Squashed commit of the following:

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