8a6
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Sep 16 11:44:24 2022 +0200

    Increase reusability of scenario code

commit 7a47f0b739b37920f77637e912edc90c5edf58e5
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Sep 16 11:00:31 2022 +0200

    enable full combation of all grid scenarios

commit fea82a8c4678d18f9c49d02b147345b07455afc0
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 75201faaca07804d8c2ee25a71b9ae24c23745a1
Merge: 3d29b765 e469b8f4
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Mon Aug 22 15:37:07 2022 +0200

    Merge pull request #574 from e0404/hotfix/dicomDoseImport

    Fix RTDose import when no RTPlan is imported

commit e469b8f4ceaff92eb2abda5cb2908786ec22cbd8
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 25ad484e233c459aaf76cfe6dbb83e27bf65d0c2
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 3de7537fc8ccb8bc9d7b0f8d40184290132759dd
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Fri Aug 5 15:17:44 2022 +0200

    Update ChangeLog.txt

    Added ChangeLog for MonteCarlo workflow Updates in Pull Request

commit 8527e90d1143665b4b01f7cd148766186a489257
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Fri Aug 5 15:01:07 2022 +0200

    TOPAS Schneider Update

    - Rearranged materials into materialConverter folder
    - Renamed density correction files
    - Removed density correction that was essentially unusable and had no reference
    - Added readme to density correction

commit 2deb2c4ad0de4e97d9bd5e31c220a6803f66ec67
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 71019963d9bfe60c09eba63a41c6b5368927fb0c
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Wed Aug 3 16:09:23 2022 +0200

    Replaced contains function by strfind for octave

    RIP contains, you were the love of my life.

commit d34b18269597a8e4599fa6426b65c8efc63b7bbb
Merge: df91e407 f5ec748a
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 1d7e81e1c71adffba034928f43410d94082a20d0
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Tue Aug 2 21:59:38 2022 +0200

    added support for 4D

commit ecf0d0b7b24d5f96592ae3e247dfd63d3db90ab7
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Tue Aug 2 11:45:32 2022 +0200

    Documentation update

commit 7a89042d2c09c48730bc9ec10f8b4b89fad560e1
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Tue Aug 2 11:44:02 2022 +0200

    remove temporary scripts

commit 0d0e61e720ca3c0e7423de38dd7d2b8ef7a06649
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Fri Jul 29 18:03:28 2022 +0200

    Merge branch 'pamede/dev_varRBErobOpt'

    Updated Example 13:
    - added function to plot particleBaseDataEntry
    - edited function to fit base data
    - added function to generate a single pencil beam

    Minor changes:
    - added variable in pln to contain an existing BDL file if available
    - Throws info where base data file is saved
    - renamed MCsquare property "Num_Primaries" -> "numHistories" to be in line with other Monte Carlo (this is written to the BDL file in original format)
    - added comments

commit f370e845bac7a4302f4fc76881af80d208f83bce
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 be48e72234318680e49dde4cabe79e76e230c7d4
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Jul 29 17:45:33 2022 +0200

    documentation and compatibility fix

commit 95ab43a15b7d6b2fbbc99662a1648828e25c048a
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Jul 29 12:03:01 2022 +0200

    Octave compatability fix

commit 5ac3cd7f797afdc4512c15e0bcb5e652950e240a
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Fri Jul 29 11:18:41 2022 +0200

    Merge branch 'pamede/dev_MonteCarloRestructured'

    Merge remote-tracking branch 'pamede/dev_MonteCarloRestructured' into dev_varRBErobOpt_Update

commit 45d414f7c9fbeafcb1ba69b2b2ba51fc15f2ebe3
Merge: ad2e93ad f5ec748a
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 4888568ccdb0790e6034695661741a29b638a7c1
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Fri Jul 29 10:32:47 2022 +0200

    Merge branch 'dev_VARBE_MC_merge_experimental' into dev_varRBErobOpt_Update

commit ad2e93ad5b316a056f5d19d6093a2ec961295654
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Jul 29 10:15:02 2022 +0200

    Include shift and range combinations

commit dba7cf45e5b5e4b2773f1cab32151c4df5e013f7
Merge: f9f6ecc6 6ef5d002
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Jul 29 10:01:07 2022 +0200

    Merge commit '6ef5d0020211c1dd4a74c9f8c30c0d543225b73b' into dev_varRBErobOpt_scen

commit f9f6ecc67d3823c2a9ac678972d9a1a2149b05e8
Merge: 00d31763 0a624cef
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Jul 29 10:00:44 2022 +0200

    Merge commit '0a624cef39f7eed970e0bba58ec8a48df2c177a7' into dev_varRBErobOpt_scen

commit c0a9f086f2a13dfb612c89d42ebe86fe14e6b1ae
Author: Niklas Wahl <niklaswahl2011@gmail.com>
Date:   Thu Jul 28 10:38:11 2022 +0200

    Remove old commented code

commit f5ec748aac7836af2bfa85a08e5bbc5c790ed7a7
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 edfef0391bcc957475c53119e10f3d89d51b7cd6
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Thu Jun 23 18:15:40 2022 +0200

    Merge additional MonteCarlo changes from dev_varRBErobOpt_experimental

    - Updated Range-Energy relationship for Helium and carbon ions
    - Added postprocessing for MCsquare dij calculation
    - added proper flag check for external calculation
    - Removed beamNum calculation in calcDoseDirectMC, this is already done in dij calculation functions

commit 6ef5d0020211c1dd4a74c9f8c30c0d543225b73b
Author: Niklas Wahl <niklaswahl2011@gmail.com>
Date:   Wed Jun 22 13:10:05 2022 +0200

    correctly set includeNominalScenario in WorstCase model

commit 0a624cef39f7eed970e0bba58ec8a48df2c177a7
Author: Niklas Wahl <niklaswahl2011@gmail.com>
Date:   Wed Jun 22 13:08:53 2022 +0200

    Add probability and weight to Nominal Scenario

commit f7ce1ee479e0ecb47d7fb1e185bb76d38085435c
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Tue Jun 21 13:42:35 2022 +0200

    Monte Carlo fix

    - Renamed numHistories back to Num_Primaries for MCsquare, since it's needed for automatic writing of the config file
    - added defaultHistories parameter in MatRad_config (Monte Carlo parameter will be overwritten if this is set)
    - added matRad_cfg to subfunctions to avoid potential matlab bug
    - renamed Monte Carlo default engines to class names

commit 1a4bfaf6101eda7a7f723c4bb93fcf51523289d1
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Wed Jun 15 17:30:27 2022 +0200

    Merge branch 'dev_VARBE_MC_merge_experimental'

    MAJOR UPDATES:
    - Added support functions for TOPAS into topasConfig class which makes usage more streamlined and uniform
    - Added support functions for MCsquare into MCsquareConfig class
    - Added class constructor for pln in MatRad_config
    - Added comments to whole TOPAS pipeline
    - edited calcParticleDoseMCtopas to generate dij in matRad format and changed calcCubes to accept a variety of differnet fields, without changing the current usage

    - minor rearrangement and whitespace changes to scorer files in TOPAS
    - minor rearrangement and whitespace changes to MCsquare scanner files
    - added multiple RBE scorer support for TOPAS
    - Changed readBinData/readCsvData files to be universally usable in matRad
    - Added functions to load class parameters and regular parameters to pln
    - edited and refined installTOPAS script
    - fixed minor bugs

commit 9a1e0714bc3d2902cd0520c6ad15ae1a8ba31ff4
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 2446784def01fd497f77a922c1a9d84fd2d3d6ce
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 a886b04d49e3e65efcad11ee37c6061973674f01
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 4cd741cee02f4cfe9a6be8ee859fc1a6017751ef
Merge: d344dad3 21f6ff80
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 00d317631b38ac3dba093347a39ff22c627d5e4c
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Jun 10 11:26:47 2022 +0200

    small update to matRadGUI

commit 99223dd1a24bbb0a8c7c7d8bdcd8d385ea8d6f60
Merge: ecd4fd0b 7b13c0e6
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 ecd4fd0b05411b9dd8adf91f6ed62eef824c3944
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Mon May 30 16:48:11 2022 +0200

    implement new interface in matRad_sampling

commit 2f957c6f4a87583ab02b7702bc3aaee1fa46663e
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Mon May 30 16:47:29 2022 +0200

    fix for downwards compatibility

commit 7b13c0e68e5580faa31da8f40cbc715590f5aec1
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 b849675c9bfe1771168b4aca70fdbab2141c5dd1
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Tue May 24 17:56:39 2022 +0200

    deprecated properties in RandomScenarios class added

commit e1b9d5e9d97bbe035ad4941f6fd98ff04a0c5551
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 3e2865d5d270cb535975bae7672e0087dedacb94
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri May 20 17:18:53 2022 +0200

    deprecation warning

commit af7719e887faf7403ea6d8252d0f7e23a4c195a7
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri May 20 17:05:43 2022 +0200

    single scenario extractor

commit e18c7ec2fc947d4b6c4844db68db379e802dc317
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri May 20 16:58:25 2022 +0200

    New Scenario update with downwards compatability

commit b38936e2cf5c99a5379767b4f324c95af9706adc
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 fbb07d5a3cbc1691997943ba7af58b9a9d5edae4
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Sun May 1 07:24:50 2022 +0200

    Update matRad_getAlphaBetaCurves.m

commit d4c4223dc2613aa90670b139c472ba06f1ba3052
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Apr 29 10:08:14 2022 +0200

    test scripts

commit df91e40747d1e84ff8ef06e59513b7b6596d0340
Merge: e0ffefeb ea37a851
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 49ccff311c5f626c9118642b07f79d2e2d5b1256
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Wed Apr 20 15:31:15 2022 +0200

    first draft of new scenario infrastructure

commit 21f6ff80c9a28eedafec8e533d527ef265f1959c
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 52e8ab72cb9df3a7e6e7da94e6f6b9b3c8938a7f
Merge: 7ba093fd ea37a851
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 64fad60ac7da768aa3567075a0b406ee78786fb8
Merge: aad8a96c ea37a851
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Tue Mar 15 17:02:08 2022 +0100

    Merge branch 'dev_varRBErobOpt' of https://github.com/e0404/matRad into pr/536

    # Conflicts:
    #	MatRad_Config.m
    #	matRad_calcParticleDose.m
    #	matRad_fluenceOptimization.m

commit ea37a851a0f122789175b0764b49dd12183432e8
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 7ba093fd37bf2e666d7cc27484f7c5fc8f4b7956
Merge: c30930e0 19ed7f61
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 19ed7f6108472753095ab3251bf16d8b46b0dcb0
Merge: 2101d8fd 4d28380b
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 e0ffefebb408a48eb1f5584cfd0a2e591691d8f5
Merge: c3844c3b c935518d
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 4d28380b193d9aa216b656a038fd2ec447d0acf4
Author: Niklas Wahl <niklaswahl2011@gmail.com>
Date:   Thu Jan 20 16:46:44 2022 +0100

    Octave compatibility

commit c93f2c48fc253b87ad4307e79ffe976f3f719862
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 87891d5e3d4a09595b6dcb0a7d802b75f53e5fb5
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 c3844c3bb297a2f6c44d8bca51f1d923291f54f3
Merge: 42d44973 2101d8fd
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 42d4497365faaf32fe0b1908397ac409e0072470
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 885aad578bb7e3f8643d7e77a4699024b471b665
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Wed Jan 19 12:04:49 2022 +0100

    fix when automatically setting the isocenter

commit 9cfba69a81a37e030d71ffdd28fb70e7e6cd114e
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 0c2c99d395d1aa81d375b118af50f4acc7c1e345
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Wed Jan 19 12:03:37 2022 +0100

    helium adaptations

commit d5418d75f4a8c037fbc5f58cdd82fe97268d8821
Author: Niklas Wahl <niklaswahl2011@gmail.com>
Date:   Fri Dec 17 14:12:22 2021 +0100

    make mean dose objective downwards compatible

commit 5d3b276fe0cecc80f959024c7a5f06fed47fd9bf
Author: Niklas Wahl <niklaswahl2011@gmail.com>
Date:   Fri Dec 17 13:20:34 2021 +0100

    better checking of DICOM RTstruct import problems

commit c30930e00675a379865db1ad5e6cd06ad907ece5
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 2101d8fd01f238e330891a58c877cff7820d2763
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 7c187f8c012c4ff933dda37d62a85f3a3ebdf1d0
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 aad8a96cc9934b7f4a5a02792b6e609eb6f73415
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Sun Dec 5 18:59:31 2021 +0100

    Extensive TOPAS workflow update:

    Major updates:
    1. installTOPAS script which installs TOPAS with the dependencies from downloaded topas.tar.gz
    2. modular Schneider Converter: Converter is now generated on demand rather than read from file which allows a variety of different options
    3. modular TOPAS scorer which can be individually turned on and off
    4. added 4D accumulation in calcDoseDirectMC
    5. implemented dij calculation in TOPAS

    Minor updates:
    1. Added optional initial weights to fluence Optimization
    2. enabled helium in calcdoseDirect
    3. implemented std of physicalDose
    4. export feature for TOPAS to run externally (includes functions to read from external folders)
    5. restructured resampling in calcParticleDoseMCtopas in separate function
    6. MCemmittanceBaseData can calculate meanEnergy and spread also for carbon and helium ions

    Bug fixes and minor changes:
    1. added flag in stf to catch specific error where no energies could be found
    2. Fixed bug in resizeCstToGrid function
    3. Fixed a number of errors in 4D calculation workflow

commit c935518d5449fd428f10dc70d6be03f313023255
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Dec 3 13:51:33 2021 +0100

    Update tests.yml

commit 82fac5059212e3ca933da6c856aebf0f3e5a5ef8
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 d63942198bba3a508b9dafa3fa16ea2d1e64a674
Merge: de4e6e1d dcded212
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Thu Dec 2 12:07:38 2021 +0100

    Merge pull request #531 from wahln/dev_varRBErobOpt

    dev_varRBErobOpt MC update

commit dcded2128a83f637b3b050bed75b9b8252042064
Merge: 02cfee9c 14f585f9
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 02cfee9cb81da01ceafef4cce5ce01decf763e64
Merge: 2b2cd50c de4e6e1d
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 50145f09875b6a301d37810325d09141a4fbc4c8
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 8740668cf5fe9dcbe384fe2137ee97dd80ced4d2
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 d08fe1d4586b89bc162174b28bb06778ccd2cb63
Merge: dbef217b f16fce3a
Author: Niklas Wahl <niklaswahl2011@gmail.com>
Date:   Thu Nov 11 13:49:39 2021 +0100

    Merge branch 'dev_optimizer' into dev

commit f16fce3a8c0f605039fbe16f091a7ee33c9030ed
Author: Niklas Wahl <niklaswahl2011@gmail.com>
Date:   Thu Nov 11 13:49:01 2021 +0100

    enable passing of initial fluence to fluence optimization

commit 97fcec604c4ef39e39747421d0af3f849b2aebf7
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 d344dad383c49e4f538746ed344ebe5b85642e3e
Merge: 041066f9 dbef217b
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 dbef217bb445e54cf08e92345264fc393c6bae19
Author: Niklas Wahl <niklaswahl2011@gmail.com>
Date:   Fri Sep 17 17:15:53 2021 +0200

    issue with the finesampling query in doseinit resolved

commit 658b390c00d03dc159e6d807f47c625fec82ee71
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 a97b6bead022b6398724fc0ea509923078dbebef
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 1db68c1bbadb5ab08114c913944e56afbbf313bd
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 11759edec63d5fcdf0f6932053d73b2b4f06e380
Merge: 8d686762 3d29b765
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 de4e6e1dd196311cc3ba404a174f194e70aa0b60
Merge: 03f60596 3ecd6dd7
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 03f60596b7704a0388a5ac20d9d14ccd4d459dc7
Merge: 27b2fe4a d36d48f5
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 3ecd6dd763152155a56cf36e16cdd57b57861f35
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 3d29b765a9a0a02a593890726102a7d9db907af7
Merge: b478ede9 be8b2bf6
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Jul 9 12:57:49 2021 +0200

    Merge pull request #506 from e0404/hotfixes/daoWithConstraints

    Fix Direct Aperture Optimization with Constraints

commit be8b2bf656024b407695c3352cf8a753d34f055e
Merge: 62c825eb b478ede9
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Jul 9 12:05:22 2021 +0200

    Merge branch 'master' into hotfixes/daoWithConstraints

commit b478ede9e6fe00544e461e9d700f0c29793da182
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Jul 9 12:05:06 2021 +0200

    Migrate from TravisCI to GitHub actions (#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 2b2cd50c7bd254d60fefc2398acb133de23fe093
Merge: 205735ab d36d48f5
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 8d68676280dbf4246c64b3ef681e7ab8e78cb5c8
Merge: f127db42 677dd905
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Mon Jun 7 10:57:42 2021 +0200

    Merge pull request #509 from NathanKunz/dev_refactorDosisCalc

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

commit d36d48f5f88d9261f1ee3683af774c1dfaa5de3f
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 f127db4286b15971312f24d6ba3f02975bd2b6aa
Merge: 27a1aef7 223fbc9d
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Mon May 17 09:32:31 2021 +0200

    Merge pull request #511 from NathanKunz/dev_exportDij_new

    Dev export dij new, second pull request

commit 223fbc9d6744d950615cca5b979b3761ad392dab
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 d73e58b317428b2680c86b25b62c2c5da0a6d284
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 #407

commit d14b334e3851898bceef8456de5b316d45580aed
Merge: 6fad1b8c 9cd1602d
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 677dd905b31363636f3b0134b7731da18c2e2686
Author: NathanKunz <nathan9kunz@gmail.com>
Date:   Wed May 5 16:55:09 2021 +0200

    Second fix #503

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

commit 6ce1e7894386464c54a116b8dc7134049cae39c8
Author: NathanKunz <nathan9kunz@gmail.com>
Date:   Tue May 4 14:40:44 2021 +0200

    Removed forgotten test code

commit 71128769473c7e5e925bb2cd3e73167461cd5cb2
Author: NathanKunz <nathan9kunz@gmail.com>
Date:   Mon May 3 16:28:43 2021 +0200

    First fix for #503 (without any GUI changes)

    Possible fix for issue #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 62c825eb7519519e2e4a21a94dd6160208d4c1b1
Merge: fe1d7e75 8669892d
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 fe1d7e7507631d6b1412e63716d9bfcfacdaa933
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 8669892dafdee2dcf8c5093622807f45fd9068f8
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Apr 30 18:06:15 2021 +0200

    explicit counter setting for better readability

commit 67638595e975f71d2c62546c6e3282a28aff1212
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 ca94c5b7e9666cb64187cfbdd20e231d08dd838f
Author: NathanKunz <nathan9kunz@gmail.com>
Date:   Thu Apr 29 12:08:21 2021 +0200

    Update LIVER.mat for issue #501

commit 27a1aef7aef75b2df872491e670e3a71034bff36
Merge: f40c9031 b1816ea7
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Wed Apr 21 10:50:49 2021 +0200

    Merge pull request #498 from NathanKunz/dev_refactorDosisCalc

    Fix for MatRad_Config downwards compatibility issue

commit 0efba94d7226bfdf80f377590dbaaa2ae60c6411
Merge: d0b59e66 972b6d5c
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Wed Apr 21 10:48:56 2021 +0200

    Merge pull request #504 from naninano1/patch-1

    Update AUTHORS.txt

commit 972b6d5cccbe2e8d53b05c6bc85169be0b06db59
Merge: fd13c0f0 d0b59e66
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Tue Apr 20 21:22:34 2021 +0200

    Merge branch 'master' into patch-1

commit d0b59e665f8eb14cfcc103015515fedb7d66f528
Merge: d10fb186 4e33ec16
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Tue Apr 20 21:21:37 2021 +0200

    Merge pull request #505 from naninano1/patch-2

    Update matRad_MeanDose.m

commit 4e33ec16e78f710447ecfb3b6e986570ad69c7b7
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 fd13c0f052a837e936244de53fef32431a71487a
Author: Navid Khaledi <77858420+naninano1@users.noreply.github.com>
Date:   Tue Apr 20 19:10:43 2021 +0430

    Update AUTHORS.txt

commit b1816ea76ae504c3e74646e7dfb71275a9fb2632
Author: NathanKunz <nathan9kunz@gmail.com>
Date:   Thu Apr 1 18:28:19 2021 +0200

    Added my name to the authors list

commit d10fb1864a7950aae6548d753ad14662803262ed
Merge: 6fad1b8c 803d0de9
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Thu Apr 1 17:15:01 2021 +0200

    Merge pull request #492 from e0404/master_hotfixEffectiveCutoff

    Fix issue with effective lateral cutoff for large photon fields

commit 8fbf0c085ba3271f0dbca9af03ccb79b10525930
Author: NathanKunz <nathan9kunz@gmail.com>
Date:   Thu Apr 1 14:04:03 2021 +0200

    Fix in MatRad_Config for Octave compatibility

commit c4c94166e8117376e24e7c2f69a6333f45dfe619
Author: NathanKunz <nathan9kunz@gmail.com>
Date:   Tue Mar 30 15:52:07 2021 +0200

    Typo fix

commit c4954c3f56ebbd6184518ff23a1888d28f0494b6
Author: NathanKunz <nathan9kunz@gmail.com>
Date:   Fri Mar 26 12:07:16 2021 +0100

    Overload loadobj function of MatRad_Config for issue #496

commit e07b2a23cc7fbd00a43d8c89c3493c9292e41a78
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 430462e2526ae61beb4a8b8f961226576519a498
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 803d0de9b0104836e599ebe5f431e80672742f73
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 14f585f92ad643b8fa921110344afd4d716bc096
Author: Niklas Wahl <niklaswahl2011@gmail.com>
Date:   Thu Mar 11 12:23:42 2021 +0100

    add configuration possibilities. Add Material Conversions HUSchneider & HUSchneiderDensity

commit 7c6f3c2c0c00aa19ad405c7a4c614f6f481ce7e6
Author: Niklas Wahl <niklaswahl2011@gmail.com>
Date:   Wed Mar 10 18:25:20 2021 +0100

    commit allow range shifters within topas

commit c51cd4b01c68e8aef0cfe71960b0adfac3f26d7a
Author: Niklas Wahl <niklaswahl2011@gmail.com>
Date:   Wed Mar 10 18:21:56 2021 +0100

    replace readHLUT with loadHLUT for automatic HLUT detection

commit f40c9031ee7f23d2c29862090644dd7557c72f9d
Merge: 0bc706d2 863e5c27
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Feb 26 16:09:55 2021 +0100

    Merge pull request #466 from pamede/dev_fineSamplingNoHistory

    Fine sampling via russo and fitted splitting

commit 863e5c274e32f9e7c2227e4a4575d8138ea25e86
Author: pamede <p.meder@protonmail.com>
Date:   Fri Feb 26 11:02:45 2021 +0100

    moved initial sigma calculation, restructured LET if statement

commit 93999fc5776fa4c4c19f5f34b57377174c66e7c3
Merge: d7355663 2317d739
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Thu Feb 25 23:44:50 2021 +0100

    Merge pull request #494 from pamede/dev_MCtmp

    fixed typo in MC example

commit 2317d7396cef80ecbdc590abe2ba1584ae6cf12d
Author: pamede <p.meder@protonmail.com>
Date:   Tue Feb 23 10:41:14 2021 +0100

    fixed typo in MC example

commit ad3f94e4801575b6e0b51899785e87aefd165a4e
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 9dc5973a5d3c9ad3844a244c895bccc246f7cebf
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 0bc706d24ddc1963cff9023d14528359aa9fbb82
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 dcda4f76c047aa42ccc3354b033c52e45a3b20b3
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 f0ad6711a4e0e72b9a4d90dc6855080e748a0702
Merge: 16af573f 34e0608d
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 d73556632448241930e8dd492f0a286ada875a15
Merge: 3eec6637 d9a1199f
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Mon Feb 8 14:38:28 2021 +0100

    Merge pull request #485 from burigolucas/dev_MonteCarlo

    Refactor HU to material conversion

commit 5af6d5b941653f24c6cdbf13ef62e6b9dfb0b9a1
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 00124b5b8d36a808e6ac7c42007d86a920e1c605
Author: pamede <p.meder@protonmail.com>
Date:   Mon Feb 1 19:05:12 2021 +0100

    deleted fine sampling example script 8

commit 4fa2394a4936ae9a825155f22d9a3fd3e0e912f3
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 d9a1199f93369c1fed53a32a3c41939c4079d661
Author: Lucas Norberto Burigo <burigolucas@gmail.com>
Date:   Sat Jan 30 03:24:09 2021 +0100

    Add option for TOPAS RSP conversion method

commit dc86a8510ae62828a4e90d666b4fea06d402eb54
Author: Lucas Norberto Burigo <burigolucas@gmail.com>
Date:   Sat Jan 30 03:22:39 2021 +0100

    Refactor HU to RSP conversion for TOPAS

commit e72651c41feb687174ca2e380173319470d35215
Author: Lucas Norberto Burigo <burigolucas@gmail.com>
Date:   Fri Jan 29 23:46:45 2021 +0100

    Redefine default matRad scanner for MCsquare

commit 36604cb8c4a194f48f55304a0a4316fa3c577ccb
Author: Lucas Norberto Burigo <burigolucas@gmail.com>
Date:   Fri Jan 29 23:35:28 2021 +0100

    Redifine HU to SPR conversion for MCsquare

commit 449a49fc86473cb29c117d57ed503a48c43b00de
Merge: b2f2c4c9 3eec6637
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 3eec6637235a3b14e9c8b75290c0283ab0ac5f03
Merge: b2f2c4c9 734c16c1
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Mon Jan 25 14:02:26 2021 +0100

    Merge pull request #483 from AdmiralHomes/dev_MonteCarlo_Master

    TOPAS: added error message for insufficient number of histories

commit 734c16c12df3bf59897588e7efda5998dbb5d9bd
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 34e0608dd27fa10b3c11a5bdc1be7f357f405048
Merge: afed8b6d 98a640e6
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Wed Jan 20 17:51:20 2021 +0100

    Merge pull request #480 from pamede/dev_varRBErobOptUpdate

    Merge master into dev_MonteCarlo into dev_varRBErobOpt

commit b2f2c4c9c2c448e3f35afe9539c59942319a768e
Merge: 93098f22 492888e5
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Wed Jan 20 17:49:58 2021 +0100

    Merge pull request #479 from pamede/dev_MonteCarloUpdate

    Merged master into dev_MonteCarlo and updated submodule

commit 98a640e640bcc056e7add9acfccf1f288188009c
Merge: afed8b6d 492888e5
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 492888e54b39918c6d4b6d933ae054e7f52be554
Merge: 93098f22 6fad1b8c
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 afed8b6d56ada6da26ee3b007c9b74583ece1a7b
Merge: c722e124 84fb2472
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Mon Jan 11 11:33:34 2021 +0100

    Merge pull request #425 from amitantony/dev_varRBErobOpt

    reshape LET cube to dose grid Correction in CalcCubes

commit 6fad1b8c07ea4d680e5c17615c5552659897e149
Merge: d930c3ec 5a0db2c0
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Mon Dec 28 15:02:49 2020 +0100

    Merge pull request #467 from e0404/dev_siggelRef

    include a download link to martin siggels thesis

commit 27b2fe4a9c90f293ee0f73fe98f89a28ccda06fc
Author: Hans-Peter Wieser <h.wieser@dkfz-heidelberg.de>
Date:   Fri Dec 18 08:16:33 2020 +0100

    added helium base data set

commit 0c6106b918e281ab60ebe5bb1e7d7c0fe125fabd
Merge: 3ab98e2b c722e124
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 16af573f5e539cbe930293520f45ca9c73d7b997
Merge: c722e124 d930c3ec
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 c722e1243453b2fbf1e2faeffdf3dc03e2e64c27
Author: Niklas Wahl <niklaswahl2011@gmail.com>
Date:   Thu Dec 10 00:38:19 2020 +0100

    fix scenForProb in scenario permuted combiantion

commit f9d4786463b59ff9738ad8e27a43e7022ff55e72
Author: Niklas Wahl <niklaswahl2011@gmail.com>
Date:   Thu Dec 10 00:29:42 2020 +0100

    fixes sorting error in multScen.scenForProb

commit 3ab98e2b332cf726cf925e1d6229c608981b7470
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 ce6c95436f75703fa8880114edafeed7f1fd6a13
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 76a22158b4d77c958ee9a7bc0ac52dd545ef45b5
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 5a0db2c01ab325473a15f5ea60dd3c8d54f813e7
Author: TURING\localbangertm <markbangert@gmail.com>
Date:   Thu Dec 3 20:48:15 2020 +0100

    include a download link to martin siggels thesis

commit 4de3ae1ae1d4b283f85092af2601859a0e3d1ef4
Author: pamede <p.meder@protonmail.com>
Date:   Thu Dec 3 19:25:09 2020 +0100

    implemented fine sampling via russo and fitted splitting

commit 4c987aa920ecfb472065da00e57cc19e104f93c8
Merge: 52e1d083 1d2bc932
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 93098f22f895f6b5bbc72360415ce33bd910abd5
Merge: 00f9a6c8 f11c42f0
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Mon Nov 23 16:01:49 2020 +0100

    Merge pull request #465 from pamede/dev_MonteCarlo

    Machine saving error

commit f11c42f09adf8b0ca61955705cfedceab47506ba
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 29e1f861a8eafc38932efa183eba2d6f799e0a8a
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 8c3cf713653de12dad2e9af138bd3676afda758d.

commit 946c025dcaeb522d595af63eb6b6740cb093cb4d
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 d930c3ec090bc89cf16eda089a80e48b6abb51f9
Merge: e3126c50 1d2bc932
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Nov 20 13:40:06 2020 +0100

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

    1st Patch Release for Blaise - v2.10.1

commit 1d2bc93264e95dd1dffc21897751b154b1522937
Author: Niklas Wahl <niklaswahl2011@gmail.com>
Date:   Fri Nov 20 11:27:45 2020 +0100

    update icons

commit c9257652b2ab5f00d7f6cfe6043a47ba5d976f3d
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Thu Nov 19 16:29:19 2020 +0100

    fix in standalone computation

commit 641fc81549adf3baa8644bad94eb1844e4c21374
Merge: 8c3cf713 00f9a6c8
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 205735ab8411a6879d55d4b1d51d63c689ff42b5
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Tue Nov 17 14:24:10 2020 +0100

    small typo in VWWC objective

commit 3051d07b38f1e7d8e3a3cb4c78b2ba3e8dd269fb
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 adb1c669615b79f90be9a9c68fb54950a3141928
Author: Niklas Wahl <niklaswahl2011@gmail.com>
Date:   Wed Nov 11 14:21:51 2020 +0100

    fix str2double in string parsing in GUI

commit 52e1d0833705e46de4e5c0d3bbc0abf7eeccd5d9
Author: Niklas Wahl <niklaswahl2011@gmail.com>
Date:   Wed Nov 11 12:51:55 2020 +0100

    fix issue in dij filling

commit cda4ac11a2bc11f946c171d5977456283989ede6
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Tue Nov 10 17:05:12 2020 +0100

    update standalone compilation

commit 8667d308ad1fb84b4113dc7f7aba6dcbdf45fb56
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Tue Nov 10 16:30:43 2020 +0100

    Configuration update

commit 42ae9e4c8930e8ba729921777c2fdf9de7ebe7b7
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Tue Nov 10 16:30:08 2020 +0100

    Update of standalone prj file.

commit ac6eda2ae0dc5cd109406c8edd9f325bd2a2d09e
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Tue Nov 10 16:27:10 2020 +0100

    remove ALDERSON phantom

commit 5636d9280e7a97bb96c19d4841489281909bbf64
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 #381)

commit 2ff35f97ab1da053488a0d55591f0945d9216b09
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 #369)

commit cacbada8c9064dcd4cd8f69bd3271860bdb81fb9
Merge: b13b4e12 55c0ba52
Author: Niklas Wahl <niklaswahl2011@gmail.com>
Date:   Mon Nov 9 10:34:42 2020 +0100

    Merge branch 'dev' into rc/v2.10.1

commit 55c0ba52ab84563aeb2df485ac99392b67ed0f7b
Author: Niklas Wahl <niklaswahl2011@gmail.com>
Date:   Mon Nov 9 10:34:08 2020 +0100

    fix indicator interface

commit b13b4e12ff0f11fc0288f34af629d49070dc62da
Author: Niklas Wahl <niklaswahl2011@gmail.com>
Date:   Thu Nov 5 16:44:07 2020 +0100

    Change version number

commit bd891b66e710e330127524305e7d1835cf8bb255
Author: Niklas Wahl <niklaswahl2011@gmail.com>
Date:   Thu Nov 5 14:26:34 2020 +0100

    update readme (Zenodo DOIs) [skip ci]

commit 89104240b5a12875ad62f7698fe9664f6ac1c5c2
Author: Niklas Wahl <niklaswahl2011@gmail.com>
Date:   Thu Nov 5 13:03:02 2020 +0100

    Update Readme

commit 1f32d39dceba47ab284698f2f03d8c9730b389c3
Author: Niklas Wahl <niklaswahl2011@gmail.com>
Date:   Thu Nov 5 12:35:58 2020 +0100

    update to changelog and fix documentation in compareDose

commit 8c11f04b2da730b8e8d859edf95bf1a7e83ce052
Merge: e01a5dc0 df2da636
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 041066f950a77080589da8e31c9f28e1a62edbda
Merge: 31645337 a0564e78
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 e01a5dc033b884979822b2206859e21d4971723c
Merge: 81aec44d fa0cf442
Author: Niklas Wahl <niklaswahl2011@gmail.com>
Date:   Wed Oct 28 11:57:29 2020 +0100

    Merge branch 'dev' into rc/v2.10.1

commit 81aec44dbf…
HomolkaN pushed a commit to HomolkaN/matRad that referenced this pull request Feb 17, 2023
Merge varRBErobOpt_Update into experimental
eef323a 
commit 9294c20
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Fri Feb 17 17:48:34 2023 +0100

    Update .gitignore

    don't add .phsp (phasespace) files to gitHub (too lage)

commit 4e87571
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Tue Dec 20 00:07:42 2022 +0100

    typo fix in MCsquare dose calculation

commit aa9fb10
Merge: a5352d9 cbc78d0
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Mon Dec 19 19:29:58 2022 +0100

    Merge branch 'dev_varRBErobOpt' into pr/536

    # Conflicts:
    #	matRad_calcParticleDoseMCsquare.m
    #	matRad_calcParticleDoseMCtopas.m
    #	matRad_calcPhotonDoseMC.m

commit cbc78d0
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Mon Dec 19 19:29:05 2022 +0100

    small fix for running index in MC scenario calculation

commit a5352d9
Merge: 0eb3d41 4453b5a
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Mon Dec 19 19:26:48 2022 +0100

    Merge branch 'dev_varRBErobOpt' into pr/536

    # Conflicts:
    #	MCsquare/matRad_writeMCsquareinputAllFiles.m
    #	matRad_calcParticleDose.m
    #	matRad_calcParticleDoseMCsquare.m
    #	matRad_calcParticleDoseMCtopas.m
    #	matRad_calcPhotonDoseMC.m

commit 4453b5a
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Mon Dec 19 18:43:02 2022 +0100

    fix MU normalization

commit cb16de9
Merge: 675ebcb 6872400
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Mon Dec 19 18:42:13 2022 +0100

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

commit 675ebcb
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Mon Dec 19 18:41:45 2022 +0100

    range scenario fix and loop simplification for MC

commit 0eb3d41
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Tue Dec 6 04:14:27 2022 +0100

    Update matRad_doseAcc.m

    Fix error in matRad_doseAcc, where the interpolation messed everything up when the phantom didn't have uniform dimensions.

commit 6872400
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Dec 2 13:52:20 2022 +0100

    Update matRad_calcParticleDose.m

    Catch failure in drawing the waitbar

commit 74f4f5d
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Thu Dec 1 05:17:30 2022 +0100

    Update matRad_fluenceOptimization.m

    Some fields necessary for RBExD optimization have to be written if initial weights are passed in

commit 093eb96
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Wed Nov 30 18:40:18 2022 +0100

    Delete protons_savedMatRadMachine.mat

commit 3782e6c
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Wed Nov 30 17:42:38 2022 +0100

    Renamed classes to follow the naming scheme

    MatRad_TopasConfig -> matRad_TopasConfig
    MatRad_HeterogeneityConfig -> matRad_HeterogeneityConfig
    MatRad_MCsquareConfig -> matRad_MCsquareConfig
    MatRad_MCsquareBaseData -> matRad_MCsquareBaseData
    matRad_bioModel -> matRad_BioModel

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 f1e446a
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Wed Nov 23 18:28:10 2022 +0100

    minor MC workflow fixes

commit 63bb149
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Tue Nov 22 17:02:52 2022 +0100

    small fix wenn getting number of emittance gaussians from the weight array

commit 348ba2f
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Tue Nov 22 16:48:04 2022 +0100

    remove weird slab file in scenarios folder

commit d81012d
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Tue Nov 22 13:43:40 2022 +0100

    make mex file compilation a static function

commit 20626d1
Merge: fcc026f 37d4129
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Tue Nov 22 13:39:35 2022 +0100

    Merge branch 'dev_varRBErobOpt' of https://github.com/e0404/matRad into pr/536

commit fcc026f
Merge: 051dfdb 93571e6
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Tue Nov 22 13:38:33 2022 +0100

    Merge branch 'dev_varRBErobOpt_Update' of https://github.com/HomolkaN/matRad into pr/536

commit 051dfdb
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Tue Nov 22 13:35:52 2022 +0100

    add different SADs for x and y to the base data class

commit 93571e6
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Fri Nov 18 18:00:07 2022 +0100

    Update MatRad_TopasConfig.m

    minor compatibility changes for TOPAS

commit 3355d05
Merge: b6188d1 c8fd302
Author: Hardt <jennifer.hardt@dkfz-heidelberg.de>
Date:   Fri Nov 18 16:45:13 2022 +0100

    Merge branch 'dev_varRBErobOpt_Update' of https://github.com/HomolkaN/matRad into dev_varRBErobOpt_Update

commit b6188d1
Author: Hardt <jennifer.hardt@dkfz-heidelberg.de>
Date:   Fri Nov 18 16:44:30 2022 +0100

    SAD and wsl fix

    SAD was wrong given in cm in header file, and phase space file location is given as a relative path, wsl dosent like the direct path

commit 277fef5
Author: Hardt <jennifer.hardt@dkfz-heidelberg.de>
Date:   Fri Nov 18 16:42:07 2022 +0100

    Phase space file starts at end of colimator

commit 16c9610
Author: Hardt <jennifer.hardt@dkfz-heidelberg.de>
Date:   Fri Nov 18 16:41:46 2022 +0100

    otherwise out and log file are the same file

commit c8fd302
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Fri Nov 18 16:06:14 2022 +0100

    Update matRad_calcPhotonDoseOmpMC.m

    Typo

commit 704d2c0
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Fri Nov 18 14:59:51 2022 +0100

    introduce ompMC class

    This change was done primarily to increase compatibility with the other MonteCarlo changes that have been done, mainly how the MC classes are currently structured and loaded.

commit 926d700
Author: Hardt <jennifer.hardt@dkfz-heidelberg.de>
Date:   Fri Nov 18 10:32:02 2022 +0100

    Update .gitignore

commit 147f058
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Fri Nov 18 10:10:18 2022 +0100

    Update matRad_runTests.m

    added small fix for runTests that couldn't find testing scripts

commit d6fd9f2
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Thu Nov 17 11:55:28 2022 +0100

    Update matRad_runTests.m

    Make sure a failing script does not get stuck in a directory

commit bb40eca
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Mon Nov 14 20:14:14 2022 +0100

    Update MatRad_TopasConfig.m

    Some more octave changes

commit 2f0b541
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Mon Nov 14 17:42:32 2022 +0100

    potential fix for testing

    renamed topas beam setup files to lowercase

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 b08ddc4
Merge: d8588e1 d0e246c
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Oct 28 14:45:19 2022 +0200

    Merge branch 'dev_varRBErobOpt_Update' of https://github.com/HomolkaN/matRad into pr/536

commit d8588e1
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Oct 28 14:44:46 2022 +0200

    change how emittance and energy spectrum should be represented in base data

commit 9b5c17a
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Oct 28 14:43:47 2022 +0200

    some technical fixes

commit ee58c3d
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Oct 28 14:43:23 2022 +0200

    remove the MCsquare MU correction as it is no longer valid

commit d0e246c
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Wed Oct 26 16:59:52 2022 +0200

    adjusted topas calcDose functions

    - streamlined topas photon calcDose function to be in line with newer function for particles
    - orderfields probably does not accept empty variables in older versions of matlab

commit d1c34ab
Merge: fe9adb8 c9d190e
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Wed Oct 26 16:35:33 2022 +0200

    Merge branch 'dev_varRBErobOpt_Update' of https://github.com/HomolkaN/matRad into dev_varRBErobOpt_Update

commit fe9adb8
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Wed Oct 26 16:35:27 2022 +0200

    added default beamProfile for photons

    - default beamProfile for photons in matRad_cfg
    - removed hardcoded beamProfile and numOfRuns in photonDoseMCtopas
    - added check if beam profile is compatible with radiationMode

commit c9d190e
Merge: f328b96 05db32a
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Wed Oct 26 16:00:39 2022 +0200

    Merge branch 'dev_varRBErobOpt' of https://github.com/e0404/matRad into pr/536

    # Conflicts:
    #	matRad_fluenceOptimization.m

commit 0af8238
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Wed Oct 26 15:58:45 2022 +0200

    small update to photons phasespace

    - set phasespace file as changable in config to maybe be implemented as a variable.
    - check is performed to see if phaseSpaceFile is available
    - Info is output if externalCalculation is turned on (manually place phaseSpace file)

commit f328b96
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Wed Oct 26 15:53:20 2022 +0200

    fix props in MatRad_Config

commit 0c2094d
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Tue Oct 25 23:36:24 2022 +0200

    Update TOPAS_beamSetup_Phasespace.txt.in

    - Fix to phaseSpace beamsetup.
    - .pshp file is still missing in order to run this properly

commit 2f53358
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Tue Oct 25 01:58:09 2022 +0200

    Finished merge of TopasConfig_Photons

    - further progression on photons for TOPAS.
    - added phasespace data SIEMENS*.header which is read through beamSetup_phasespace. If the file can be found by TOPAS in the subfolder has to be checked.
    - time feature splitting for dij calculation is turned off for now, this has to be discussed further

commit 93233d1
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Mon Oct 24 22:05:25 2022 +0200

    Update MatRad_Config.m

    disabled ompMC for now and change default photon engine to TOPAS. This can be reverted at a later stage when this is properly implemented.

commit 4b59c62
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Mon Oct 24 18:03:04 2022 +0200

    Merge piastammer/dev_varRBErobOpt_photonsTopas into dev_varRBErobOpt_Update

    This is a preliminary implementation. Next, I will implement this properly into the updated TOPAS structure.

    commit 0b82924
    Author: pia.stammer <pia.stammer@kit.edu>
    Date:   Fri Oct 21 16:09:00 2022 +0200

        Added phase space source
        *need testing!*
        -load phase space from source file SIEMENS_PRIMUS_6.0_0.10_15.0x15.0 available at https://www-nds.iaea.org/phsp/photon/SIEMENS_Primus_6MV/
        -added beamProfile 'phasespace' and appropriate input file
        -no pencil beam scanning supported, only single angle/position atm
        ToDo: Check geometry, especially distances between nozzle, phase space, MLC and patient (surface/isocenter?)

    commit 5ee5467
    Author: Noa Homolka <n.homolka@dkfz.de>
    Date:   Fri Sep 16 17:19:28 2022 +0200

        PhotonTOPAS Update

        - export leafWidth from aperture2collimation
        - small bug with additional "end" fix in ParticleDoseMCtopas
        - added switch for uniform weights in case of ~calcDoseDirect
        - changed materialConversion to 'RSP'
        - renamed numOfLeaves and leafTimes parameters for easier understanding
        - Translated MLC so that the Nozzle lies at beginning of MLC, not centered

    commit d43b80c
    Author: pia.stammer <pia.stammer@kit.edu>
    Date:   Fri Sep 16 14:47:50 2022 +0200

        Reduced size of source, increased number of histories

    commit 9067aa9
    Author: pia.stammer <pia.stammer@kit.edu>
    Date:   Fri Sep 16 11:31:06 2022 +0200

        Add uniform source and rotate MLC

    commit e7031b1
    Author: Noa Homolka <n.homolka@dkfz.de>
    Date:   Fri Sep 16 10:30:36 2022 +0200

        disabled tracking of MCrun folder

    commit 23b517a
    Author: pia.stammer <pia.stammer@kit.edu>
    Date:   Fri Sep 16 09:57:44 2022 +0200

        Status 2nd Hackday: Some corrections, TOPAS runs through, results mediocre

    commit bd68b3b
    Author: pia.stammer <pia.stammer@kit.edu>
    Date:   Fri Jun 10 17:00:17 2022 +0200

        Initial commit: Added MLC shape capabilities for TOPAS
        - shapes generated by matRad_aperture2collimation are written into TOPAS config file
        - use class matRad_TopasConfigPhotons with "virtualGaussian" beam and "mlc" Multileaf collimator set-up if corresponding info exists
        - TOPAS config files for several beams, rays, leafs and shapes are created and run through
        !!Caution: Results not yet validated!!

    commit c6dd0cb
    Author: Niklas Wahl <n.wahl@dkfz.de>
    Date:   Fri Apr 29 09:49:26 2022 +0200

        added basic photon infrastructure

    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 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 3610bf5
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Wed Oct 12 13:57:57 2022 +0200

    Update TopasConfig

    - added output of numOfBixels that did not meet the minimum numOfParticles required
    - removed unnecessary statement regarding alpha beta parameters
    - added comment to externalCalculation

commit 834bb1f
Merge: 19e22df 1b13404
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Wed Oct 5 17:21:33 2022 +0200

    Merge branch 'master' into pr/536

    # Conflicts:
    #	README.md

commit 19e22df
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Wed Oct 5 16:36:42 2022 +0200

    reset to old bixelwidth-dependent dij sampling

commit 1ee132d
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Tue Oct 4 20:31:30 2022 +0200

    Merge dev_varRBErobOpt_experimental

     Important branch Bug Fix:

        - fixed 2 major bugs in matRad_calcCubes!
        - fixed bug in TopasConfig, where the empty preallocated dij field was used to calculate tallies instead of the actual dose
        - made beamSetup more concise with shorter spaces between numbers
        - added fix for selection of focusIndex for generated phaseSpace data
        - changed handling of 0 fields
        - use isprop instead of isfield now that the class system is used
        - removed several statements that are no longer used or required

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 4a3e73a
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Thu Sep 22 21:35:00 2022 +0200

    Update to emittanceBaseData energyspread handling

commit 87bf5fe
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Sep 23 15:25:24 2022 +0200

    Fix indent

commit 37d3c58
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Thu Sep 22 20:53:11 2022 +0200

    Update to matRad_calcCubes.m

    - removed section that added "non-processed MC tallies", not needed anymore
    - removed 2 lines from MCsquare calculation that still referenced the outdated MC_tallies system

commit dc9552e
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Thu Sep 22 13:45:13 2022 +0200

    MC dij update calcDoseDirect

    - renamed topasCubes variable into dij to make it clearer (used to be a relict from deprecated workflow)
    - Brought dij generation of MCsquare and TOPAS in line for calcDoseDirect (all beam/ray/bixel fields are 1)

commit be032cc
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Thu Sep 22 13:42:04 2022 +0200

    bug fix for recent resampling update

    - fixed resampleCTtoGrid function being called incorrectly
    - fixed input

commit 45b6517
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Wed Sep 21 16:44:07 2022 +0200

    Merge dev_varRBErobOpt_experimental -> dev_varRBErobOpt_Update

    Update PR:
    - removed TOPAS scripts
    - added compatibility patch
    - Added patch for fluence Optimization and input of precalculated weigths
    - Added input of LET into calcLQParameter function
    - Moved resampling function from TOPASconfig in general tools
    - made externalCalculation parameter clearer to use and saved folder is output to the console
    -

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 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 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 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
HomolkaN pushed a commit to HomolkaN/matRad that referenced this pull request May 15, 2023
Merge dev_varRBErobOpt_Update >> dev_varRBErobOpt_experimental
319f850 
commit 8ca3b98
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Mon May 15 14:58:52 2023 +0200

    Merge E0404/dev_varRBErobOpt >> dev_varRBErobOpt_Update

    commit 58362ac
    Author: Niklas Wahl <n.wahl@dkfz.de>
    Date:   Wed May 10 12:08:26 2023 +0200

        correct for reading x and y spot sizes from emittance data in topas interface

    commit c0c8353
    Author: Niklas Wahl <n.wahl@dkfz.de>
    Date:   Tue Mar 7 01:50:55 2023 +0100

        remove phsp-header

    commit b85ec2c
    Author: Niklas Wahl <n.wahl@dkfz.de>
    Date:   Wed Jan 25 23:04:36 2023 +0100

        Downwards compatibility of biological model

    commit 5663803
    Author: Niklas Wahl <n.wahl@dkfz.de>
    Date:   Wed Jan 25 18:11:35 2023 +0100

        fix missing extractBetween function in Octave

    commit 64ce14c
    Merge: d3625aa 4e87571
    Author: Niklas Wahl <n.wahl@dkfz.de>
    Date:   Tue Jan 24 15:55:11 2023 +0100

        Merge pull request e0404#536 from HomolkaN/dev_varRBErobOpt_Update

        Extensive TOPAS workflow update:

    commit d3625aa
    Author: Niklas Wahl <n.wahl@dkfz.de>
    Date:   Thu Jan 19 13:41:47 2023 +0100

        Remove opengl software rendering query due to deprecation

    commit 3e427cf
    Author: Niklas Wahl <n.wahl@dkfz.de>
    Date:   Thu Jan 19 01:44:05 2023 +0100

        Avoid erroring on opengl in matRadGUI

    commit 894211d
    Author: Niklas Wahl <n.wahl@dkfz.de>
    Date:   Wed Dec 21 18:34:02 2022 +0100

        improve dicom import handling for RTPlan and RTDose

commit 7c2a36f
Author: Homolka <n.homolka@dkfz.de>
Date:   Fri Apr 28 14:55:37 2023 +0200

    update patient voxelSize handling in TOPAS

    - Removed vector from Z corrdinate of the VoxelSize (it's not written anyways and it's therefore not needed now)

commit 32e8341
Author: Homolka <n.homolka@dkfz.de>
Date:   Fri Apr 28 14:46:30 2023 +0200

    Important fix for TOPAS for multiple RBE scorers

    shared subscorer was only written once if multiple RBE models were requested!

commit 52487a6
Author: Homolka <n.homolka@dkfz.de>
Date:   Fri Apr 28 14:16:16 2023 +0200

    Merge dev_varRBErobOpt_experimental > dev_varRBErobOpt_Update

    matRad_bioModel:
    - change default Helium model to "HEL"
    - Change description option error to a warning because that would often crash loading in saved pln

    calcDoseDirectMC:
    - add passthrough of numOfDiscardedSpots, a new variable introduced to track how many spots didn't pass the minimum particle requirement by TOPAS

    calcParticleDoseMCsquare:
    - Add externalCalculation files (copy all necessary txt files to MCrun folder). This change was made so any MC simulation does not have to be rerun, even with externalCalculation turned off

    calcParticleDoseMCtopas:
    - add RBEmodel to workingDirectory name to be more distinguishable
    - add workingDirectory naming for phaseSpace
    - add pass through of DiscardedSpots
    - fix initialization of dij struct to use struct() instead of struct([]), could not assign new fields

    calcPhotonDoseOmpMC:
    - added pln variable needed to parse lateralCutoff into the class

    calcQualityIndicators:
    - only calculate QIs of fields that have the .Visible = true!
    - some minor bug fixes mostly with run variables

    fluenceOptimization
    - parse RemovedSpots from dij to resultGUI (only MC)

    generateStfSinglePencilBeam:
    - removed, because more modular version available

    MCemittanceBaseData:
    - Added comments to every substep
    - removed unnecessary counter
    - made whole fitting process more concise and easier to understand
    - added (commented out) alternative for proton rangeEnergyFit based on PSTAR Database instead of MC simulations
    - changed some variable names so their reason is clearer

    MCinit:
    - Remove as it is not needed anymore

    showDVH:
    - added output option to access the individual DVHs when plotting
    - font size reduced to 12
    - added manual setting of grid options to work properly when plotting multiple DVHs

    showQualityIndicators:
    - Added preliminary title with inputname

    ompConfig:
    - parse lateralCutOff with pln

    SimplePhantom_3mm:
    - add simple small phantom to test single pencil beams or small fields (faster than regular Boxphantom)

    compareDose:
    - move to plotting folder

    plotVoiContourSlice:
    - changed ct variable name to ctCube, since it's not the structure parsed in
    - add statement where only the fields are plotted with .Visible = true.

    generateStfPencilBeam:
    - add function to generate simple pencil beam and select energyIx for selected energy

    topasCheckComputationTime:
    - add simple function that reads out the complete duration of a TOPAS simulation (by parsing the foldername)

    TOPAS_beamSetup_*:
    - cleaned up beamSetup a bit (cosmetic)
    - added second file for internally scored phaseSpace and renamed "phaseSpace" into "genericPhaseSpace"

    topas\materialConverter\definedMaterials\*:
    - cosmetic changes for the files to be readable more clearly

    Topas_Config:
    - change default runs back to 5
    - increase parameterizationErrorMaxEnergy to not cancel TOPAS simulation due to that error
    - PhaseSpace presimulation: added new scorer field
    - PhaseSpace presimulation: added new files to infilenames struct
    - added parsion of pln.bioParam.model into TOPAS instead of only the default values
    - PhaseSpace presimulation: added new function to writeStfPhaseSpace
    - added maskDij function to remove dose from voxels outside of the patient geometry
    - added support to read_in standard deviation that has been scored separately
    - added check for NaNs in each readOut
    - display projected number of bixels that are to be discarded to console
    - added function to initialize MCparam (to have it at once place)

    topas\scorers\*:
    - cosmetic changes for the files to be readable more clearly
    - PhaseSpace presimulation: added scorer for phaseSpaceSurface

    topas\world\matRad_geometry:
    - cosmetic changes for the files to be readable more clearly
    - rearrange ordering to reflect hirarchie

    topas\world\matRad_geometry_read/score phaseSpace:
    - PhaseSpace presimulation: added new scorer files that use the phaseSpaceSurface to score a phaseSpace for later easier dose calculation

commit ab88a0f
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Mon Feb 27 15:38:53 2023 +0100

    Add readme reagarding topas phasespace file

commit b6c8e64
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Sun Feb 19 16:11:26 2023 +0100

    small additions and fixes to last merge

commit 63e9e2d
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Sun Feb 19 15:42:11 2023 +0100

    Merge dev_varRBErobOpt_experimental

    - Extension of calcDoseDirectMC to photons
    - External calculation of MCsquare
    - max_iter flag in fluence optimization (through pln.propOpt.max_iter)
    - TOPAS: add option to read in separate scorer file and not use constructor

commit 9294c20
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Fri Feb 17 17:48:34 2023 +0100

    Update .gitignore

    don't add .phsp (phasespace) files to gitHub (too lage)

commit 4e87571
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Tue Dec 20 00:07:42 2022 +0100

    typo fix in MCsquare dose calculation

commit aa9fb10
Merge: a5352d9 cbc78d0
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Mon Dec 19 19:29:58 2022 +0100

    Merge branch 'dev_varRBErobOpt' into pr/536

    # Conflicts:
    #	matRad_calcParticleDoseMCsquare.m
    #	matRad_calcParticleDoseMCtopas.m
    #	matRad_calcPhotonDoseMC.m

commit cbc78d0
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Mon Dec 19 19:29:05 2022 +0100

    small fix for running index in MC scenario calculation

commit a5352d9
Merge: 0eb3d41 4453b5a
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Mon Dec 19 19:26:48 2022 +0100

    Merge branch 'dev_varRBErobOpt' into pr/536

    # Conflicts:
    #	MCsquare/matRad_writeMCsquareinputAllFiles.m
    #	matRad_calcParticleDose.m
    #	matRad_calcParticleDoseMCsquare.m
    #	matRad_calcParticleDoseMCtopas.m
    #	matRad_calcPhotonDoseMC.m

commit 4453b5a
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Mon Dec 19 18:43:02 2022 +0100

    fix MU normalization

commit cb16de9
Merge: 675ebcb 6872400
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Mon Dec 19 18:42:13 2022 +0100

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

commit 675ebcb
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Mon Dec 19 18:41:45 2022 +0100

    range scenario fix and loop simplification for MC

commit 0eb3d41
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Tue Dec 6 04:14:27 2022 +0100

    Update matRad_doseAcc.m

    Fix error in matRad_doseAcc, where the interpolation messed everything up when the phantom didn't have uniform dimensions.

commit 6872400
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Dec 2 13:52:20 2022 +0100

    Update matRad_calcParticleDose.m

    Catch failure in drawing the waitbar

commit 74f4f5d
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Thu Dec 1 05:17:30 2022 +0100

    Update matRad_fluenceOptimization.m

    Some fields necessary for RBExD optimization have to be written if initial weights are passed in

commit 093eb96
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Wed Nov 30 18:40:18 2022 +0100

    Delete protons_savedMatRadMachine.mat

commit 3782e6c
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Wed Nov 30 17:42:38 2022 +0100

    Renamed classes to follow the naming scheme

    MatRad_TopasConfig -> matRad_TopasConfig
    MatRad_HeterogeneityConfig -> matRad_HeterogeneityConfig
    MatRad_MCsquareConfig -> matRad_MCsquareConfig
    MatRad_MCsquareBaseData -> matRad_MCsquareBaseData
    matRad_bioModel -> matRad_BioModel

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 f1e446a
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Wed Nov 23 18:28:10 2022 +0100

    minor MC workflow fixes

commit 63bb149
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Tue Nov 22 17:02:52 2022 +0100

    small fix wenn getting number of emittance gaussians from the weight array

commit 348ba2f
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Tue Nov 22 16:48:04 2022 +0100

    remove weird slab file in scenarios folder

commit d81012d
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Tue Nov 22 13:43:40 2022 +0100

    make mex file compilation a static function

commit 20626d1
Merge: fcc026f 37d4129
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Tue Nov 22 13:39:35 2022 +0100

    Merge branch 'dev_varRBErobOpt' of https://github.com/e0404/matRad into pr/536

commit fcc026f
Merge: 051dfdb 93571e6
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Tue Nov 22 13:38:33 2022 +0100

    Merge branch 'dev_varRBErobOpt_Update' of https://github.com/HomolkaN/matRad into pr/536

commit 051dfdb
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Tue Nov 22 13:35:52 2022 +0100

    add different SADs for x and y to the base data class

commit 93571e6
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Fri Nov 18 18:00:07 2022 +0100

    Update MatRad_TopasConfig.m

    minor compatibility changes for TOPAS

commit 3355d05
Merge: b6188d1 c8fd302
Author: Hardt <jennifer.hardt@dkfz-heidelberg.de>
Date:   Fri Nov 18 16:45:13 2022 +0100

    Merge branch 'dev_varRBErobOpt_Update' of https://github.com/HomolkaN/matRad into dev_varRBErobOpt_Update

commit b6188d1
Author: Hardt <jennifer.hardt@dkfz-heidelberg.de>
Date:   Fri Nov 18 16:44:30 2022 +0100

    SAD and wsl fix

    SAD was wrong given in cm in header file, and phase space file location is given as a relative path, wsl dosent like the direct path

commit 277fef5
Author: Hardt <jennifer.hardt@dkfz-heidelberg.de>
Date:   Fri Nov 18 16:42:07 2022 +0100

    Phase space file starts at end of colimator

commit 16c9610
Author: Hardt <jennifer.hardt@dkfz-heidelberg.de>
Date:   Fri Nov 18 16:41:46 2022 +0100

    otherwise out and log file are the same file

commit c8fd302
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Fri Nov 18 16:06:14 2022 +0100

    Update matRad_calcPhotonDoseOmpMC.m

    Typo

commit 704d2c0
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Fri Nov 18 14:59:51 2022 +0100

    introduce ompMC class

    This change was done primarily to increase compatibility with the other MonteCarlo changes that have been done, mainly how the MC classes are currently structured and loaded.

commit 926d700
Author: Hardt <jennifer.hardt@dkfz-heidelberg.de>
Date:   Fri Nov 18 10:32:02 2022 +0100

    Update .gitignore

commit 147f058
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Fri Nov 18 10:10:18 2022 +0100

    Update matRad_runTests.m

    added small fix for runTests that couldn't find testing scripts

commit d6fd9f2
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Thu Nov 17 11:55:28 2022 +0100

    Update matRad_runTests.m

    Make sure a failing script does not get stuck in a directory

commit bb40eca
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Mon Nov 14 20:14:14 2022 +0100

    Update MatRad_TopasConfig.m

    Some more octave changes

commit 2f0b541
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Mon Nov 14 17:42:32 2022 +0100

    potential fix for testing

    renamed topas beam setup files to lowercase

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 b08ddc4
Merge: d8588e1 d0e246c
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Oct 28 14:45:19 2022 +0200

    Merge branch 'dev_varRBErobOpt_Update' of https://github.com/HomolkaN/matRad into pr/536

commit d8588e1
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Oct 28 14:44:46 2022 +0200

    change how emittance and energy spectrum should be represented in base data

commit 9b5c17a
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Oct 28 14:43:47 2022 +0200

    some technical fixes

commit ee58c3d
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Oct 28 14:43:23 2022 +0200

    remove the MCsquare MU correction as it is no longer valid

commit d0e246c
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Wed Oct 26 16:59:52 2022 +0200

    adjusted topas calcDose functions

    - streamlined topas photon calcDose function to be in line with newer function for particles
    - orderfields probably does not accept empty variables in older versions of matlab

commit d1c34ab
Merge: fe9adb8 c9d190e
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Wed Oct 26 16:35:33 2022 +0200

    Merge branch 'dev_varRBErobOpt_Update' of https://github.com/HomolkaN/matRad into dev_varRBErobOpt_Update

commit fe9adb8
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Wed Oct 26 16:35:27 2022 +0200

    added default beamProfile for photons

    - default beamProfile for photons in matRad_cfg
    - removed hardcoded beamProfile and numOfRuns in photonDoseMCtopas
    - added check if beam profile is compatible with radiationMode

commit c9d190e
Merge: f328b96 05db32a
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Wed Oct 26 16:00:39 2022 +0200

    Merge branch 'dev_varRBErobOpt' of https://github.com/e0404/matRad into pr/536

    # Conflicts:
    #	matRad_fluenceOptimization.m

commit 0af8238
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Wed Oct 26 15:58:45 2022 +0200

    small update to photons phasespace

    - set phasespace file as changable in config to maybe be implemented as a variable.
    - check is performed to see if phaseSpaceFile is available
    - Info is output if externalCalculation is turned on (manually place phaseSpace file)

commit f328b96
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Wed Oct 26 15:53:20 2022 +0200

    fix props in MatRad_Config

commit 0c2094d
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Tue Oct 25 23:36:24 2022 +0200

    Update TOPAS_beamSetup_Phasespace.txt.in

    - Fix to phaseSpace beamsetup.
    - .pshp file is still missing in order to run this properly

commit 2f53358
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Tue Oct 25 01:58:09 2022 +0200

    Finished merge of TopasConfig_Photons

    - further progression on photons for TOPAS.
    - added phasespace data SIEMENS*.header which is read through beamSetup_phasespace. If the file can be found by TOPAS in the subfolder has to be checked.
    - time feature splitting for dij calculation is turned off for now, this has to be discussed further

commit 93233d1
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Mon Oct 24 22:05:25 2022 +0200

    Update MatRad_Config.m

    disabled ompMC for now and change default photon engine to TOPAS. This can be reverted at a later stage when this is properly implemented.

commit 4b59c62
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Mon Oct 24 18:03:04 2022 +0200

    Merge piastammer/dev_varRBErobOpt_photonsTopas into dev_varRBErobOpt_Update

    This is a preliminary implementation. Next, I will implement this properly into the updated TOPAS structure.

    commit 0b82924
    Author: pia.stammer <pia.stammer@kit.edu>
    Date:   Fri Oct 21 16:09:00 2022 +0200

        Added phase space source
        *need testing!*
        -load phase space from source file SIEMENS_PRIMUS_6.0_0.10_15.0x15.0 available at https://www-nds.iaea.org/phsp/photon/SIEMENS_Primus_6MV/
        -added beamProfile 'phasespace' and appropriate input file
        -no pencil beam scanning supported, only single angle/position atm
        ToDo: Check geometry, especially distances between nozzle, phase space, MLC and patient (surface/isocenter?)

    commit 5ee5467
    Author: Noa Homolka <n.homolka@dkfz.de>
    Date:   Fri Sep 16 17:19:28 2022 +0200

        PhotonTOPAS Update

        - export leafWidth from aperture2collimation
        - small bug with additional "end" fix in ParticleDoseMCtopas
        - added switch for uniform weights in case of ~calcDoseDirect
        - changed materialConversion to 'RSP'
        - renamed numOfLeaves and leafTimes parameters for easier understanding
        - Translated MLC so that the Nozzle lies at beginning of MLC, not centered

    commit d43b80c
    Author: pia.stammer <pia.stammer@kit.edu>
    Date:   Fri Sep 16 14:47:50 2022 +0200

        Reduced size of source, increased number of histories

    commit 9067aa9
    Author: pia.stammer <pia.stammer@kit.edu>
    Date:   Fri Sep 16 11:31:06 2022 +0200

        Add uniform source and rotate MLC

    commit e7031b1
    Author: Noa Homolka <n.homolka@dkfz.de>
    Date:   Fri Sep 16 10:30:36 2022 +0200

        disabled tracking of MCrun folder

    commit 23b517a
    Author: pia.stammer <pia.stammer@kit.edu>
    Date:   Fri Sep 16 09:57:44 2022 +0200

        Status 2nd Hackday: Some corrections, TOPAS runs through, results mediocre

    commit bd68b3b
    Author: pia.stammer <pia.stammer@kit.edu>
    Date:   Fri Jun 10 17:00:17 2022 +0200

        Initial commit: Added MLC shape capabilities for TOPAS
        - shapes generated by matRad_aperture2collimation are written into TOPAS config file
        - use class matRad_TopasConfigPhotons with "virtualGaussian" beam and "mlc" Multileaf collimator set-up if corresponding info exists
        - TOPAS config files for several beams, rays, leafs and shapes are created and run through
        !!Caution: Results not yet validated!!

    commit c6dd0cb
    Author: Niklas Wahl <n.wahl@dkfz.de>
    Date:   Fri Apr 29 09:49:26 2022 +0200

        added basic photon infrastructure

    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 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 3610bf5
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Wed Oct 12 13:57:57 2022 +0200

    Update TopasConfig

    - added output of numOfBixels that did not meet the minimum numOfParticles required
    - removed unnecessary statement regarding alpha beta parameters
    - added comment to externalCalculation

commit 834bb1f
Merge: 19e22df 1b13404
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Wed Oct 5 17:21:33 2022 +0200

    Merge branch 'master' into pr/536

    # Conflicts:
    #	README.md

commit 19e22df
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Wed Oct 5 16:36:42 2022 +0200

    reset to old bixelwidth-dependent dij sampling

commit 1ee132d
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Tue Oct 4 20:31:30 2022 +0200

    Merge dev_varRBErobOpt_experimental

     Important branch Bug Fix:

        - fixed 2 major bugs in matRad_calcCubes!
        - fixed bug in TopasConfig, where the empty preallocated dij field was used to calculate tallies instead of the actual dose
        - made beamSetup more concise with shorter spaces between numbers
        - added fix for selection of focusIndex for generated phaseSpace data
        - changed handling of 0 fields
        - use isprop instead of isfield now that the class system is used
        - removed several statements that are no longer used or required

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 4a3e73a
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Thu Sep 22 21:35:00 2022 +0200

    Update to emittanceBaseData energyspread handling

commit 87bf5fe
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Sep 23 15:25:24 2022 +0200

    Fix indent

commit 37d3c58
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Thu Sep 22 20:53:11 2022 +0200

    Update to matRad_calcCubes.m

    - removed section that added "non-processed MC tallies", not needed anymore
    - removed 2 lines from MCsquare calculation that still referenced the outdated MC_tallies system

commit dc9552e
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Thu Sep 22 13:45:13 2022 +0200

    MC dij update calcDoseDirect

    - renamed topasCubes variable into dij to make it clearer (used to be a relict from deprecated workflow)
    - Brought dij generation of MCsquare and TOPAS in line for calcDoseDirect (all beam/ray/bixel fields are 1)

commit be032cc
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Thu Sep 22 13:42:04 2022 +0200

    bug fix for recent resampling update

    - fixed resampleCTtoGrid function being called incorrectly
    - fixed input

commit 45b6517
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Wed Sep 21 16:44:07 2022 +0200

    Merge dev_varRBErobOpt_experimental -> dev_varRBErobOpt_Update

    Update PR:
    - removed TOPAS scripts
    - added compatibility patch
    - Added patch for fluence Optimization and input of precalculated weigths
    - Added input of LET into calcLQParameter function
    - Moved resampling function from TOPASconfig in general tools
    - made externalCalculation parameter clearer to use and saved folder is output to the console
    -

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 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 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 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
HomolkaN pushed a commit to HomolkaN/matRad that referenced this pull request May 17, 2023
Fixed merge issue with bioModel
13d3926 
commit 8ca3b98
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Mon May 15 14:58:52 2023 +0200

    Merge E0404/dev_varRBErobOpt >> dev_varRBErobOpt_Update

    commit 58362ac
    Author: Niklas Wahl <n.wahl@dkfz.de>
    Date:   Wed May 10 12:08:26 2023 +0200

        correct for reading x and y spot sizes from emittance data in topas interface

    commit c0c8353
    Author: Niklas Wahl <n.wahl@dkfz.de>
    Date:   Tue Mar 7 01:50:55 2023 +0100

        remove phsp-header

    commit b85ec2c
    Author: Niklas Wahl <n.wahl@dkfz.de>
    Date:   Wed Jan 25 23:04:36 2023 +0100

        Downwards compatibility of biological model

    commit 5663803
    Author: Niklas Wahl <n.wahl@dkfz.de>
    Date:   Wed Jan 25 18:11:35 2023 +0100

        fix missing extractBetween function in Octave

    commit 64ce14c
    Merge: d3625aa 4e87571
    Author: Niklas Wahl <n.wahl@dkfz.de>
    Date:   Tue Jan 24 15:55:11 2023 +0100

        Merge pull request e0404#536 from HomolkaN/dev_varRBErobOpt_Update

        Extensive TOPAS workflow update:

    commit d3625aa
    Author: Niklas Wahl <n.wahl@dkfz.de>
    Date:   Thu Jan 19 13:41:47 2023 +0100

        Remove opengl software rendering query due to deprecation

    commit 3e427cf
    Author: Niklas Wahl <n.wahl@dkfz.de>
    Date:   Thu Jan 19 01:44:05 2023 +0100

        Avoid erroring on opengl in matRadGUI

    commit 894211d
    Author: Niklas Wahl <n.wahl@dkfz.de>
    Date:   Wed Dec 21 18:34:02 2022 +0100

        improve dicom import handling for RTPlan and RTDose

commit 7c2a36f
Author: Homolka <n.homolka@dkfz.de>
Date:   Fri Apr 28 14:55:37 2023 +0200

    update patient voxelSize handling in TOPAS

    - Removed vector from Z corrdinate of the VoxelSize (it's not written anyways and it's therefore not needed now)

commit 32e8341
Author: Homolka <n.homolka@dkfz.de>
Date:   Fri Apr 28 14:46:30 2023 +0200

    Important fix for TOPAS for multiple RBE scorers

    shared subscorer was only written once if multiple RBE models were requested!

commit 52487a6
Author: Homolka <n.homolka@dkfz.de>
Date:   Fri Apr 28 14:16:16 2023 +0200

    Merge dev_varRBErobOpt_experimental > dev_varRBErobOpt_Update

    matRad_bioModel:
    - change default Helium model to "HEL"
    - Change description option error to a warning because that would often crash loading in saved pln

    calcDoseDirectMC:
    - add passthrough of numOfDiscardedSpots, a new variable introduced to track how many spots didn't pass the minimum particle requirement by TOPAS

    calcParticleDoseMCsquare:
    - Add externalCalculation files (copy all necessary txt files to MCrun folder). This change was made so any MC simulation does not have to be rerun, even with externalCalculation turned off

    calcParticleDoseMCtopas:
    - add RBEmodel to workingDirectory name to be more distinguishable
    - add workingDirectory naming for phaseSpace
    - add pass through of DiscardedSpots
    - fix initialization of dij struct to use struct() instead of struct([]), could not assign new fields

    calcPhotonDoseOmpMC:
    - added pln variable needed to parse lateralCutoff into the class

    calcQualityIndicators:
    - only calculate QIs of fields that have the .Visible = true!
    - some minor bug fixes mostly with run variables

    fluenceOptimization
    - parse RemovedSpots from dij to resultGUI (only MC)

    generateStfSinglePencilBeam:
    - removed, because more modular version available

    MCemittanceBaseData:
    - Added comments to every substep
    - removed unnecessary counter
    - made whole fitting process more concise and easier to understand
    - added (commented out) alternative for proton rangeEnergyFit based on PSTAR Database instead of MC simulations
    - changed some variable names so their reason is clearer

    MCinit:
    - Remove as it is not needed anymore

    showDVH:
    - added output option to access the individual DVHs when plotting
    - font size reduced to 12
    - added manual setting of grid options to work properly when plotting multiple DVHs

    showQualityIndicators:
    - Added preliminary title with inputname

    ompConfig:
    - parse lateralCutOff with pln

    SimplePhantom_3mm:
    - add simple small phantom to test single pencil beams or small fields (faster than regular Boxphantom)

    compareDose:
    - move to plotting folder

    plotVoiContourSlice:
    - changed ct variable name to ctCube, since it's not the structure parsed in
    - add statement where only the fields are plotted with .Visible = true.

    generateStfPencilBeam:
    - add function to generate simple pencil beam and select energyIx for selected energy

    topasCheckComputationTime:
    - add simple function that reads out the complete duration of a TOPAS simulation (by parsing the foldername)

    TOPAS_beamSetup_*:
    - cleaned up beamSetup a bit (cosmetic)
    - added second file for internally scored phaseSpace and renamed "phaseSpace" into "genericPhaseSpace"

    topas\materialConverter\definedMaterials\*:
    - cosmetic changes for the files to be readable more clearly

    Topas_Config:
    - change default runs back to 5
    - increase parameterizationErrorMaxEnergy to not cancel TOPAS simulation due to that error
    - PhaseSpace presimulation: added new scorer field
    - PhaseSpace presimulation: added new files to infilenames struct
    - added parsion of pln.bioParam.model into TOPAS instead of only the default values
    - PhaseSpace presimulation: added new function to writeStfPhaseSpace
    - added maskDij function to remove dose from voxels outside of the patient geometry
    - added support to read_in standard deviation that has been scored separately
    - added check for NaNs in each readOut
    - display projected number of bixels that are to be discarded to console
    - added function to initialize MCparam (to have it at once place)

    topas\scorers\*:
    - cosmetic changes for the files to be readable more clearly
    - PhaseSpace presimulation: added scorer for phaseSpaceSurface

    topas\world\matRad_geometry:
    - cosmetic changes for the files to be readable more clearly
    - rearrange ordering to reflect hirarchie

    topas\world\matRad_geometry_read/score phaseSpace:
    - PhaseSpace presimulation: added new scorer files that use the phaseSpaceSurface to score a phaseSpace for later easier dose calculation

commit ab88a0f
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Mon Feb 27 15:38:53 2023 +0100

    Add readme reagarding topas phasespace file

commit b6c8e64
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Sun Feb 19 16:11:26 2023 +0100

    small additions and fixes to last merge

commit 63e9e2d
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Sun Feb 19 15:42:11 2023 +0100

    Merge dev_varRBErobOpt_experimental

    - Extension of calcDoseDirectMC to photons
    - External calculation of MCsquare
    - max_iter flag in fluence optimization (through pln.propOpt.max_iter)
    - TOPAS: add option to read in separate scorer file and not use constructor

commit 9294c20
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Fri Feb 17 17:48:34 2023 +0100

    Update .gitignore

    don't add .phsp (phasespace) files to gitHub (too lage)

commit 4e87571
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Tue Dec 20 00:07:42 2022 +0100

    typo fix in MCsquare dose calculation

commit aa9fb10
Merge: a5352d9 cbc78d0
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Mon Dec 19 19:29:58 2022 +0100

    Merge branch 'dev_varRBErobOpt' into pr/536

    # Conflicts:
    #	matRad_calcParticleDoseMCsquare.m
    #	matRad_calcParticleDoseMCtopas.m
    #	matRad_calcPhotonDoseMC.m

commit cbc78d0
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Mon Dec 19 19:29:05 2022 +0100

    small fix for running index in MC scenario calculation

commit a5352d9
Merge: 0eb3d41 4453b5a
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Mon Dec 19 19:26:48 2022 +0100

    Merge branch 'dev_varRBErobOpt' into pr/536

    # Conflicts:
    #	MCsquare/matRad_writeMCsquareinputAllFiles.m
    #	matRad_calcParticleDose.m
    #	matRad_calcParticleDoseMCsquare.m
    #	matRad_calcParticleDoseMCtopas.m
    #	matRad_calcPhotonDoseMC.m

commit 4453b5a
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Mon Dec 19 18:43:02 2022 +0100

    fix MU normalization

commit cb16de9
Merge: 675ebcb 6872400
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Mon Dec 19 18:42:13 2022 +0100

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

commit 675ebcb
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Mon Dec 19 18:41:45 2022 +0100

    range scenario fix and loop simplification for MC

commit 0eb3d41
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Tue Dec 6 04:14:27 2022 +0100

    Update matRad_doseAcc.m

    Fix error in matRad_doseAcc, where the interpolation messed everything up when the phantom didn't have uniform dimensions.

commit 6872400
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Dec 2 13:52:20 2022 +0100

    Update matRad_calcParticleDose.m

    Catch failure in drawing the waitbar

commit 74f4f5d
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Thu Dec 1 05:17:30 2022 +0100

    Update matRad_fluenceOptimization.m

    Some fields necessary for RBExD optimization have to be written if initial weights are passed in

commit 093eb96
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Wed Nov 30 18:40:18 2022 +0100

    Delete protons_savedMatRadMachine.mat

commit 3782e6c
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Wed Nov 30 17:42:38 2022 +0100

    Renamed classes to follow the naming scheme

    MatRad_TopasConfig -> matRad_TopasConfig
    MatRad_HeterogeneityConfig -> matRad_HeterogeneityConfig
    MatRad_MCsquareConfig -> matRad_MCsquareConfig
    MatRad_MCsquareBaseData -> matRad_MCsquareBaseData
    matRad_bioModel -> matRad_BioModel

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 f1e446a
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Wed Nov 23 18:28:10 2022 +0100

    minor MC workflow fixes

commit 63bb149
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Tue Nov 22 17:02:52 2022 +0100

    small fix wenn getting number of emittance gaussians from the weight array

commit 348ba2f
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Tue Nov 22 16:48:04 2022 +0100

    remove weird slab file in scenarios folder

commit d81012d
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Tue Nov 22 13:43:40 2022 +0100

    make mex file compilation a static function

commit 20626d1
Merge: fcc026f 37d4129
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Tue Nov 22 13:39:35 2022 +0100

    Merge branch 'dev_varRBErobOpt' of https://github.com/e0404/matRad into pr/536

commit fcc026f
Merge: 051dfdb 93571e6
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Tue Nov 22 13:38:33 2022 +0100

    Merge branch 'dev_varRBErobOpt_Update' of https://github.com/HomolkaN/matRad into pr/536

commit 051dfdb
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Tue Nov 22 13:35:52 2022 +0100

    add different SADs for x and y to the base data class

commit 93571e6
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Fri Nov 18 18:00:07 2022 +0100

    Update MatRad_TopasConfig.m

    minor compatibility changes for TOPAS

commit 3355d05
Merge: b6188d1 c8fd302
Author: Hardt <jennifer.hardt@dkfz-heidelberg.de>
Date:   Fri Nov 18 16:45:13 2022 +0100

    Merge branch 'dev_varRBErobOpt_Update' of https://github.com/HomolkaN/matRad into dev_varRBErobOpt_Update

commit b6188d1
Author: Hardt <jennifer.hardt@dkfz-heidelberg.de>
Date:   Fri Nov 18 16:44:30 2022 +0100

    SAD and wsl fix

    SAD was wrong given in cm in header file, and phase space file location is given as a relative path, wsl dosent like the direct path

commit 277fef5
Author: Hardt <jennifer.hardt@dkfz-heidelberg.de>
Date:   Fri Nov 18 16:42:07 2022 +0100

    Phase space file starts at end of colimator

commit 16c9610
Author: Hardt <jennifer.hardt@dkfz-heidelberg.de>
Date:   Fri Nov 18 16:41:46 2022 +0100

    otherwise out and log file are the same file

commit c8fd302
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Fri Nov 18 16:06:14 2022 +0100

    Update matRad_calcPhotonDoseOmpMC.m

    Typo

commit 704d2c0
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Fri Nov 18 14:59:51 2022 +0100

    introduce ompMC class

    This change was done primarily to increase compatibility with the other MonteCarlo changes that have been done, mainly how the MC classes are currently structured and loaded.

commit 926d700
Author: Hardt <jennifer.hardt@dkfz-heidelberg.de>
Date:   Fri Nov 18 10:32:02 2022 +0100

    Update .gitignore

commit 147f058
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Fri Nov 18 10:10:18 2022 +0100

    Update matRad_runTests.m

    added small fix for runTests that couldn't find testing scripts

commit d6fd9f2
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Thu Nov 17 11:55:28 2022 +0100

    Update matRad_runTests.m

    Make sure a failing script does not get stuck in a directory

commit bb40eca
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Mon Nov 14 20:14:14 2022 +0100

    Update MatRad_TopasConfig.m

    Some more octave changes

commit 2f0b541
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Mon Nov 14 17:42:32 2022 +0100

    potential fix for testing

    renamed topas beam setup files to lowercase

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 b08ddc4
Merge: d8588e1 d0e246c
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Oct 28 14:45:19 2022 +0200

    Merge branch 'dev_varRBErobOpt_Update' of https://github.com/HomolkaN/matRad into pr/536

commit d8588e1
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Oct 28 14:44:46 2022 +0200

    change how emittance and energy spectrum should be represented in base data

commit 9b5c17a
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Oct 28 14:43:47 2022 +0200

    some technical fixes

commit ee58c3d
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Oct 28 14:43:23 2022 +0200

    remove the MCsquare MU correction as it is no longer valid

commit d0e246c
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Wed Oct 26 16:59:52 2022 +0200

    adjusted topas calcDose functions

    - streamlined topas photon calcDose function to be in line with newer function for particles
    - orderfields probably does not accept empty variables in older versions of matlab

commit d1c34ab
Merge: fe9adb8 c9d190e
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Wed Oct 26 16:35:33 2022 +0200

    Merge branch 'dev_varRBErobOpt_Update' of https://github.com/HomolkaN/matRad into dev_varRBErobOpt_Update

commit fe9adb8
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Wed Oct 26 16:35:27 2022 +0200

    added default beamProfile for photons

    - default beamProfile for photons in matRad_cfg
    - removed hardcoded beamProfile and numOfRuns in photonDoseMCtopas
    - added check if beam profile is compatible with radiationMode

commit c9d190e
Merge: f328b96 05db32a
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Wed Oct 26 16:00:39 2022 +0200

    Merge branch 'dev_varRBErobOpt' of https://github.com/e0404/matRad into pr/536

    # Conflicts:
    #	matRad_fluenceOptimization.m

commit 0af8238
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Wed Oct 26 15:58:45 2022 +0200

    small update to photons phasespace

    - set phasespace file as changable in config to maybe be implemented as a variable.
    - check is performed to see if phaseSpaceFile is available
    - Info is output if externalCalculation is turned on (manually place phaseSpace file)

commit f328b96
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Wed Oct 26 15:53:20 2022 +0200

    fix props in MatRad_Config

commit 0c2094d
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Tue Oct 25 23:36:24 2022 +0200

    Update TOPAS_beamSetup_Phasespace.txt.in

    - Fix to phaseSpace beamsetup.
    - .pshp file is still missing in order to run this properly

commit 2f53358
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Tue Oct 25 01:58:09 2022 +0200

    Finished merge of TopasConfig_Photons

    - further progression on photons for TOPAS.
    - added phasespace data SIEMENS*.header which is read through beamSetup_phasespace. If the file can be found by TOPAS in the subfolder has to be checked.
    - time feature splitting for dij calculation is turned off for now, this has to be discussed further

commit 93233d1
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Mon Oct 24 22:05:25 2022 +0200

    Update MatRad_Config.m

    disabled ompMC for now and change default photon engine to TOPAS. This can be reverted at a later stage when this is properly implemented.

commit 4b59c62
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Mon Oct 24 18:03:04 2022 +0200

    Merge piastammer/dev_varRBErobOpt_photonsTopas into dev_varRBErobOpt_Update

    This is a preliminary implementation. Next, I will implement this properly into the updated TOPAS structure.

    commit 0b82924
    Author: pia.stammer <pia.stammer@kit.edu>
    Date:   Fri Oct 21 16:09:00 2022 +0200

        Added phase space source
        *need testing!*
        -load phase space from source file SIEMENS_PRIMUS_6.0_0.10_15.0x15.0 available at https://www-nds.iaea.org/phsp/photon/SIEMENS_Primus_6MV/
        -added beamProfile 'phasespace' and appropriate input file
        -no pencil beam scanning supported, only single angle/position atm
        ToDo: Check geometry, especially distances between nozzle, phase space, MLC and patient (surface/isocenter?)

    commit 5ee5467
    Author: Noa Homolka <n.homolka@dkfz.de>
    Date:   Fri Sep 16 17:19:28 2022 +0200

        PhotonTOPAS Update

        - export leafWidth from aperture2collimation
        - small bug with additional "end" fix in ParticleDoseMCtopas
        - added switch for uniform weights in case of ~calcDoseDirect
        - changed materialConversion to 'RSP'
        - renamed numOfLeaves and leafTimes parameters for easier understanding
        - Translated MLC so that the Nozzle lies at beginning of MLC, not centered

    commit d43b80c
    Author: pia.stammer <pia.stammer@kit.edu>
    Date:   Fri Sep 16 14:47:50 2022 +0200

        Reduced size of source, increased number of histories

    commit 9067aa9
    Author: pia.stammer <pia.stammer@kit.edu>
    Date:   Fri Sep 16 11:31:06 2022 +0200

        Add uniform source and rotate MLC

    commit e7031b1
    Author: Noa Homolka <n.homolka@dkfz.de>
    Date:   Fri Sep 16 10:30:36 2022 +0200

        disabled tracking of MCrun folder

    commit 23b517a
    Author: pia.stammer <pia.stammer@kit.edu>
    Date:   Fri Sep 16 09:57:44 2022 +0200

        Status 2nd Hackday: Some corrections, TOPAS runs through, results mediocre

    commit bd68b3b
    Author: pia.stammer <pia.stammer@kit.edu>
    Date:   Fri Jun 10 17:00:17 2022 +0200

        Initial commit: Added MLC shape capabilities for TOPAS
        - shapes generated by matRad_aperture2collimation are written into TOPAS config file
        - use class matRad_TopasConfigPhotons with "virtualGaussian" beam and "mlc" Multileaf collimator set-up if corresponding info exists
        - TOPAS config files for several beams, rays, leafs and shapes are created and run through
        !!Caution: Results not yet validated!!

    commit c6dd0cb
    Author: Niklas Wahl <n.wahl@dkfz.de>
    Date:   Fri Apr 29 09:49:26 2022 +0200

        added basic photon infrastructure

    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 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 3610bf5
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Wed Oct 12 13:57:57 2022 +0200

    Update TopasConfig

    - added output of numOfBixels that did not meet the minimum numOfParticles required
    - removed unnecessary statement regarding alpha beta parameters
    - added comment to externalCalculation

commit 834bb1f
Merge: 19e22df 1b13404
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Wed Oct 5 17:21:33 2022 +0200

    Merge branch 'master' into pr/536

    # Conflicts:
    #	README.md

commit 19e22df
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Wed Oct 5 16:36:42 2022 +0200

    reset to old bixelwidth-dependent dij sampling

commit 1ee132d
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Tue Oct 4 20:31:30 2022 +0200

    Merge dev_varRBErobOpt_experimental

     Important branch Bug Fix:

        - fixed 2 major bugs in matRad_calcCubes!
        - fixed bug in TopasConfig, where the empty preallocated dij field was used to calculate tallies instead of the actual dose
        - made beamSetup more concise with shorter spaces between numbers
        - added fix for selection of focusIndex for generated phaseSpace data
        - changed handling of 0 fields
        - use isprop instead of isfield now that the class system is used
        - removed several statements that are no longer used or required

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 4a3e73a
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Thu Sep 22 21:35:00 2022 +0200

    Update to emittanceBaseData energyspread handling

commit 87bf5fe
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Fri Sep 23 15:25:24 2022 +0200

    Fix indent

commit 37d3c58
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Thu Sep 22 20:53:11 2022 +0200

    Update to matRad_calcCubes.m

    - removed section that added "non-processed MC tallies", not needed anymore
    - removed 2 lines from MCsquare calculation that still referenced the outdated MC_tallies system

commit dc9552e
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Thu Sep 22 13:45:13 2022 +0200

    MC dij update calcDoseDirect

    - renamed topasCubes variable into dij to make it clearer (used to be a relict from deprecated workflow)
    - Brought dij generation of MCsquare and TOPAS in line for calcDoseDirect (all beam/ray/bixel fields are 1)

commit be032cc
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Thu Sep 22 13:42:04 2022 +0200

    bug fix for recent resampling update

    - fixed resampleCTtoGrid function being called incorrectly
    - fixed input

commit 45b6517
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Wed Sep 21 16:44:07 2022 +0200

    Merge dev_varRBErobOpt_experimental -> dev_varRBErobOpt_Update

    Update PR:
    - removed TOPAS scripts
    - added compatibility patch
    - Added patch for fluence Optimization and input of precalculated weigths
    - Added input of LET into calcLQParameter function
    - Moved resampling function from TOPASconfig in general tools
    - made externalCalculation parameter clearer to use and saved folder is output to the console
    -

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 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 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 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
HomolkaN pushed a commit to HomolkaN/matRad that referenced this pull request Aug 29, 2023
Merge varRBErobOpt_experimental into varRBErobOpt_Update
646ca07 
commit 2e2823bd78dd85a296e271c0d88b50d22db7f796
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Tue Aug 29 18:26:33 2023 +0200

    merge changes to MCemittanceBaseData from master/dev_varRBErobOpt

commit 86cecacc25dfce80132ced66dabdae93b18b84c8
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Sat Aug 12 17:07:32 2023 +0200

    add water- and lung equivalent sampling in topas

    lungEquivalent as default

commit 589205c818d7872dee8a98ac3336c66402a958dc
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Sat Aug 12 17:01:41 2023 +0200

    change how dates are named in external calculation (more readable)

commit ad9bf5ca892ff01af67a365899188f6fedebca24
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Sat Aug 12 17:01:24 2023 +0200

    add complete external calculation for MCsquare

commit 170127d16ff598f10d2e5e61d9b314b44cbb0bc5
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Sat Aug 12 17:01:08 2023 +0200

    change sampling material converter to default (correct sampling this way)

commit 5758017ea5f2b4b1149d28b40b2101b5d20a4984
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Thu Aug 10 18:32:01 2023 +0200

    remove HLUT from phantoms

commit 74717188cc853ee85690174e35f2cd09eeb4fe65
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Thu Aug 10 18:31:34 2023 +0200

    change MCsquare sampling to use lung material like TOPAS

commit 58fdddc26d0497b22977d35768eec5f7a97526e4
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Thu Aug 10 18:31:20 2023 +0200

    add specific error message to heterogeneity correction

commit d8520c80bf36f770a19b58a71db08184c286d117
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Mon Aug 7 23:25:07 2023 +0200

    Update MCsquare default HLUT

    Use actual matRad HLUT because the default HLUT wasn't the default HLUT -.-

commit e629bdba85f8116e55dae34e825c9f231583bb6e
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Fri Jul 21 14:17:37 2023 +0200

    update phantoms to characterize base data sets

commit e4b3b16f01a4ee25a0f5abfba3cd4562f91267f7
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Fri Jul 21 14:16:41 2023 +0200

    Update matRadGUI.m

    At least load ct and cst if it can't find some fields in the pln? Maybe get some default values instead. maybe this is fixed in a new GUI version already!

commit 687e758e0e84664b0b61f4ccf84b2d8baece1b7d
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Fri Jul 21 14:15:24 2023 +0200

    HC: fix for error with empty propHeterogeneity field upon loading

commit 023a70e63818afbddc7e8b848128138026431428
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Wed Jul 19 15:56:01 2023 +0200

    fix crucial bug for analytical lung heterogeneity correction

    - the way it was implemented, the algorithm only chose the first lung entry of the cst instead of all of them, because of a mixup with the scenarios (I know -.-)
    - this section has to be updated if going to 4D calculation, because THERE you actually need the cell structure for the scenarios

commit 96bb9e9d190794e8177465c402b65db77044cb8b
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Wed Jul 12 16:41:03 2023 +0200

    Update matRad_downsampleMachineFile.m

commit 3d451cd541d3f284d644623d9853941084507529
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Wed Jul 12 16:25:23 2023 +0200

    Update protons_generic_TOPAS_APM.mat

commit af2786366d5d6c97a1e8bd56ed5f626cb99e4b3a
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Fri Jul 7 19:17:14 2023 +0200

    update TopasConfig with potential Fix for HLUTs that do not contain an air section

commit 0a7fc8259f4f9255ce9499cc8c239ee95841e65f
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Thu Jul 6 16:43:28 2023 +0200

    Update plotIDD.m

commit d72c04672bc707875cff3ccb700926e397162da1
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Thu Jul 6 16:26:41 2023 +0200

    update matRad_calcIDD_pencil with option for peakPos

commit 5c0baea6fa9f1f7c88c9d3fb60619b52fdaf65fa
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Thu Jul 6 16:21:56 2023 +0200

    update energyspread estimation to be physically correct

    The calculation of the energySpread is now in line with Bortfeld1997:
    1. Estimation of the totalSigma by calculation from the FWHM
    2. Estimate the pathSigma from Eq.17 (Bortfeld1997)
    3. Actually calculate Energyspread relative to the current nominalEnergy

    Note: it is believed that both TOPAS and MCsquare actually take the relative energySpread as number rather than the % mantioned in the documentation

commit e6d6401b3cd2e0ca5594c77c892e7f115907d859
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Wed Jul 5 00:56:27 2023 +0200

    small fix so TOPAS heterogeneity correction is skipped properly

commit 54c2f628b90b21f932fbea9b2ebb0fcf15a771f7
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Tue Jul 4 20:45:32 2023 +0200

    further improvements to matRad_MCemittanceBaseData

    - improved range-energy fit
    - added energy-range fit to replace values from bortfeld paper (new updated NIST data and should make more sense to include values that are fitted analogously to range-energy)

commit 4e24eea5351676b7534199d50ef5b5d28602e7cd
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Tue Jul 4 18:22:11 2023 +0200

    clean up MCemittanceBaseData a bit

commit 8f89f9c945d72f863684fe70952ae7e2dfc2b592
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Tue Jun 27 21:16:02 2023 +0200

    added stf dependeny in MCsquareBaseData, added preliminary try catch to save the matRadMachine

commit 6d41e375314cfd7a10df2d3fb28bc5824efae216
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Tue Jun 27 21:15:25 2023 +0200

    Update matRad_MCemittanceBaseData.m

    Add dependence of the emittance with the selectedFocus (new Base data)

commit da3254404bc0f2080f466f218644fefa392911dc
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Tue Jun 27 21:14:46 2023 +0200

    Update matRad_downsampleMachineFile.m

    - Added option to finesample the whole grid first. Especially for small energies where the smoothing doesn't work correctly if there aren't enough entries
    - Added option to only run downsampling for a single energy

commit 8e4e37ec380c218d920b3e494f817a0aaf8eade9
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Tue Jun 27 21:13:07 2023 +0200

    Fitted 8 lower energies to generic_TOPAS base data

    - Simulations were done in TOPAS using the preset energySpectrum and emittance
    - Z, weight, sigma1 and sigma2 fitted by Remo
    - added APM fit and LET to new data
    - improved APM fit marginally by further adjusting the initial weights

commit 8ec9e70f017788e43d94e14d938d4dde4fa85222
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Thu Jun 22 15:48:13 2023 +0200

    slightly update particleMonteCarlo example

commit a1a4d15a764c5eff84188c071128891d1fc64c94
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Thu Jun 22 15:44:27 2023 +0200

    changed BioModel to lowercase bioModel

commit 37f6bc9c2b343b8c08c281b1f86c7c16fe7fee86
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Thu Jun 22 15:17:10 2023 +0200

    cleaned up topasConfig a bit

commit 12226807f289824fc1569c561b96c8704a5ae127
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Thu Jun 22 15:15:05 2023 +0200

    Added 2 small phantoms to efficiently test pencil beams with

commit f319e2c5629a542a401633192760f8eafa7e8064
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Thu Jun 22 15:03:30 2023 +0200

    fixed cst struct in lung phantoms

commit 021b482269dde0ecb9112a475eeeccff2337a780
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Thu Jun 22 14:57:02 2023 +0200

    added numerical convolution to heterogeneity correction

commit 3ba235c66265732171cad7f1c672a529771feac4
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Mon Jun 19 19:42:59 2023 +0200

    Create SimplePhantom_1mm_longwide.mat

commit 87df060a6ab6a3021507691a98e06e0b21f610a3
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Mon Jun 19 19:41:01 2023 +0200

    change BAMStoIsoDist in generic_TOPAS_APM base data and adjust sigma

commit 16050191366b87304e874a09813bbb4b035c945b
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Sun Jun 18 17:56:50 2023 +0200

    complete protons_generic_TOPAS_APM base data that includes all changes

commit beea16a026fb64cc0cc7a85e0fee2b34d4f6ad02
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Sat Jun 17 15:34:40 2023 +0200

    density fix for TOPAS

    fix addresses shifts in the peaks with depth that originated from a broken schneider converter
    - set Schneider converter to use rspHLUT from matRad with simple HUsections (straightforward conversion)
    - changed minHU in rspHLUT to -1000 since TOPAS will use that internally anyways and otherwise the indices are wrong

commit 9f8ce1f36edf52c340f7942f223b7dd822ef2789
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Thu Jun 15 22:27:46 2023 +0200

    Create SimplePhantom_1mm_long.mat

    Create simplePhantom_1mm_long in order to characterize pencil beams on a very long and narrow phantom with 1mm voxel

commit 8ddc3118f5e08128f7ab81fb6e8ca7f5ca99c553
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Thu Jun 15 22:26:01 2023 +0200

    in particleDose calculation, always override APM data if not needed

commit ab96a105318dd17281a60f941b22400875ce68c8
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Thu Jun 15 22:25:38 2023 +0200

    Update matRad_calcIDD_pencil.m

commit 9a6a660cec64f1f5fbc26f7062b3ad51f98348fa
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Thu Jun 15 22:20:21 2023 +0200

    merge MC interface changes from dev_varRBErobOpt

    - Merge MC interface changes (mostly air offset, mex files)
    - merge biologicalModel
    - merge minor optimization change

commit 625f0befdad32945c8e5ddbef54f38022e21c0e6
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Thu Jun 15 21:09:14 2023 +0200

    merge testing and optimization changes from dev_varRBErobOpt

commit 7448b9312294e1d1c3f734e004dc4117d734fa32
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Thu Jun 15 15:47:37 2023 +0200

    added function to calculate the distal fall-off

    fall-off distance from 80% to 20% of the max dose

commit aa4dc8df3012c8e084d7402e6b4ec1d8765d2c88
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Wed Jun 14 16:31:37 2023 +0200

    PRIV: added calcIDD_pencil function to properly take lateral profiles into account for pencil beams (at iso)

commit 8dd66c87d6d926681b26c54222fde77ad90badfc
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Wed Jun 14 16:30:34 2023 +0200

    refined generic_TOPAS baseData and added APM

    - Contains APM
    - Contains LET
    - Contains new InitFocus
    - Contains correct energySpectrum

commit 2cbe674a1300105e35c52dda78b10bf14b6205d4
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Wed Jun 14 16:29:23 2023 +0200

    save numOfSamples in dose modulation

commit d1fd9af3de87c0937bc85d148bac3f8216e980d5
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Wed Jun 14 16:28:53 2023 +0200

    update machine downsampling

    downsample first, and then truncate!

commit c484bca7e57cdfbc7a26149cb9a78460ba53ad16
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Fri Jun 9 12:36:11 2023 +0200

    fix another bug in phaseSpace splitting pipeline

commit ca1644b828429d755abb9fddbe01c83188616ab6
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Thu Jun 8 22:24:50 2023 +0200

    update genericTOPAS LET

commit 90932c312717913935923753d60b35e53bcafab3
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Thu Jun 8 22:13:18 2023 +0200

    fixed typo in TOPAS phaseSpace

commit 1c6b5ca2efdde6c99a769a2f76532368802684be
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Wed Jun 7 13:39:14 2023 +0200

    Fix for separated phaseSpace calculation (heterogeneity correction)

commit 56116e662a8851f40338fd5788f1d35de7fb80b0
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Wed Jun 7 11:20:33 2023 +0200

    Update protons_generic_TOPAS_LET with updated sigma

commit f9cf6836f122ea143e9c63cc63c68b7c17ebed78
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Tue Jun 6 21:56:41 2023 +0200

    Create protons_generic_TOPAS_newInitFocus.mat

commit 96082d4e9a8199bf4317370f25950ee4d7431ba4
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Tue Jun 6 21:06:14 2023 +0200

    fix bug in emittanceBaseData

commit 02a2a11af396af2965bd445243843996038e172e
Author: Niklas Wahl <n.wahl@dkfz.de>
Date:   Tue Jun 6 14:13:01 2023 +0200

    add empirical correction for MCS in air when approximating beam model

commit 65dccf6624307708a656c65f8c27eda93020229d
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Tue Jun 6 14:33:31 2023 +0200

    added 2 additional LEM scorers based on the V79 cell line

    one with 5µm LEM radius and one with 8µm LEM radius

commit 8a5cbf34d64b633ff7d9c37b84a53add57d8bf87
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Tue Jun 6 14:29:58 2023 +0200

    fix so that phaseSpace will run automatically (still not correct though)

commit 909238ccc909db3fe5c9249b4d30cb22d2b71f08
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Tue Jun 6 14:25:25 2023 +0200

    update machineData downsampling with gradual grid

commit 81276fc0e6b6e4ab511d91d970cf14d19f9bfab0
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Tue Jun 6 14:19:15 2023 +0200

    update genericTOPAS with LET

commit ef068390531105e6a657428bda9c0750dcd85676
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Wed May 31 14:00:12 2023 +0200

    Create protons_generic_TOPAS_LET.mat

    Added generic LET based on TOPAS simulations to protons_generic_TOPAS
    - Contains downsampled values, LET and a fixed 3% energy spread

commit 4e61b59a9f6c14a15515fb00358c5cc6a0f2d783
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Wed May 31 13:53:42 2023 +0200

    Update matRad_downsampleMachineFile.m

    refined downsampling with a fine grid at peak and a smooth gradient to the rest of the base data (maximal agreement)

commit 873ea32b91b6a852a18b09ed808035eaeba752cc
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Wed May 31 12:51:21 2023 +0200

    set RBE for TOPAS as default

commit c47ef526381de7ca05119955b4894f6e47822fdb
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Wed May 31 12:36:28 2023 +0200

    TopasConfig further automate phaseSpace splitting

commit 530fa40d2ac88750593ab49b576bcb00edc3e4ee
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Wed May 31 12:34:20 2023 +0200

    Update matRad_readBinData.m

    add option to read everything in one vector if cubeDim isn't set

commit eca3d90989bf6da177944df35b6926cdca568dfd
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Wed May 31 12:32:49 2023 +0200

    Update matRad_example12_simpleParticleMonteCarlo.m

commit 01463de09c4def8580b02e71db66b52021745762
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Thu May 25 12:35:31 2023 +0200

    actually name the base data set accordingly

commit 63ea625f779ac395f9c1dd702d9b5c4e3461e195
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Thu May 25 12:34:28 2023 +0200

    Create protons_generic_TOPAS with fixed 3% energy spread

commit 48a09f433702f091364f24405f65ecdb66ec14d1
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Thu May 25 12:33:23 2023 +0200

    Fix typo in calcParticleDoseMCtopas for phaseSpace

commit 5feb58a66d783e684109cd920b864c5adf4151d4
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Thu May 25 12:33:05 2023 +0200

    update phaseSpaceScorer to output the phasespace in an above directory

    -> the subsequent samples can use the scorer then

commit 2d239ff74f64da024c5f81b3d464afed0ed65257
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Thu May 25 12:32:12 2023 +0200

    Use rangeEnergy fit for protons based on NIST tables

commit 13d39263c2e2a9303cf852bd4a82f59bd2bf3951
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Wed May 17 16:58:42 2023 +0200

    Fixed merge issue with bioModel

    commit 8ca3b98198321714bb4a88c183bc65d359f42f80
    Author: Noa Homolka <n.homolka@dkfz.de>
    Date:   Mon May 15 14:58:52 2023 +0200

        Merge E0404/dev_varRBErobOpt >> dev_varRBErobOpt_Update

        commit 58362ac810fafea3ada04a93c9af319fd6d91a13
        Author: Niklas Wahl <n.wahl@dkfz.de>
        Date:   Wed May 10 12:08:26 2023 +0200

            correct for reading x and y spot sizes from emittance data in topas interface

        commit c0c8353793a6809b64d9d3245681175333855d50
        Author: Niklas Wahl <n.wahl@dkfz.de>
        Date:   Tue Mar 7 01:50:55 2023 +0100

            remove phsp-header

        commit b85ec2c1d50cb67d5e0be75dcce21f61bf3701e4
        Author: Niklas Wahl <n.wahl@dkfz.de>
        Date:   Wed Jan 25 23:04:36 2023 +0100

            Downwards compatibility of biological model

        commit 56638039c2d46e96c7de1ff0e8aaef0c3be247ab
        Author: Niklas Wahl <n.wahl@dkfz.de>
        Date:   Wed Jan 25 18:11:35 2023 +0100

            fix missing extractBetween function in Octave

        commit 64ce14ca2b7337c8d141bcd1ca9dba5c2bf79a48
        Merge: d3625aad 4e875716
        Author: Niklas Wahl <n.wahl@dkfz.de>
        Date:   Tue Jan 24 15:55:11 2023 +0100

            Merge pull request #536 from HomolkaN/dev_varRBErobOpt_Update

            Extensive TOPAS workflow update:

        commit d3625aadb81af29df92ecba1823a998f33163fe5
        Author: Niklas Wahl <n.wahl@dkfz.de>
        Date:   Thu Jan 19 13:41:47 2023 +0100

            Remove opengl software rendering query due to deprecation

        commit 3e427cfa7595986d32555beae70fe16178cd99a4
        Author: Niklas Wahl <n.wahl@dkfz.de>
        Date:   Thu Jan 19 01:44:05 2023 +0100

            Avoid erroring on opengl in matRadGUI

        commit 894211de77e83de4cc586251ecd1eadf3c4e2793
        Author: Niklas Wahl <n.wahl@dkfz.de>
        Date:   Wed Dec 21 18:34:02 2022 +0100

            improve dicom import handling for RTPlan and RTDose

    commit 7c2a36f29af48d66f9b9638ce48929a378ae9a97
    Author: Homolka <n.homolka@dkfz.de>
    Date:   Fri Apr 28 14:55:37 2023 +0200

        update patient voxelSize handling in TOPAS

        - Removed vector from Z corrdinate of the VoxelSize (it's not written anyways and it's therefore not needed now)

    commit 32e83416c339965f55a10325900ddc849aa92803
    Author: Homolka <n.homolka@dkfz.de>
    Date:   Fri Apr 28 14:46:30 2023 +0200

        Important fix for TOPAS for multiple RBE scorers

        shared subscorer was only written once if multiple RBE models were requested!

    commit 52487a6b8120e8337abfb4676a71bd88dc57c4eb
    Author: Homolka <n.homolka@dkfz.de>
    Date:   Fri Apr 28 14:16:16 2023 +0200

        Merge dev_varRBErobOpt_experimental > dev_varRBErobOpt_Update

        matRad_bioModel:
        - change default Helium model to "HEL"
        - Change description option error to a warning because that would often crash loading in saved pln

        calcDoseDirectMC:
        - add passthrough of numOfDiscardedSpots, a new variable introduced to track how many spots didn't pass the minimum particle requirement by TOPAS

        calcParticleDoseMCsquare:
        - Add externalCalculation files (copy all necessary txt files to MCrun folder). This change was made so any MC simulation does not have to be rerun, even with externalCalculation turned off

        calcParticleDoseMCtopas:
        - add RBEmodel to workingDirectory name to be more distinguishable
        - add workingDirectory naming for phaseSpace
        - add pass through of DiscardedSpots
        - fix initialization of dij struct to use struct() instead of struct([]), could not assign new fields

        calcPhotonDoseOmpMC:
        - added pln variable needed to parse lateralCutoff into the class

        calcQualityIndicators:
        - only calculate QIs of fields that have the .Visible = true!
        - some minor bug fixes mostly with run variables

        fluenceOptimization
        - parse RemovedSpots from dij to resultGUI (only MC)

        generateStfSinglePencilBeam:
        - removed, because more modular version available

        MCemittanceBaseData:
        - Added comments to every substep
        - removed unnecessary counter
        - made whole fitting process more concise and easier to understand
        - added (commented out) alternative for proton rangeEnergyFit based on PSTAR Database instead of MC simulations
        - changed some variable names so their reason is clearer

        MCinit:
        - Remove as it is not needed anymore

        showDVH:
        - added output option to access the individual DVHs when plotting
        - font size reduced to 12
        - added manual setting of grid options to work properly when plotting multiple DVHs

        showQualityIndicators:
        - Added preliminary title with inputname

        ompConfig:
        - parse lateralCutOff with pln

        SimplePhantom_3mm:
        - add simple small phantom to test single pencil beams or small fields (faster than regular Boxphantom)

        compareDose:
        - move to plotting folder

        plotVoiContourSlice:
        - changed ct variable name to ctCube, since it's not the structure parsed in
        - add statement where only the fields are plotted with .Visible = true.

        generateStfPencilBeam:
        - add function to generate simple pencil beam and select energyIx for selected energy

        topasCheckComputationTime:
        - add simple function that reads out the complete duration of a TOPAS simulation (by parsing the foldername)

        TOPAS_beamSetup_*:
        - cleaned up beamSetup a bit (cosmetic)
        - added second file for internally scored phaseSpace and renamed "phaseSpace" into "genericPhaseSpace"

        topas\materialConverter\definedMaterials\*:
        - cosmetic changes for the files to be readable more clearly

        Topas_Config:
        - change default runs back to 5
        - increase parameterizationErrorMaxEnergy to not cancel TOPAS simulation due to that error
        - PhaseSpace presimulation: added new scorer field
        - PhaseSpace presimulation: added new files to infilenames struct
        - added parsion of pln.bioParam.model into TOPAS instead of only the default values
        - PhaseSpace presimulation: added new function to writeStfPhaseSpace
        - added maskDij function to remove dose from voxels outside of the patient geometry
        - added support to read_in standard deviation that has been scored separately
        - added check for NaNs in each readOut
        - display projected number of bixels that are to be discarded to console
        - added function to initialize MCparam (to have it at once place)

        topas\scorers\*:
        - cosmetic changes for the files to be readable more clearly
        - PhaseSpace presimulation: added scorer for phaseSpaceSurface

        topas\world\matRad_geometry:
        - cosmetic changes for the files to be readable more clearly
        - rearrange ordering to reflect hirarchie

        topas\world\matRad_geometry_read/score phaseSpace:
        - PhaseSpace presimulation: added new scorer files that use the phaseSpaceSurface to score a phaseSpace for later easier dose calculation

    commit ab88a0fa75e830a9aa7fad140e52919bc088bcec
    Author: Noa Homolka <n.homolka@dkfz.de>
    Date:   Mon Feb 27 15:38:53 2023 +0100

        Add readme reagarding topas phasespace file

    commit b6c8e6477ba320a1d3d7efea84e3b87f9298e71d
    Author: Noa Homolka <n.homolka@dkfz.de>
    Date:   Sun Feb 19 16:11:26 2023 +0100

        small additions and fixes to last merge

    commit 63e9e2dc3438da5a78fc0936dab9c80c51755278
    Author: Noa Homolka <n.homolka@dkfz.de>
    Date:   Sun Feb 19 15:42:11 2023 +0100

        Merge dev_varRBErobOpt_experimental

        - Extension of calcDoseDirectMC to photons
        - External calculation of MCsquare
        - max_iter flag in fluence optimization (through pln.propOpt.max_iter)
        - TOPAS: add option to read in separate scorer file and not use constructor

    commit 9294c202eebd336a981b711ce3e1aa5ca64dbf6d
    Author: Noa Homolka <n.homolka@dkfz.de>
    Date:   Fri Feb 17 17:48:34 2023 +0100

        Update .gitignore

        don't add .phsp (phasespace) files to gitHub (too lage)

    commit 4e8757165cbf339d3f20dfaa109a325979f1efc2
    Author: Niklas Wahl <n.wahl@dkfz.de>
    Date:   Tue Dec 20 00:07:42 2022 +0100

        typo fix in MCsquare dose calculation

    commit aa9fb10200ba52d3fde335ad1c60831100302aae
    Merge: a5352d99 cbc78d07
    Author: Niklas Wahl <n.wahl@dkfz.de>
    Date:   Mon Dec 19 19:29:58 2022 +0100

        Merge branch 'dev_varRBErobOpt' into pr/536

        # Conflicts:
        #	matRad_calcParticleDoseMCsquare.m
        #	matRad_calcParticleDoseMCtopas.m
        #	matRad_calcPhotonDoseMC.m

    commit cbc78d07f392ea76a9ce37291d851882b0c0627b
    Author: Niklas Wahl <n.wahl@dkfz.de>
    Date:   Mon Dec 19 19:29:05 2022 +0100

        small fix for running index in MC scenario calculation

    commit a5352d99ffb4bab28b5a7b4a68d843ec4cc3a92a
    Merge: 0eb3d41b 4453b5ae
    Author: Niklas Wahl <n.wahl@dkfz.de>
    Date:   Mon Dec 19 19:26:48 2022 +0100

        Merge branch 'dev_varRBErobOpt' into pr/536

        # Conflicts:
        #	MCsquare/matRad_writeMCsquareinputAllFiles.m
        #	matRad_calcParticleDose.m
        #	matRad_calcParticleDoseMCsquare.m
        #	matRad_calcParticleDoseMCtopas.m
        #	matRad_calcPhotonDoseMC.m

    commit 4453b5ae89b0fbdd3ed534bd141ebb89cc770241
    Author: Niklas Wahl <n.wahl@dkfz.de>
    Date:   Mon Dec 19 18:43:02 2022 +0100

        fix MU normalization

    commit cb16de9c1aea902d21241446cfeee13a8ac92ce4
    Merge: 675ebcb0 68724001
    Author: Niklas Wahl <n.wahl@dkfz.de>
    Date:   Mon Dec 19 18:42:13 2022 +0100

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

    commit 675ebcb07a1820916292d45b3ca3c8be70e77096
    Author: Niklas Wahl <n.wahl@dkfz.de>
    Date:   Mon Dec 19 18:41:45 2022 +0100

        range scenario fix and loop simplification for MC

    commit 0eb3d41b3418e8ec84cc062ac6ed279dafe59c9a
    Author: Noa Homolka <n.homolka@dkfz.de>
    Date:   Tue Dec 6 04:14:27 2022 +0100

        Update matRad_doseAcc.m

        Fix error in matRad_doseAcc, where the interpolation messed everything up when the phantom didn't have uniform dimensions.

    commit 6872400174d738b1e4e14140c3573a47d17b3745
    Author: Niklas Wahl <n.wahl@dkfz.de>
    Date:   Fri Dec 2 13:52:20 2022 +0100

        Update matRad_calcParticleDose.m

        Catch failure in drawing the waitbar

    commit 74f4f5d44401e77d8b7a14fa68dbce3f4ecf37dd
    Author: Noa Homolka <n.homolka@dkfz.de>
    Date:   Thu Dec 1 05:17:30 2022 +0100

        Update matRad_fluenceOptimization.m

        Some fields necessary for RBExD optimization have to be written if initial weights are passed in

    commit 093eb964deb62133ae0dcf3f0b15edfbc3616e6c
    Author: Noa Homolka <n.homolka@dkfz.de>
    Date:   Wed Nov 30 18:40:18 2022 +0100

        Delete protons_savedMatRadMachine.mat

    commit 3782e6c7fe2b125e3911b2537869b491e7024b22
    Author: Noa Homolka <n.homolka@dkfz.de>
    Date:   Wed Nov 30 17:42:38 2022 +0100

        Renamed classes to follow the naming scheme

        MatRad_TopasConfig -> matRad_TopasConfig
        MatRad_HeterogeneityConfig -> matRad_HeterogeneityConfig
        MatRad_MCsquareConfig -> matRad_MCsquareConfig
        MatRad_MCsquareBaseData -> matRad_MCsquareBaseData
        matRad_bioModel -> matRad_BioModel

    commit 7cd7879fa8ab542abd35d200b171cf77f5d7c0ad
    Merge: 37d41298 cb6b04a6
    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 cb6b04a603533a5906617d489eb36e4a054eaa3a
    Author: Niklas Wahl <n.wahl@dkfz.de>
    Date:   Tue Nov 29 20:26:59 2022 +0100

        Update README.md

        Update Cancer Aid Funding

    commit 538f08b63ee433e96c4b3f2fea2ac2253a9b60e6
    Author: Niklas Wahl <n.wahl@dkfz.de>
    Date:   Tue Nov 29 20:23:17 2022 +0100

        Update README.md

        Add funding information

    commit f1e446a8d06eff73e8224a59498bbfde53bc4456
    Author: Noa Homolka <n.homolka@dkfz.de>
    Date:   Wed Nov 23 18:28:10 2022 +0100

        minor MC workflow fixes

    commit 63bb149b191840e240e21e07f257f6172241f8f8
    Author: Niklas Wahl <n.wahl@dkfz.de>
    Date:   Tue Nov 22 17:02:52 2022 +0100

        small fix wenn getting number of emittance gaussians from the weight array

    commit 348ba2fee095ced97e2d957b674a24c9812310a8
    Author: Niklas Wahl <n.wahl@dkfz.de>
    Date:   Tue Nov 22 16:48:04 2022 +0100

        remove weird slab file in scenarios folder

    commit d81012dd18badb6fcb74dacf5518c9fd267ef99c
    Author: Niklas Wahl <n.wahl@dkfz.de>
    Date:   Tue Nov 22 13:43:40 2022 +0100

        make mex file compilation a static function

    commit 20626d1e4321e2b3d9e5887d4904c1f5c5f5f9b3
    Merge: fcc026f0 37d41298
    Author: Niklas Wahl <n.wahl@dkfz.de>
    Date:   Tue Nov 22 13:39:35 2022 +0100

        Merge branch 'dev_varRBErobOpt' of https://github.com/e0404/matRad into pr/536

    commit fcc026f01709beef78f2ea861dceb6054af00d49
    Merge: 051dfdbd 93571e61
    Author: Niklas Wahl <n.wahl@dkfz.de>
    Date:   Tue Nov 22 13:38:33 2022 +0100

        Merge branch 'dev_varRBErobOpt_Update' of https://github.com/HomolkaN/matRad into pr/536

    commit 051dfdbd9f8eb6bb60ecfbb258eef310115bd0a5
    Author: Niklas Wahl <n.wahl@dkfz.de>
    Date:   Tue Nov 22 13:35:52 2022 +0100

        add different SADs for x and y to the base data class

    commit 93571e61baa9a4d4a8b89b0883f92893b0ee84cf
    Author: Noa Homolka <n.homolka@dkfz.de>
    Date:   Fri Nov 18 18:00:07 2022 +0100

        Update MatRad_TopasConfig.m

        minor compatibility changes for TOPAS

    commit 3355d0519af14942d4201ff4220c1fcaa19c5292
    Merge: b6188d1f c8fd3029
    Author: Hardt <jennifer.hardt@dkfz-heidelberg.de>
    Date:   Fri Nov 18 16:45:13 2022 +0100

        Merge branch 'dev_varRBErobOpt_Update' of https://github.com/HomolkaN/matRad into dev_varRBErobOpt_Update

    commit b6188d1f5c0df47a808392290feaf12705190989
    Author: Hardt <jennifer.hardt@dkfz-heidelberg.de>
    Date:   Fri Nov 18 16:44:30 2022 +0100

        SAD and wsl fix

        SAD was wrong given in cm in header file, and phase space file location is given as a relative path, wsl dosent like the direct path

    commit 277fef513dbc2bb972b77521dcfd342cefaa576e
    Author: Hardt <jennifer.hardt@dkfz-heidelberg.de>
    Date:   Fri Nov 18 16:42:07 2022 +0100

        Phase space file starts at end of colimator

    commit 16c9610a9b65ad45b1dabbea5ddd155e2019eb80
    Author: Hardt <jennifer.hardt@dkfz-heidelberg.de>
    Date:   Fri Nov 18 16:41:46 2022 +0100

        otherwise out and log file are the same file

    commit c8fd30297275590ef6f390239267c1f49f10d4a5
    Author: Noa Homolka <n.homolka@dkfz.de>
    Date:   Fri Nov 18 16:06:14 2022 +0100

        Update matRad_calcPhotonDoseOmpMC.m

        Typo

    commit 704d2c08ae503705d87dafc8af8a65f223754ec6
    Author: Noa Homolka <n.homolka@dkfz.de>
    Date:   Fri Nov 18 14:59:51 2022 +0100

        introduce ompMC class

        This change was done primarily to increase compatibility with the other MonteCarlo changes that have been done, mainly how the MC classes are currently structured and loaded.

    commit 926d70097867a9bac85f1bb4f78684a4cfaaf503
    Author: Hardt <jennifer.hardt@dkfz-heidelberg.de>
    Date:   Fri Nov 18 10:32:02 2022 +0100

        Update .gitignore

    commit 147f0582bfc487378ea651bce4d2ff1e185698bb
    Author: Noa Homolka <n.homolka@dkfz.de>
    Date:   Fri Nov 18 10:10:18 2022 +0100

        Update matRad_runTests.m

        added small fix for runTests that couldn't find testing scripts

    commit d6fd9f2997881af72985c5df0a1562880e9eb48b
    Author: Niklas Wahl <n.wahl@dkfz.de>
    Date:   Thu Nov 17 11:55:28 2022 +0100

        Update matRad_runTests.m

        Make sure a failing script does not get stuck in a directory

    commit bb40ecab977e8992c17cbb093a726499328fb0f1
    Author: Noa Homolka <n.homolka@dkfz.de>
    Date:   Mon Nov 14 20:14:14 2022 +0100

        Update MatRad_TopasConfig.m

        Some more octave changes

    commit 2f0b541a6791c340b316a7f5db275e8a1304f913
    Author: Noa Homolka <n.homolka@dkfz.de>
    Date:   Mon Nov 14 17:42:32 2022 +0100

        potential fix for testing

        renamed topas beam setup files to lowercase

    commit 37d412983857db3c163b8b5a4b4719a55a989207
    Author: Niklas Wahl <n.wahl@dkfz.de>
    Date:   Fri Nov 11 18:05:52 2022 +0100

        add some compatibility functions to scenarioModel

    commit 2c576ab155599f00650d408fe9089cae999bde21
    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 b08ddc49c7f84cec4df56bc5213c4ef726609be3
    Merge: d8588e13 d0e246c6
    Author: Niklas Wahl <n.wahl@dkfz.de>
    Date:   Fri Oct 28 14:45:19 2022 +0200

        Merge branch 'dev_varRBErobOpt_Update' of https://github.com/HomolkaN/matRad into pr/536

    commit d8588e131751fdff71389f7cfab2f13b69ff1e9e
    Author: Niklas Wahl <n.wahl@dkfz.de>
    Date:   Fri Oct 28 14:44:46 2022 +0200

        change how emittance and energy spectrum should be represented in base data

    commit 9b5c17af4cc000483a46989fc51d8609129412ea
    Author: Niklas Wahl <n.wahl@dkfz.de>
    Date:   Fri Oct 28 14:43:47 2022 +0200

        some technical fixes

    commit ee58c3d155a7b33ac44c60753b35d48fcb409904
    Author: Niklas Wahl <n.wahl@dkfz.de>
    Date:   Fri Oct 28 14:43:23 2022 +0200

        remove the MCsquare MU correction as it is no longer valid

    commit d0e246c6da2c53bfab2389cb4b7271b3fb9ce495
    Author: Noa Homolka <n.homolka@dkfz.de>
    Date:   Wed Oct 26 16:59:52 2022 +0200

        adjusted topas calcDose functions

        - streamlined topas photon calcDose function to be in line with newer function for particles
        - orderfields probably does not accept empty variables in older versions of matlab

    commit d1c34aba8a11fdcb86c80e271c2e844d0c5fcba6
    Merge: fe9adb80 c9d190e1
    Author: Noa Homolka <n.homolka@dkfz.de>
    Date:   Wed Oct 26 16:35:33 2022 +0200

        Merge branch 'dev_varRBErobOpt_Update' of https://github.com/HomolkaN/matRad into dev_varRBErobOpt_Update

    commit fe9adb804144f5739ed541bdc290c9d9aa1961de
    Author: Noa Homolka <n.homolka@dkfz.de>
    Date:   Wed Oct 26 16:35:27 2022 +0200

        added default beamProfile for photons

        - default beamProfile for photons in matRad_cfg
        - removed hardcoded beamProfile and numOfRuns in photonDoseMCtopas
        - added check if beam profile is compatible with radiationMode

    commit c9d190e16c784994989bcb1c1d69a311522ab61c
    Merge: f328b964 05db32a3
    Author: Niklas Wahl <n.wahl@dkfz.de>
    Date:   Wed Oct 26 16:00:39 2022 +0200

        Merge branch 'dev_varRBErobOpt' of https://github.com/e0404/matRad into pr/536

        # Conflicts:
        #	matRad_fluenceOptimization.m

    commit 0af8238dd63ad051b446253682dd30d96abad8ca
    Author: Noa Homolka <n.homolka@dkfz.de>
    Date:   Wed Oct 26 15:58:45 2022 +0200

        small update to photons phasespace

        - set phasespace file as changable in config to maybe be implemented as a variable.
        - check is performed to see if phaseSpaceFile is available
        - Info is output if externalCalculation is turned on (manually place phaseSpace file)

    commit f328b96408e79750aea512e85d27344c0ec65fc2
    Author: Niklas Wahl <n.wahl@dkfz.de>
    Date:   Wed Oct 26 15:53:20 2022 +0200

        fix props in MatRad_Config

    commit 0c2094d33ba42566fb7a186b81975bdb93288105
    Author: Noa Homolka <n.homolka@dkfz.de>
    Date:   Tue Oct 25 23:36:24 2022 +0200

        Update TOPAS_beamSetup_Phasespace.txt.in

        - Fix to phaseSpace beamsetup.
        - .pshp file is still missing in order to run this properly

    commit 2f53358537c4fb6e9d1c46c43649b739493338dc
    Author: Noa Homolka <n.homolka@dkfz.de>
    Date:   Tue Oct 25 01:58:09 2022 +0200

        Finished merge of TopasConfig_Photons

        - further progression on photons for TOPAS.
        - added phasespace data SIEMENS*.header which is read through beamSetup_phasespace. If the file can be found by TOPAS in the subfolder has to be checked.
        - time feature splitting for dij calculation is turned off for now, this has to be discussed further

    commit 93233d1d4a7fa58c3bffdab8476d00fc2ea3d367
    Author: Noa Homolka <n.homolka@dkfz.de>
    Date:   Mon Oct 24 22:05:25 2022 +0200

        Update MatRad_Config.m

        disabled ompMC for now and change default photon engine to TOPAS. This can be reverted at a later stage when this is properly implemented.

    commit 4b59c62b782844cfe98e4f335cffb1363a181bef
    Author: Noa Homolka <n.homolka@dkfz.de>
    Date:   Mon Oct 24 18:03:04 2022 +0200

        Merge piastammer/dev_varRBErobOpt_photonsTopas into dev_varRBErobOpt_Update

        This is a preliminary implementation. Next, I will implement this properly into the updated TOPAS structure.

        commit 0b82924cb06e43568801ae97cddc67bd7316f814
        Author: pia.stammer <pia.stammer@kit.edu>
        Date:   Fri Oct 21 16:09:00 2022 +0200

            Added phase space source
            *need testing!*
            -load phase space from source file SIEMENS_PRIMUS_6.0_0.10_15.0x15.0 available at https://www-nds.iaea.org/phsp/photon/SIEMENS_Primus_6MV/
            -added beamProfile 'phasespace' and appropriate input file
            -no pencil beam scanning supported, only single angle/position atm
            ToDo: Check geometry, especially distances between nozzle, phase space, MLC and patient (surface/isocenter?)

        commit 5ee546711c2bda90eec3fef84726eecbab61fd05
        Author: Noa Homolka <n.homolka@dkfz.de>
        Date:   Fri Sep 16 17:19:28 2022 +0200

            PhotonTOPAS Update

            - export leafWidth from aperture2collimation
            - small bug with additional "end" fix in ParticleDoseMCtopas
            - added switch for uniform weights in case of ~calcDoseDirect
            - changed materialConversion to 'RSP'
            - renamed numOfLeaves and leafTimes parameters for easier understanding
            - Translated MLC so that the Nozzle lies at beginning of MLC, not centered

        commit d43b80cc5f7a58dcd781d5d986aa4b7842bcb2e3
        Author: pia.stammer <pia.stammer@kit.edu>
        Date:   Fri Sep 16 14:47:50 2022 +0200

            Reduced size of source, increased number of histories

        commit 9067aa9c7ea33be6c219b98ca260a35e1f6357d6
        Author: pia.stammer <pia.stammer@kit.edu>
        Date:   Fri Sep 16 11:31:06 2022 +0200

            Add uniform source and rotate MLC

        commit e7031b191568979b54bdc2c89811d0248f59d5d2
        Author: Noa Homolka <n.homolka@dkfz.de>
        Date:   Fri Sep 16 10:30:36 2022 +0200

            disabled tracking of MCrun folder

        commit 23b517aa56a9cb88b1e65d12c91cff6cbf1fa056
        Author: pia.stammer <pia.stammer@kit.edu>
        Date:   Fri Sep 16 09:57:44 2022 +0200

            Status 2nd Hackday: Some corrections, TOPAS runs through, results mediocre

        commit bd68b3b70aa41321ec69248f748f1c8696b3811d
        Author: pia.stammer <pia.stammer@kit.edu>
        Date:   Fri Jun 10 17:00:17 2022 +0200

            Initial commit: Added MLC shape capabilities for TOPAS
            - shapes generated by matRad_aperture2collimation are written into TOPAS config file
            - use class matRad_TopasConfigPhotons with "virtualGaussian" beam and "mlc" Multileaf collimator set-up if corresponding info exists
            - TOPAS config files for several beams, rays, leafs and shapes are created and run through
            !!Caution: Results not yet validated!!

        commit c6dd0cb6ddbe9ee8ddb502c5db66b4dc4b87fa6c
        Author: Niklas Wahl <n.wahl@dkfz.de>
        Date:   Fri Apr 29 09:49:26 2022 +0200

            added basic photon infrastructure

        commit df91e40747d1e84ff8ef06e59513b7b6596d0340
        Merge: e0ffefeb ea37a851
        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 05db32a31303bb78c9f2cc70feab9ea0f1af31e3
    Merge: d34b1826 9a431cdb
    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 3610bf50d710d0370e6e306393ea6e2f11905372
    Author: Noa Homolka <n.homolka@dkfz.de>
    Date:   Wed Oct 12 13:57:57 2022 +0200

        Update TopasConfig

        - added output of numOfBixels that did not meet the minimum numOfParticles required
        - removed unnecessary statement regarding alpha beta parameters
        - added comment to externalCalculation

    commit 834bb1f651137e8ff1c1ac3d441157bfd3dd7a76
    Merge: 19e22df3 1b13404b
    Author: Niklas Wahl <n.wahl@dkfz.de>
    Date:   Wed Oct 5 17:21:33 2022 +0200

        Merge branch 'master' into pr/536

        # Conflicts:
        #	README.md

    commit 19e22df3ba1553adb14b516fbe4d674ebd221b64
    Author: Niklas Wahl <n.wahl@dkfz.de>
    Date:   Wed Oct 5 16:36:42 2022 +0200

        reset to old bixelwidth-dependent dij sampling

    commit 1ee132d5e2b85176681cdaf86ce06946164d0688
    Author: Noa Homolka <n.homolka@dkfz.de>
    Date:   Tue Oct 4 20:31:30 2022 +0200

        Merge dev_varRBErobOpt_experimental

         Important branch Bug Fix:

            - fixed 2 major bugs in matRad_calcCubes!
            - fixed bug in TopasConfig, where the empty preallocated dij field was used to calculate tallies instead of the actual dose
            - made beamSetup more concise with shorter spaces between numbers
            - added fix for selection of focusIndex for generated phaseSpace data
            - changed handling of 0 fields
            - use isprop instead of isfield now that the class system is used
            - removed several statements that are no longer used or required

    commit 1b13404b357f07245869dfa2c815a016d0a5c84c
    Author: Niklas Wahl <n.wahl@dkfz.de>
    Date:   Sat Sep 24 00:39:04 2022 +0200

        Update tests.yml

    commit d24dc5faa966e63a93643c0aacdab98379bd0f84
    Author: Niklas Wahl <n.wahl@dkfz.de>
    Date:   Sat Sep 24 00:14:14 2022 +0200

        Update README.md

    commit 4a3e73a9cb4f825214478ebfc5ef43e60ca9cc42
    Author: Noa Homolka <n.homolka@dkfz.de>
    Date:   Thu Sep 22 21:35:00 2022 +0200

        Update to emittanceBaseData energyspread handling

    commit 87bf5febf8bc02481a17c7c72de09ecafbb4622c
    Author: Niklas Wahl <n.wahl@dkfz.de>
    Date:   Fri Sep 23 15:25:24 2022 +0200

        Fix indent

    commit 37d3c58f3ce42427ba3717002202b50cfa17335b
    Author: Noa Homolka <n.homolka@dkfz.de>
    Date:   Thu Sep 22 20:53:11 2022 +0200

        Update to matRad_calcCubes.m

        - removed section that added "non-processed MC tallies", not needed anymore
        - removed 2 lines from MCsquare calculation that still referenced the outdated MC_tallies system

    commit dc9552e4b26a8645385ea4e369338dd6b4764045
    Author: Noa Homolka <n.homolka@dkfz.de>
    Date:   Thu Sep 22 13:45:13 2022 +0200

        MC dij update calcDoseDirect

        - renamed topasCubes variable into dij to make it clearer (used to be a relict from deprecated workflow)
        - Brought dij generation of MCsquare and TOPAS in line for calcDoseDirect (all beam/ray/bixel fields are 1)

    commit be032ccbd9b3ef6568c37c81cf191af6392a6c8b
    Author: Noa Homolka <n.homolka@dkfz.de>
    Date:   Thu Sep 22 13:42:04 2022 +0200

        bug fix for recent resampling update

        - fixed resampleCTtoGrid function being called incorrectly
        - fixed input

    commit 45b651788dbacf15b4fd09c60f7ebbeb3511fe5d
    Author: Noa Homolka <n.homolka@dkfz.de>
    Date:   Wed Sep 21 16:44:07 2022 +0200

        Merge dev_varRBErobOpt_experimental -> dev_varRBErobOpt_Update

        Update PR:
        - removed TOPAS scripts
        - added compatibility patch
        - Added patch for fluence Optimization and input of precalculated weigths
        - Added input of LET into calcLQParameter function
        - Moved resampling function from TOPASconfig in general tools
        - made externalCalculation parameter clearer to use and saved folder is output to the console
        -

    commit 942ea448cc43dd4ac3c00d7760499d228f68efa7
    Merge: 75201faa f69a0076
    Author: Niklas Wahl <n.wahl@dkfz.de>
    Date:   Sat Sep 17 01:33:39 2022 +0200

        Merge pull request #579 from wahln/master

        Create CITATION.cff

    commit f69a0076a11dfbcf4e3d642c8453f2ed94e2f553
    Author: Niklas Wahl <n.wahl@dkfz.de>
    Date:   Sat Sep 17 01:28:31 2022 +0200

        Create CITATION.cff

    commit 9a431cdb86096f4776135ad8591077d1fa49312b
    Merge: 3ae8fc1e 54a6dfc6
    Author: Niklas Wahl <n.wahl@dkfz.de>
    Date:   Fri Sep 16 18:23:49 2022 +0200

        Merge pull request #537 from HomolkaN/dev_varRBErobOpt_ToolUpdate

        Tool update

    commit 75201faaca07804d8c2ee25a71b9ae24c23745a1
    Merge: 3d29b765 e469b8f4
    Author: Niklas Wahl <n.wahl@dkfz.de>
    Date:   Mon Aug 22 15:37:07 2022 +0200

        Merge pull request #574 from e0404/hotfix/dicomDoseImport

        Fix RTDose import when no RTPlan is imported

    commit e469b8f4ceaff92eb2abda5cb2908786ec22cbd8
    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 d34b18269597a8e4599fa6426b65c8efc63b7bbb
    Merge: df91e407 f5ec748a
    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 df91e40747d1e84ff8ef06e59513b7b6596d0340
    Merge: e0ffefeb ea37a851
    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 465c36b07cedeac9e66cac454d738d5ba990b8a8
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Tue May 16 12:48:10 2023 +0200

    Update TOPAS_scorer_doseRBE_LEM1_survival.txt.in

    fix typo (Protons instead of Proton) that crashes topas

commit 319f8506170956956bac51538d8f0717cae142cf
Author: Noa Homolka <n.homolka@dkfz.de>
Date:   Mon May 15 15:08:41 2023 +0200

    Merge dev_varRBErobOpt_Update >> dev_varRBErobOpt_experimental

    commit 8ca3b98198321714bb4a88c183bc65d359f42f80
    Author: Noa Homolka <n.homolka@dkfz.de>
    Date:   Mon May 15 14:58:52 2023 +0200

        Merge E0404/dev_varRBErobOpt >> dev_varRBErobOpt_Update

        commit 58362ac810fafea3ada04a93c9af319fd6d91a13
        Author: Niklas Wahl <n.wahl@dkfz.de>
        Date:   Wed May 10 12:08:26 2023 +0200

            correct for reading x and y spot sizes from emittance data in topas interface

        commit c0c8353793a6809b64d9d3245681175333855d50
        Author: Niklas Wahl <n.wahl@dkfz.de>
        Date:   Tue Mar 7 01:50:55 2023 +0100

            remove phsp-header

        commit b85ec2c1d50cb67d5e0be75dcce21f61bf3701e4
        Author: Niklas Wahl <n.wahl@dkfz.de>
        Date:   Wed Jan 25 23:04:36 2023 +0100

            Downwards compatibility of biological model

        commit 56638039c2d46e96c7de1ff0e8aaef0c3be247ab
        Author: Niklas Wahl <n.wahl@dkfz.de>
        Date:   Wed Jan 25 18:11:35 2023 +0100

            fix missing extractBetween function in Octave

        commit 64ce14ca2b7337c8d141bcd1ca9dba5c2bf79a48
        Merge: d3625aad 4e875716
        Author: Niklas Wahl <n.wahl@dkfz.de>
        Date:   Tue Jan 24 15:55:11 2023 +0100

            Merge pull request #536 from HomolkaN/dev_varRBErobOpt_Update

            Extensive TOPAS workflow update:

        commit d3625aadb81af29df92ecba1823a998f33163fe5
        Author: Niklas Wahl <n.wahl@dkfz.de>
        Date:   Thu Jan 19 13:41:47 2023 +0100

            Remove opengl software rendering query due to deprecation

        commit 3e427cfa7595986d32555beae70fe16178cd99a4
        Author: Niklas Wahl <n.wahl@dkfz.de>
        Date:   Thu Jan 19 01:44:05 2023 +0100

            Avoid erroring on opengl in matRadGUI

        commit 894211de77e83de4cc586251ecd1eadf3c4e2793
        Author: Niklas Wahl <n.wahl@dkfz.de>
        Date:   Wed Dec 21 18:34:02 2022 +0100

            improve dicom import handling for RTPlan and RTDose

    commit 7c2a36f29af48d66f9b9638ce48929a378ae9a97
    Author: Homolka <n.homolka@dkfz.de>
    Date:   Fri Apr 28 14:55:37 2023 +0200

        update patient voxelSize handling in TOPAS

        - Removed vector from Z corrdinate of the VoxelSize (it's not written anyways and it's therefore not needed now)

    commit 32e83416c339965f55a10325900ddc849aa92803
    Author: Homolka <n.homolka@dkfz.de>
    Date:   Fri Apr 28 14:46:30 2023 +0200

        Important fix for TOPAS for multiple RBE scorers

        shared subscorer was only written once if multiple RBE models were requested!

    commit 52487a6b8120e8337abfb4676a71bd88dc57c4eb
    Author: Homolka <n.homolka@dkfz.de>
    Date:   Fri Apr 28 14:16:16 2023 +0200

        Merge dev_varRBErobOpt_experimental > dev_varRBErobOpt_Update

        matRad_bioModel:
        - change default Helium model to "HEL"
        - Change description option error to a warning because that would often crash loading in saved pln

        calcDoseDirectMC:
        - add passthrough of numOfDiscardedSpots, a new variable introduced to track how many spots didn't pass the minimum particle requirement by TOPAS

        calcParticleDoseMCsquare:
        - Add externalCalculation files (copy all necessary txt files to MCrun folder). This change was made so any MC simulation does not have to be rerun, even with externalCalculation turned off

        calcParticleDoseMCtopas:
        - add RBEmodel to workingDirectory name to be more distinguishable
        - add workingDirectory naming for phaseSpace
        - add pass through of DiscardedSpots
        - fix initialization of dij struct to use struct() instead of struct([]), could not assign new fields

        calcPhotonDoseOmpMC:
        - added pln variable needed to parse lateralCutoff into the class

        calcQualityIndicators:
        - only calculate QIs of fields that have the .Visible = true!
        - some minor bug fixes mostly with run variables

        fluenceOptimization
        - parse RemovedSpots from dij to resultGUI (only MC)

        generateStfSinglePencilBeam:
        - removed, because more modular version available

        MCemittanceBaseData:
        - Added comments to every substep
        - removed unnecessary counter
        - made whole fitting process more concise and easier to understand
        - added (commented out) alternative for proton rangeEnergyFit based on PSTAR Database instead of MC simulations
        - changed some variable names so their reason is clearer

        MCinit:
        - Remove as it is not needed anymore

        showDVH:
        - added output option to access the individual DVHs when plotting
        - font size reduced to 12
        - added manual setting of grid options to work properly when plotting multiple DVHs

        showQualityIndicators:
        - Added preliminary title with inputname

        ompConfig:
        - parse lateralCutOff with pln

        SimplePhantom_3mm:
        - add simple small phantom to test single pencil beams or small fields (faster than regular Boxphantom)

        compareDose:
        - move to plotting folder

        plotVoiContourSlice:
        - changed ct variable name to ctCube, since it's not the structure parsed in
        - add statement where only the fields are plotted with .Visible = true.

        generateStfPencilBeam:
        - add function to generate simple pencil beam and select energyIx for selected energy

        topasCheckComputationTime:
        - add simple function that reads out the complete duration of a TOPAS simulation (by parsing the foldername)

        TOPAS_beamSetup_*:
        - cleaned up beamSetup a bit (cosmetic)
        - added second file for internally scored phaseSpace and renamed "phaseSpace" into "genericPhaseSpace"

        topas\materialConverter\definedMaterials\*:
        - cosmetic changes for the files to be readable more clearly

        Topas_Config:
        - change default runs back to 5
        - increase parameterizationErrorMaxEnergy to not cancel TOPAS simulation due to that error
        - PhaseSpace presimulation: added new scorer field
        - PhaseSpace presimulation: added new files to infilenames struct
        - added parsion of pln.bioParam.model into TOPAS instead of only the default values
        - PhaseSpace presimulation: added new function to writeStfPhaseSpace
        - added maskDij function to remove dose from voxels outside of the patient geometry
        - added support to read_in standard deviation that has been scored separately
        - added check for NaNs in each readOut
        - display projected number of bixels that are to be discarded to console
        - added function to initialize MCparam (to have it at once place)

        topas\scorers\*:
        - cosmetic changes for the files to be readable more clearly
        - PhaseSpace presimulation: added scorer for phaseSpaceSurface

        topas\world\matRad_geometry:
        - cosmetic changes for the files to be readable more clearly
        - rearrange ordering to reflect hirarchie

        topas\world\matRad_geometry_read/score phaseSpace:
        - PhaseSpace presimulation: added new scorer files that use the phaseSpaceSurface to score a phaseSpace for later easier dose calculation

    commit ab88a0fa75e830a9aa7fad140e52919bc088bcec
    Author: Noa Homolka <n.homolka@dkfz.de>
    Date:   Mon Feb 27 15:38:53 2023 +0100

        Add readme reagarding topas phasespace file

    commit b6c8e6477ba320a1d3d7efea84e3b87f9298e71d
    Author: Noa Homolka <n.homolka@dkfz.de>
    Date:   Sun Feb 19 16:11:26 2023 +0100

        small additions and fixes to last merge

    commit 63e9e2dc3438da5a78fc0936dab9c80c51755278
    Author: Noa Homolka <n.homolka@dkfz.de>
    Date:   Sun Feb 19 15:42:11 2023 +0100

        Merge dev_varRBErobOpt_experimental

        - Extension of calcDoseDirectMC to photons
        - External calculation of MCsquare
        - max_iter flag in fluence optimization (through pln.propOpt.max_iter)
        - TOPAS: add option to read in separate scorer file and not use constructor

    commit 9294c202eebd336a981b711ce3e1aa5ca64dbf6d
    Author: Noa Homolka <n.homolka@dkfz.de>
    Date:   Fri Feb 17 17:48:34 2023 +0100

        Update .gitignore

        don't add .phsp (phasespace) files to gitHub (too lage)

    commit 4e8757165cbf339d3f20dfaa109a325979f1efc2
    Author: Niklas Wahl <n.wahl@dkfz.de>
    Date:   Tue Dec 20 00:07:42 2022 +0100

        typo fix in MCsquare dose calculation

    commit aa9fb10200ba52d3fde335ad1c60831100302aae
    Merge: a5352d99 cbc78d07
    Author: Niklas Wahl <n.wahl@dkfz.de>
    Date:   Mon Dec 19 19:29:58 2022 +0100

        Merge branch 'dev_varRBErobOpt' into pr/536

        # Conflicts:
        #	matRad_calcParticleDoseMCsquare.m
        #	matRad_calcParticleDoseMCtopas.m
        #	matRad_calcPhotonDoseMC.m

    commit cbc78d07f392ea76a9ce37291d851882b0c0627b
    Author: Niklas Wahl <n.wahl@dkfz.de>
    Date:   Mon Dec 19 19:29:05 2022 +0100

        small fix for running index in MC scenario calculation

    commit a5352d99ffb4bab28b5a7b4a68d843ec4cc3a92a
    Merge: 0eb3d41b 4453b5ae
    Author: Niklas Wahl <n.wahl@dkfz.de>
    Date:   Mon Dec 19 19:26:48 2022 +0100

        Merge branch 'dev_varRBErobOpt' into pr/536

        # Conflicts:
        #	MCsquare/matRad_writeMCsquareinputAllFiles.m
        #	matRad_calcParticleDose.m
        #	matRad_calcParticleDoseMCsquare.m
        #	matRad_calcParticleDoseMCtopas.m
        #	matRad_calcPhotonDoseMC.m

    commit 4453b5ae89b0fbdd3ed534bd141ebb89cc770241
    Author: Niklas Wahl <n.wahl@dkfz.de>
    Date:   Mon Dec 19 18:43:02 2022 +0100

        fix MU normalization

    commit cb16de9c1aea902d21241446cfeee13a8ac92ce4
    Merge: 675ebcb0 68724001
    Author: Niklas Wahl <n.wahl@dkfz.de>
    Date:   Mon Dec 19 18:42:13 2022 +0100

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

    commit 675ebcb07a1820916292d45b3ca3c8be70e77096
    Author: Niklas Wahl <n.wahl@dkfz.de>
    Date:   Mon Dec 19 18:41:45 2022 +0100

        range scenario fix and loop simplification for MC

    commit 0eb3d41b3418e8ec84cc062ac6ed279dafe59c9a
    Author: Noa Homolka <n.homolka@dkfz.de>
    Date:   Tue Dec 6 04:14:27 2022 +0100

        Update matRad_doseAcc.m

        Fix error in matRad_doseAcc, where the interpolation messed everything up when the phantom didn't have uniform dimensions.

    commit 6872400174d738b1e4e14140c3573a47d17b3745
    Author: Niklas Wahl <n.wahl@dkfz.de>
    Date:   Fri Dec 2 13:52:20 2022 +0100

        Update matRad_calcParticleDose.m

        Catch failure in drawing the waitbar

    commit 74f4f5d44401e77d8b7a14fa68dbce3f4ecf37dd
    Author: Noa Homolka <n.homolka@dkfz.de>
    Date:   Thu Dec 1 05:17:30 2022 +0100

        Update matRad_fluenceOptimization.m

        Some fields necessary for RBExD optimization have to be written if initial weights are passed in

    commit 093eb964deb62133ae0dcf3f0b15edfbc3616e6c
    Author: Noa Homolka <n.homolka@dkfz.de>
    Date:   Wed Nov 30 18:40:18 2022 +0100

        Delete protons_savedMatRadMachine.mat

    commit 3782e6c7fe2b125e3911b2537869b491e7024b22
    Author: Noa Homolka <n.homolka@dkfz.de>
    Date:   Wed Nov 30 17:42:38 2022 +0100

        Renamed classes to follow the naming scheme

        MatRad_TopasConfig -> matRad_TopasConfig
        MatRad_HeterogeneityConfig -> matRad_HeterogeneityConfig
        MatRad_MCsquareConfig -> matRad_MCsquareConfig
        MatRad_MCsquareBaseData -> matRad_MCsquareBaseData
        matRad_bioModel -> matRad_BioModel

    commit 7cd7879fa8ab542abd35d200b171cf77f5d7c0ad
    Merge: 37d41298 cb6b04a6
    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 cb6b04a603533a5906617d489eb36e4a054eaa3a
    Author: Niklas Wahl <n.wahl@dkfz.de>
    Date:   Tue Nov 29 20:26:59 2022 +0100

        Update README.md

        Update Cancer Aid Funding

    commit 538f08b63ee433e96c4b3f2fea2ac2253a9b60e6
    Author: Niklas Wahl <n.wahl@dkfz.de>
    Date:   Tue Nov 29 20:23:17 2022 +0100

        Update README.md

        Add funding information

    commit f1e446a8d06eff73e8224a59498bbfde53bc4456
    Author: Noa Homolka <n.homolka@dkfz.de>
    Date:   Wed Nov 23 18:28:10 2022 +0100

        minor MC workflow fixes

    commit 63bb149b191840e240e21e07f257f6172241f8f8
    Author: Niklas Wahl <n.wahl@dkfz.de>
    Date:   Tue Nov 22 17:02:52 2022 +0100

        small fix wenn getting number of emittance gaussians from the weight array

    commit 348ba2fee095ced97e2d957b674a24c9812310a8
    Author: Niklas Wahl <n.wahl@dkfz.de>
    Date:   Tue Nov 22 16:48:04 2022 +0100

        remove weird slab file in scenarios folder

    commit d81012dd18badb6fcb74dacf5518c9fd267ef99c
    Author: Niklas Wahl <n.wahl@dkfz.de>
    Date:   Tue Nov 22 13:43:40 2022 +0100

        make mex file compilation a static function

    commit 20626d1e4321e2b3d9e5887d4904c1f5c5f5f9b3
    Merge: fcc026f0 37d41298
    Author: Niklas Wahl <n.wahl@dkfz.de>
    Date:   Tue Nov 22 13:39:35 2022 +0100

        Merge branch 'dev_varRBErobOpt' of https://github.com/e0404/matRad into pr/536

    commit fcc026f01709beef78f2ea861dceb6054af00d49
    Merge: 051dfdbd 93571e61
    Author: Niklas Wahl <n.wahl@dkfz.de>
    Date:   Tue Nov 22 13:38:33 2022 +0100

        Merge branch 'dev_varRBErobOpt_Update' of https://github.com/HomolkaN/matRad into pr/536

    commit 051dfdbd9f8eb6bb60ecfbb258eef310115bd0a5
    Author: Niklas Wahl <n.wahl@dkfz.de>
    Date:   Tue Nov 22 13:35:52 2022 +0100

        add different SADs for x and y to the base data class

    commit 93571e61baa9a4d4a8b89b0883f92893b0ee84cf
    Author: Noa Homolka <n.homolka@dkfz.de>
    Date:   Fri Nov 18 18:00:07 2022 +0100

        Update MatRad_TopasConfig.m

        minor compatibility changes for TOPAS

    commit 3355d0519af14942d4201ff4220c1fcaa19c5292
    Merge: b6188d1f c8fd3029
    Author: Hardt <jennifer.hardt@dkfz-heidelberg.de>
    Date:   Fri Nov 18 16:45:13 2022 +0100

        Merge branch 'dev_varRBErobOpt_Update' of https://github.com/HomolkaN/matRad into dev_varRBErobOpt_Update

    commit b6188d1f5c0df47a808392290feaf12705190989
    Author: Hardt <jennifer.hardt@dkfz-heidelberg.de>
    Date:   Fri Nov 18 16:44:30 2022 +0100

        SAD and wsl fix

        SAD was wrong given in cm in header file, and phase space file location is given as a relative path, wsl dosent like the direct path

    commit 277fef513dbc2bb972b77521dcfd342cefaa576e
    Author: Hardt <jennifer.hardt@dkfz-heidelberg.de>
    Date:   Fri Nov 18 16:42:07 2022 +0100

        Phase space file starts at end of colimator

    commit 16c9610a9b65ad45b1dabbea5ddd155e2019eb80
    Author: Hardt <jennifer.hardt@dkfz-heidelberg.de>
    Date:   Fri Nov 18 16:41:46 2022 +0100

        otherwise out and log file are the same file

    commit c8fd30297275590ef6f390239267c1f49f10d4a5
    Author: Noa Homolka <n.homolka@dkfz.de>
    Date:   Fri Nov 18 16:06:14 2022 +0100

        Update matRad_calcPhotonDoseOmpMC.m

        Typo

    commit 704d2c08ae503705d87dafc8af8a65f223754ec6
    Author: Noa Homolka <n.homolka@dkfz.de>
    Date:   Fri Nov 18 14:59:51 2022 +0100

        introduce ompMC class

        This change was done primarily to increase compatibility with the other MonteCarlo changes that have been done, mainly how the MC classes are currently structured and loaded.

    commit 926d70097867a9bac85f1bb4f78684a4cfaaf503
    Author: Hardt <jennifer.hardt@dkfz-heidelberg.de>
    Date:   Fri Nov 18 10:32:02 2022 +0100

        Update .gitignore

    commit 147f0582bfc487378ea651bce4d2ff1e185698bb
    Author: Noa Homolka <n.homolka@dkfz.de>
    Date:   Fri Nov 18 10:10:18 2022 +0100

        Update matRad_runTests.m

        added small fix for runTests that couldn't find testing scripts

    commit d6fd9f2997881af72985c5df0a1562880e9eb48b
    Author: Niklas Wahl <n.wahl@dkfz.de>
    Date:   Thu Nov 17 11:55:28 2022 +0100

        Update matRad_runTests.m

        Make sure a failing script does not get stuck in a directory

    commit bb40ecab977e8992c17cbb093a726499328fb0f1
    Author: Noa Homolka <n.homolka@dkfz.de>
    Date:   Mon Nov 14 20:14:14 2022 +0100

        Update MatRad_TopasConfig.m

        Some more octave changes

    commit 2f0b541a6791c340b316a7f5db275e8a1304f913
    Author: Noa Homolka <n.homolka@dkfz.de>
    Date:   Mon Nov 14 17:42:32 2022 +0100

        potential fix for testing

        renamed topas beam setup files to lowercase

    commit 37d412983857db3c163b8b5a4b4719a55a989207
    Author: Niklas Wahl <n.wahl@dkfz.de>
    Date:   Fri Nov 11 18:05:52 2022 +0100

        add some compatibility functions to scenarioModel

    commit 2c576ab155599f00650d408fe9089cae999bde21
    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 b08ddc49c7f84cec4df56bc5213c4ef726609be3
    Merge: d8588e13 d0e246c6
    Author: Niklas Wahl <n.wahl@dkfz.de>
    Date:   Fri Oct 28 14:45:19 2022 +0200

        Merge branch 'dev_varRBErobOpt_Update' of https://github.com/HomolkaN/matRad into pr/536

    commit d8588e131751fdff71389f7cfab2f13b69ff1e9e
    Author: Niklas Wahl <n.wahl@dkfz.de>
    Date:   Fri Oct 28 14:44:46 2022 +0200

        change how emittance and energy spectrum should be represented in base data

    commit 9b5c17af4cc000483a46989fc51d8609129412ea
    Author: Niklas Wahl <n.wahl@dkfz.de>
    Date:   Fri Oct 28 14:43:47 2022 +0200

        some technical fixes

    commit ee58c3d155a7b33ac44c60753b35d48fcb409904
    Author: Niklas Wahl <n.wahl@dkfz.de>
    Date:   Fri Oct 28 14:43:23 2022 +0200

        remove the MCsquare MU correction as it is no longer valid

    commit d0e…
@wahln wahln deleted the hotfix/dicomDoseImport branch May 22, 2024 12:43
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers
No reviews
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
1 participant
@wahln