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Extensive TOPAS workflow update: #536

Merged
merged 68 commits into from
Jan 24, 2023
Merged

Extensive TOPAS workflow update: #536

merged 68 commits into from
Jan 24, 2023

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HomolkaN
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@HomolkaN HomolkaN commented Dec 5, 2021 •
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New pull request, because changes made to the dev_MC master branch had not been implemented.

2nd August 2022: Merged pull requests #470 and #524, Added support for 4D

Major changes:

  1. Restructured the MCEmittanceBaseData class, fit and calculation pipeline
  2. Added example 13 for generating analytical data file by fitting to given machine emittance
    2.1. added function to plot particleBaseDataEntry
    2.2. edited function to fit base data
    2.3. added function to generate a single pencil beam
  3. Added support for 4D calculation

Minor changes:

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

15th June 2022: Added merge commit from my main branch

Major changes to Monte Carlo pipeline:

-> This change was done to make usage more streamlined and uniform as well as be in line with future changes

  1. Merged support functions for TOPAS into topasConfig class
  2. Merged support functions for MCsquare into MCsquareConfig class
  3. Added a class constructor for pln in MatRad_config, which loads requested classes in pln and writes default values that were not

Futher changes:

  1. Added comments to whole TOPAS pipeline
  2. calcParticleDoseMCtopas now generates dij in matRad format
  3. Changed matRad_calcCubes to accept a variety of differnet fields for Monte Carlo, without changing the current usage

5th December 2021

Major updates:

  1. installTOPAS script which installs TOPAS with the dependencies from downloaded topas.tar.gz
  2. modular Schneider Converter: Converter is 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

HomolkaN and others added 2 commits December 5, 2021 18:59
@HomolkaN
Extensive TOPAS workflow update:
aad8a96 
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
@wahln
Merge branch 'dev_varRBErobOpt' of https://github.com/e0404/matRad in…
64fad60 
…to pr/536

# Conflicts:
#	MatRad_Config.m
#	matRad_calcParticleDose.m
#	matRad_fluenceOptimization.m
wahln
wahln requested changes Mar 16, 2022
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Good work. Some documentation missing and some additions are not quite clear to me yet.

topas/install/installTopas.sh Outdated Show resolved Hide resolved
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MatRad_Config.m Outdated Show resolved Hide resolved
topas/matRad_resampleTopasGrid.m Outdated Show resolved Hide resolved
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@HomolkaN
Merge branch 'dev_VARBE_MC_merge_experimental'
1a4bfaf 
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
@HomolkaN
Monte Carlo fix
f7ce1ee 
- 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
@HomolkaN
Merge additional MonteCarlo changes from dev_varRBErobOpt_experimental
edfef03 
- 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
@HomolkaN
Merge branch 'dev_VARBE_MC_merge_experimental' into dev_varRBErobOpt_…
4888568 
…Update
@HomolkaN
Merge branch 'pamede/dev_MonteCarloRestructured'
5ac3cd7 
Merge remote-tracking branch 'pamede/dev_MonteCarloRestructured' into dev_varRBErobOpt_Update
@HomolkaN
Merge branch 'pamede/dev_varRBErobOpt'
0d0e61e 
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
This was referenced Jul 29, 2022
Closed
Closed
Merged
HomolkaN and others added 5 commits August 2, 2022 21:59
@HomolkaN
added support for 4D
1d7e81e
@HomolkaN
Replaced contains function by strfind for octave
7101996 
RIP contains, you were the love of my life.
@HomolkaN
TOPAS Schneider Update
8527e90 
- 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
@HomolkaN
Update ChangeLog.txt
3de7537 
Added ChangeLog for MonteCarlo workflow Updates in Pull Request
@wahln
Merge branch 'dev_varRBErobOpt' into pr/536
80d1396 
# Conflicts:
#	MatRad_Config.m
#	matRad_calcCubes.m
#	matRad_calcParticleDose.m
#	matRad_fluenceOptimization.m
#	matRad_generateStf.m
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@HomolkaN
Update matRad_calcDoseDirectMC.m
9b968e8 
small bug fix that should also resolve this iteration of unit testing
wahln
wahln reviewed Sep 19, 2022
View reviewed changes
matRad_calcDoseDirectMC.m Outdated Show resolved Hide resolved
@HomolkaN
Merge dev_varRBErobOpt_experimental -> dev_varRBErobOpt_Update
45b6517 
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
-
JenHardt and others added 10 commits November 18, 2022 16:42
@JenHardt
Phase space file starts at end of colimator
277fef5
@JenHardt
SAD and wsl fix
b6188d1 
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
@JenHardt
Merge branch 'dev_varRBErobOpt_Update' of https://github.com/HomolkaN…
3355d05 
…/matRad into dev_varRBErobOpt_Update
@HomolkaN
Update MatRad_TopasConfig.m
93571e6 
minor compatibility changes for TOPAS
@wahln
add different SADs for x and y to the base data class
051dfdb
@wahln
Merge branch 'dev_varRBErobOpt_Update' of https://github.com/HomolkaN…
fcc026f 
…/matRad into pr/536
@wahln
Merge branch 'dev_varRBErobOpt' of https://github.com/e0404/matRad in…
20626d1 
…to pr/536
@wahln
make mex file compilation a static function
d81012d
@wahln
remove weird slab file in scenarios folder
348ba2f
@wahln
small fix wenn getting number of emittance gaussians from the weight …
63bb149 
…array
@wahln wahln self-assigned this Nov 23, 2022
HomolkaN and others added 8 commits November 23, 2022 18:28
@HomolkaN
minor MC workflow fixes
f1e446a
@HomolkaN
Renamed classes to follow the naming scheme
3782e6c 
MatRad_TopasConfig -> matRad_TopasConfig
MatRad_HeterogeneityConfig -> matRad_HeterogeneityConfig
MatRad_MCsquareConfig -> matRad_MCsquareConfig
MatRad_MCsquareBaseData -> matRad_MCsquareBaseData
matRad_bioModel -> matRad_BioModel
@HomolkaN
Delete protons_savedMatRadMachine.mat
093eb96
@HomolkaN
Update matRad_fluenceOptimization.m
74f4f5d 
Some fields necessary for RBExD optimization have to be written if initial weights are passed in
@HomolkaN
Update matRad_doseAcc.m
0eb3d41 
Fix error in matRad_doseAcc, where the interpolation messed everything up when the phantom didn't have uniform dimensions.
@wahln
Merge branch 'dev_varRBErobOpt' into pr/536
a5352d9 
# Conflicts:
#	MCsquare/matRad_writeMCsquareinputAllFiles.m
#	matRad_calcParticleDose.m
#	matRad_calcParticleDoseMCsquare.m
#	matRad_calcParticleDoseMCtopas.m
#	matRad_calcPhotonDoseMC.m
@wahln
Merge branch 'dev_varRBErobOpt' into pr/536
aa9fb10 
# Conflicts:
#	matRad_calcParticleDoseMCsquare.m
#	matRad_calcParticleDoseMCtopas.m
#	matRad_calcPhotonDoseMC.m
@wahln
typo fix in MCsquare dose calculation
4e87571
@wahln wahln merged commit 64ce14c into e0404:dev_varRBErobOpt Jan 24, 2023
HomolkaN added a commit to HomolkaN/matRad that referenced this pull request May 15, 2023
@HomolkaN
Merge E0404/dev_varRBErobOpt >> dev_varRBErobOpt_Update
8ca3b98 
commit 58362ac
Author: Niklas Wahl <[email protected]>
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 <[email protected]>
Date:   Tue Mar 7 01:50:55 2023 +0100

    remove phsp-header

commit b85ec2c
Author: Niklas Wahl <[email protected]>
Date:   Wed Jan 25 23:04:36 2023 +0100

    Downwards compatibility of biological model

commit 5663803
Author: Niklas Wahl <[email protected]>
Date:   Wed Jan 25 18:11:35 2023 +0100

    fix missing extractBetween function in Octave

commit 64ce14c
Merge: d3625aa 4e87571
Author: Niklas Wahl <[email protected]>
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 <[email protected]>
Date:   Thu Jan 19 13:41:47 2023 +0100

    Remove opengl software rendering query due to deprecation

commit 3e427cf
Author: Niklas Wahl <[email protected]>
Date:   Thu Jan 19 01:44:05 2023 +0100

    Avoid erroring on opengl in matRadGUI

commit 894211d
Author: Niklas Wahl <[email protected]>
Date:   Wed Dec 21 18:34:02 2022 +0100

    improve dicom import handling for RTPlan and RTDose
HomolkaN added a commit to HomolkaN/matRad that referenced this pull request May 15, 2023
@HomolkaN
Merge dev_varRBErobOpt_Update >> dev_varRBErobOpt_experimental
319f850 
commit 8ca3b98
Author: Noa Homolka <[email protected]>
Date:   Mon May 15 14:58:52 2023 +0200

    Merge E0404/dev_varRBErobOpt >> dev_varRBErobOpt_Update

    commit 58362ac
    Author: Niklas Wahl <[email protected]>
    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 <[email protected]>
    Date:   Tue Mar 7 01:50:55 2023 +0100

        remove phsp-header

    commit b85ec2c
    Author: Niklas Wahl <[email protected]>
    Date:   Wed Jan 25 23:04:36 2023 +0100

        Downwards compatibility of biological model

    commit 5663803
    Author: Niklas Wahl <[email protected]>
    Date:   Wed Jan 25 18:11:35 2023 +0100

        fix missing extractBetween function in Octave

    commit 64ce14c
    Merge: d3625aa 4e87571
    Author: Niklas Wahl <[email protected]>
    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 <[email protected]>
    Date:   Thu Jan 19 13:41:47 2023 +0100

        Remove opengl software rendering query due to deprecation

    commit 3e427cf
    Author: Niklas Wahl <[email protected]>
    Date:   Thu Jan 19 01:44:05 2023 +0100

        Avoid erroring on opengl in matRadGUI

    commit 894211d
    Author: Niklas Wahl <[email protected]>
    Date:   Wed Dec 21 18:34:02 2022 +0100

        improve dicom import handling for RTPlan and RTDose

commit 7c2a36f
Author: Homolka <[email protected]>
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 <[email protected]>
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 <[email protected]>
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 <[email protected]>
Date:   Mon Feb 27 15:38:53 2023 +0100

    Add readme reagarding topas phasespace file

commit b6c8e64
Author: Noa Homolka <[email protected]>
Date:   Sun Feb 19 16:11:26 2023 +0100

    small additions and fixes to last merge

commit 63e9e2d
Author: Noa Homolka <[email protected]>
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 <[email protected]>
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 <[email protected]>
Date:   Tue Dec 20 00:07:42 2022 +0100

    typo fix in MCsquare dose calculation

commit aa9fb10
Merge: a5352d9 cbc78d0
Author: Niklas Wahl <[email protected]>
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 <[email protected]>
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 <[email protected]>
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 <[email protected]>
Date:   Mon Dec 19 18:43:02 2022 +0100

    fix MU normalization

commit cb16de9
Merge: 675ebcb 6872400
Author: Niklas Wahl <[email protected]>
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 <[email protected]>
Date:   Mon Dec 19 18:41:45 2022 +0100

    range scenario fix and loop simplification for MC

commit 0eb3d41
Author: Noa Homolka <[email protected]>
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 <[email protected]>
Date:   Fri Dec 2 13:52:20 2022 +0100

    Update matRad_calcParticleDose.m

    Catch failure in drawing the waitbar

commit 74f4f5d
Author: Noa Homolka <[email protected]>
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 <[email protected]>
Date:   Wed Nov 30 18:40:18 2022 +0100

    Delete protons_savedMatRadMachine.mat

commit 3782e6c
Author: Noa Homolka <[email protected]>
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 <[email protected]>
Date:   Tue Nov 29 20:32:15 2022 +0100

    Merge branch 'master' into dev_varRBErobOpt

    # Conflicts:
    #	README.md

commit cb6b04a
Author: Niklas Wahl <[email protected]>
Date:   Tue Nov 29 20:26:59 2022 +0100

    Update README.md

    Update Cancer Aid Funding

commit 538f08b
Author: Niklas Wahl <[email protected]>
Date:   Tue Nov 29 20:23:17 2022 +0100

    Update README.md

    Add funding information

commit f1e446a
Author: Noa Homolka <[email protected]>
Date:   Wed Nov 23 18:28:10 2022 +0100

    minor MC workflow fixes

commit 63bb149
Author: Niklas Wahl <[email protected]>
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 <[email protected]>
Date:   Tue Nov 22 16:48:04 2022 +0100

    remove weird slab file in scenarios folder

commit d81012d
Author: Niklas Wahl <[email protected]>
Date:   Tue Nov 22 13:43:40 2022 +0100

    make mex file compilation a static function

commit 20626d1
Merge: fcc026f 37d4129
Author: Niklas Wahl <[email protected]>
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 <[email protected]>
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 <[email protected]>
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 <[email protected]>
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 <[email protected]>
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 <[email protected]>
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 <[email protected]>
Date:   Fri Nov 18 16:42:07 2022 +0100

    Phase space file starts at end of colimator

commit 16c9610
Author: Hardt <[email protected]>
Date:   Fri Nov 18 16:41:46 2022 +0100

    otherwise out and log file are the same file

commit c8fd302
Author: Noa Homolka <[email protected]>
Date:   Fri Nov 18 16:06:14 2022 +0100

    Update matRad_calcPhotonDoseOmpMC.m

    Typo

commit 704d2c0
Author: Noa Homolka <[email protected]>
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 <[email protected]>
Date:   Fri Nov 18 10:32:02 2022 +0100

    Update .gitignore

commit 147f058
Author: Noa Homolka <[email protected]>
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 <[email protected]>
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 <[email protected]>
Date:   Mon Nov 14 20:14:14 2022 +0100

    Update MatRad_TopasConfig.m

    Some more octave changes

commit 2f0b541
Author: Noa Homolka <[email protected]>
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 <[email protected]>
Date:   Fri Nov 11 18:05:52 2022 +0100

    add some compatibility functions to scenarioModel

commit 2c576ab
Author: Niklas Wahl <[email protected]>
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 <[email protected]>
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 <[email protected]>
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 <[email protected]>
Date:   Fri Oct 28 14:43:47 2022 +0200

    some technical fixes

commit ee58c3d
Author: Niklas Wahl <[email protected]>
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 <[email protected]>
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 <[email protected]>
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 <[email protected]>
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 <[email protected]>
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 <[email protected]>
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 <[email protected]>
Date:   Wed Oct 26 15:53:20 2022 +0200

    fix props in MatRad_Config

commit 0c2094d
Author: Noa Homolka <[email protected]>
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 <[email protected]>
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 <[email protected]>
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 <[email protected]>
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 <[email protected]>
    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 <[email protected]>
    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 <[email protected]>
    Date:   Fri Sep 16 14:47:50 2022 +0200

        Reduced size of source, increased number of histories

    commit 9067aa9
    Author: pia.stammer <[email protected]>
    Date:   Fri Sep 16 11:31:06 2022 +0200

        Add uniform source and rotate MLC

    commit e7031b1
    Author: Noa Homolka <[email protected]>
    Date:   Fri Sep 16 10:30:36 2022 +0200

        disabled tracking of MCrun folder

    commit 23b517a
    Author: pia.stammer <[email protected]>
    Date:   Fri Sep 16 09:57:44 2022 +0200

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

    commit bd68b3b
    Author: pia.stammer <[email protected]>
    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 <[email protected]>
    Date:   Fri Apr 29 09:49:26 2022 +0200

        added basic photon infrastructure

    commit df91e40
    Merge: e0ffefe ea37a85
    Author: Niklas Wahl <[email protected]>
    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 <[email protected]>
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 <[email protected]>
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 <[email protected]>
Date:   Wed Oct 5 17:21:33 2022 +0200

    Merge branch 'master' into pr/536

    # Conflicts:
    #	README.md

commit 19e22df
Author: Niklas Wahl <[email protected]>
Date:   Wed Oct 5 16:36:42 2022 +0200

    reset to old bixelwidth-dependent dij sampling

commit 1ee132d
Author: Noa Homolka <[email protected]>
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 <[email protected]>
Date:   Sat Sep 24 00:39:04 2022 +0200

    Update tests.yml

commit d24dc5f
Author: Niklas Wahl <[email protected]>
Date:   Sat Sep 24 00:14:14 2022 +0200

    Update README.md

commit 4a3e73a
Author: Noa Homolka <[email protected]>
Date:   Thu Sep 22 21:35:00 2022 +0200

    Update to emittanceBaseData energyspread handling

commit 87bf5fe
Author: Niklas Wahl <[email protected]>
Date:   Fri Sep 23 15:25:24 2022 +0200

    Fix indent

commit 37d3c58
Author: Noa Homolka <[email protected]>
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 <[email protected]>
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 <[email protected]>
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 <[email protected]>
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 <[email protected]>
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 <[email protected]>
Date:   Sat Sep 17 01:28:31 2022 +0200

    Create CITATION.cff

commit 9a431cd
Merge: 3ae8fc1 54a6dfc
Author: Niklas Wahl <[email protected]>
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 <[email protected]>
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 <[email protected]>
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 <[email protected]>
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 <[email protected]>
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 added a commit to HomolkaN/matRad that referenced this pull request May 17, 2023
@HomolkaN
Fixed merge issue with bioModel
13d3926 
commit 8ca3b98
Author: Noa Homolka <[email protected]>
Date:   Mon May 15 14:58:52 2023 +0200

    Merge E0404/dev_varRBErobOpt >> dev_varRBErobOpt_Update

    commit 58362ac
    Author: Niklas Wahl <[email protected]>
    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 <[email protected]>
    Date:   Tue Mar 7 01:50:55 2023 +0100

        remove phsp-header

    commit b85ec2c
    Author: Niklas Wahl <[email protected]>
    Date:   Wed Jan 25 23:04:36 2023 +0100

        Downwards compatibility of biological model

    commit 5663803
    Author: Niklas Wahl <[email protected]>
    Date:   Wed Jan 25 18:11:35 2023 +0100

        fix missing extractBetween function in Octave

    commit 64ce14c
    Merge: d3625aa 4e87571
    Author: Niklas Wahl <[email protected]>
    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 <[email protected]>
    Date:   Thu Jan 19 13:41:47 2023 +0100

        Remove opengl software rendering query due to deprecation

    commit 3e427cf
    Author: Niklas Wahl <[email protected]>
    Date:   Thu Jan 19 01:44:05 2023 +0100

        Avoid erroring on opengl in matRadGUI

    commit 894211d
    Author: Niklas Wahl <[email protected]>
    Date:   Wed Dec 21 18:34:02 2022 +0100

        improve dicom import handling for RTPlan and RTDose

commit 7c2a36f
Author: Homolka <[email protected]>
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 <[email protected]>
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 <[email protected]>
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 <[email protected]>
Date:   Mon Feb 27 15:38:53 2023 +0100

    Add readme reagarding topas phasespace file

commit b6c8e64
Author: Noa Homolka <[email protected]>
Date:   Sun Feb 19 16:11:26 2023 +0100

    small additions and fixes to last merge

commit 63e9e2d
Author: Noa Homolka <[email protected]>
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 <[email protected]>
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 <[email protected]>
Date:   Tue Dec 20 00:07:42 2022 +0100

    typo fix in MCsquare dose calculation

commit aa9fb10
Merge: a5352d9 cbc78d0
Author: Niklas Wahl <[email protected]>
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 <[email protected]>
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 <[email protected]>
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 <[email protected]>
Date:   Mon Dec 19 18:43:02 2022 +0100

    fix MU normalization

commit cb16de9
Merge: 675ebcb 6872400
Author: Niklas Wahl <[email protected]>
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 <[email protected]>
Date:   Mon Dec 19 18:41:45 2022 +0100

    range scenario fix and loop simplification for MC

commit 0eb3d41
Author: Noa Homolka <[email protected]>
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 <[email protected]>
Date:   Fri Dec 2 13:52:20 2022 +0100

    Update matRad_calcParticleDose.m

    Catch failure in drawing the waitbar

commit 74f4f5d
Author: Noa Homolka <[email protected]>
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 <[email protected]>
Date:   Wed Nov 30 18:40:18 2022 +0100

    Delete protons_savedMatRadMachine.mat

commit 3782e6c
Author: Noa Homolka <[email protected]>
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 <[email protected]>
Date:   Tue Nov 29 20:32:15 2022 +0100

    Merge branch 'master' into dev_varRBErobOpt

    # Conflicts:
    #	README.md

commit cb6b04a
Author: Niklas Wahl <[email protected]>
Date:   Tue Nov 29 20:26:59 2022 +0100

    Update README.md

    Update Cancer Aid Funding

commit 538f08b
Author: Niklas Wahl <[email protected]>
Date:   Tue Nov 29 20:23:17 2022 +0100

    Update README.md

    Add funding information

commit f1e446a
Author: Noa Homolka <[email protected]>
Date:   Wed Nov 23 18:28:10 2022 +0100

    minor MC workflow fixes

commit 63bb149
Author: Niklas Wahl <[email protected]>
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 <[email protected]>
Date:   Tue Nov 22 16:48:04 2022 +0100

    remove weird slab file in scenarios folder

commit d81012d
Author: Niklas Wahl <[email protected]>
Date:   Tue Nov 22 13:43:40 2022 +0100

    make mex file compilation a static function

commit 20626d1
Merge: fcc026f 37d4129
Author: Niklas Wahl <[email protected]>
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 <[email protected]>
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 <[email protected]>
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 <[email protected]>
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 <[email protected]>
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 <[email protected]>
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 <[email protected]>
Date:   Fri Nov 18 16:42:07 2022 +0100

    Phase space file starts at end of colimator

commit 16c9610
Author: Hardt <[email protected]>
Date:   Fri Nov 18 16:41:46 2022 +0100

    otherwise out and log file are the same file

commit c8fd302
Author: Noa Homolka <[email protected]>
Date:   Fri Nov 18 16:06:14 2022 +0100

    Update matRad_calcPhotonDoseOmpMC.m

    Typo

commit 704d2c0
Author: Noa Homolka <[email protected]>
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 <[email protected]>
Date:   Fri Nov 18 10:32:02 2022 +0100

    Update .gitignore

commit 147f058
Author: Noa Homolka <[email protected]>
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 <[email protected]>
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 <[email protected]>
Date:   Mon Nov 14 20:14:14 2022 +0100

    Update MatRad_TopasConfig.m

    Some more octave changes

commit 2f0b541
Author: Noa Homolka <[email protected]>
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 <[email protected]>
Date:   Fri Nov 11 18:05:52 2022 +0100

    add some compatibility functions to scenarioModel

commit 2c576ab
Author: Niklas Wahl <[email protected]>
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 <[email protected]>
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 <[email protected]>
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 <[email protected]>
Date:   Fri Oct 28 14:43:47 2022 +0200

    some technical fixes

commit ee58c3d
Author: Niklas Wahl <[email protected]>
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 <[email protected]>
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 <[email protected]>
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 <[email protected]>
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 <[email protected]>
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 <[email protected]>
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 <[email protected]>
Date:   Wed Oct 26 15:53:20 2022 +0200

    fix props in MatRad_Config

commit 0c2094d
Author: Noa Homolka <[email protected]>
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 <[email protected]>
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 <[email protected]>
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 <[email protected]>
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 <[email protected]>
    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 <[email protected]>
    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 <[email protected]>
    Date:   Fri Sep 16 14:47:50 2022 +0200

        Reduced size of source, increased number of histories

    commit 9067aa9
    Author: pia.stammer <[email protected]>
    Date:   Fri Sep 16 11:31:06 2022 +0200

        Add uniform source and rotate MLC

    commit e7031b1
    Author: Noa Homolka <[email protected]>
    Date:   Fri Sep 16 10:30:36 2022 +0200

        disabled tracking of MCrun folder

    commit 23b517a
    Author: pia.stammer <[email protected]>
    Date:   Fri Sep 16 09:57:44 2022 +0200

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

    commit bd68b3b
    Author: pia.stammer <[email protected]>
    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 <[email protected]>
    Date:   Fri Apr 29 09:49:26 2022 +0200

        added basic photon infrastructure

    commit df91e40
    Merge: e0ffefe ea37a85
    Author: Niklas Wahl <[email protected]>
    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 <[email protected]>
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 <[email protected]>
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 <[email protected]>
Date:   Wed Oct 5 17:21:33 2022 +0200

    Merge branch 'master' into pr/536

    # Conflicts:
    #	README.md

commit 19e22df
Author: Niklas Wahl <[email protected]>
Date:   Wed Oct 5 16:36:42 2022 +0200

    reset to old bixelwidth-dependent dij sampling

commit 1ee132d
Author: Noa Homolka <[email protected]>
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 <[email protected]>
Date:   Sat Sep 24 00:39:04 2022 +0200

    Update tests.yml

commit d24dc5f
Author: Niklas Wahl <[email protected]>
Date:   Sat Sep 24 00:14:14 2022 +0200

    Update README.md

commit 4a3e73a
Author: Noa Homolka <[email protected]>
Date:   Thu Sep 22 21:35:00 2022 +0200

    Update to emittanceBaseData energyspread handling

commit 87bf5fe
Author: Niklas Wahl <[email protected]>
Date:   Fri Sep 23 15:25:24 2022 +0200

    Fix indent

commit 37d3c58
Author: Noa Homolka <[email protected]>
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 <[email protected]>
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 <[email protected]>
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 <[email protected]>
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 <[email protected]>
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 <[email protected]>
Date:   Sat Sep 17 01:28:31 2022 +0200

    Create CITATION.cff

commit 9a431cd
Merge: 3ae8fc1 54a6dfc
Author: Niklas Wahl <[email protected]>
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 <[email protected]>
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 <[email protected]>
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 <[email protected]>
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 <[email protected]>
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 added a commit to HomolkaN/matRad that referenced this pull request Aug 29, 2023
@HomolkaN
Merge varRBErobOpt_experimental into varRBErobOpt_Update
646ca07 
commit 2e2823bd78dd85a296e271c0d88b50d22db7f796
Author: Noa Homolka <[email protected]>
Date:   Tue Aug 29 18:26:33 2023 +0200

    merge changes to MCemittanceBaseData from master/dev_varRBErobOpt

commit 86cecacc25dfce80132ced66dabdae93b18b84c8
Author: Noa Homolka <[email protected]>
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 <[email protected]>
Date:   Sat Aug 12 17:01:41 2023 +0200

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

commit ad9bf5ca892ff01af67a365899188f6fedebca24
Author: Noa Homolka <[email protected]>
Date:   Sat Aug 12 17:01:24 2023 +0200

    add complete external calculation for MCsquare

commit 170127d16ff598f10d2e5e61d9b314b44cbb0bc5
Author: Noa Homolka <[email protected]>
Date:   Sat Aug 12 17:01:08 2023 +0200

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

commit 5758017ea5f2b4b1149d28b40b2101b5d20a4984
Author: Noa Homolka <[email protected]>
Date:   Thu Aug 10 18:32:01 2023 +0200

    remove HLUT from phantoms

commit 74717188cc853ee85690174e35f2cd09eeb4fe65
Author: Noa Homolka <[email protected]>
Date:   Thu Aug 10 18:31:34 2023 +0200

    change MCsquare sampling to use lung material like TOPAS

commit 58fdddc26d0497b22977d35768eec5f7a97526e4
Author: Noa Homolka <[email protected]>
Date:   Thu Aug 10 18:31:20 2023 +0200

    add specific error message to heterogeneity correction

commit d8520c80bf36f770a19b58a71db08184c286d117
Author: Noa Homolka <[email protected]>
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 <[email protected]>
Date:   Fri Jul 21 14:17:37 2023 +0200

    update phantoms to characterize base data sets

commit e4b3b16f01a4ee25a0f5abfba3cd4562f91267f7
Author: Noa Homolka <[email protected]>
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 <[email protected]>
Date:   Fri Jul 21 14:15:24 2023 +0200

    HC: fix for error with empty propHeterogeneity field upon loading

commit 023a70e63818afbddc7e8b848128138026431428
Author: Noa Homolka <[email protected]>
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 <[email protected]>
Date:   Wed Jul 12 16:41:03 2023 +0200

    Update matRad_downsampleMachineFile.m

commit 3d451cd541d3f284d644623d9853941084507529
Author: Noa Homolka <[email protected]>
Date:   Wed Jul 12 16:25:23 2023 +0200

    Update protons_generic_TOPAS_APM.mat

commit af2786366d5d6c97a1e8bd56ed5f626cb99e4b3a
Author: Noa Homolka <[email protected]>
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 <[email protected]>
Date:   Thu Jul 6 16:43:28 2023 +0200

    Update plotIDD.m

commit d72c04672bc707875cff3ccb700926e397162da1
Author: Noa Homolka <[email protected]>
Date:   Thu Jul 6 16:26:41 2023 +0200

    update matRad_calcIDD_pencil with option for peakPos

commit 5c0baea6fa9f1f7c88c9d3fb60619b52fdaf65fa
Author: Noa Homolka <[email protected]>
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 <[email protected]>
Date:   Wed Jul 5 00:56:27 2023 +0200

    small fix so TOPAS heterogeneity correction is skipped properly

commit 54c2f628b90b21f932fbea9b2ebb0fcf15a771f7
Author: Noa Homolka <[email protected]>
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 <[email protected]>
Date:   Tue Jul 4 18:22:11 2023 +0200

    clean up MCemittanceBaseData a bit

commit 8f89f9c945d72f863684fe70952ae7e2dfc2b592
Author: Noa Homolka <[email protected]>
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 <[email protected]>
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 <[email protected]>
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 <[email protected]>
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 <[email protected]>
Date:   Thu Jun 22 15:48:13 2023 +0200

    slightly update particleMonteCarlo example

commit a1a4d15a764c5eff84188c071128891d1fc64c94
Author: Noa Homolka <[email protected]>
Date:   Thu Jun 22 15:44:27 2023 +0200

    changed BioModel to lowercase bioModel

commit 37f6bc9c2b343b8c08c281b1f86c7c16fe7fee86
Author: Noa Homolka <[email protected]>
Date:   Thu Jun 22 15:17:10 2023 +0200

    cleaned up topasConfig a bit

commit 12226807f289824fc1569c561b96c8704a5ae127
Author: Noa Homolka <[email protected]>
Date:   Thu Jun 22 15:15:05 2023 +0200

    Added 2 small phantoms to efficiently test pencil beams with

commit f319e2c5629a542a401633192760f8eafa7e8064
Author: Noa Homolka <[email protected]>
Date:   Thu Jun 22 15:03:30 2023 +0200

    fixed cst struct in lung phantoms

commit 021b482269dde0ecb9112a475eeeccff2337a780
Author: Noa Homolka <[email protected]>
Date:   Thu Jun 22 14:57:02 2023 +0200

    added numerical convolution to heterogeneity correction

commit 3ba235c66265732171cad7f1c672a529771feac4
Author: Noa Homolka <[email protected]>
Date:   Mon Jun 19 19:42:59 2023 +0200

    Create SimplePhantom_1mm_longwide.mat

commit 87df060a6ab6a3021507691a98e06e0b21f610a3
Author: Noa Homolka <[email protected]>
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 <[email protected]>
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 <[email protected]>
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 <[email protected]>
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 <[email protected]>
Date:   Thu Jun 15 22:26:01 2023 +0200

    in particleDose calculation, always override APM data if not needed

commit ab96a105318dd17281a60f941b22400875ce68c8
Author: Noa Homolka <[email protected]>
Date:   Thu Jun 15 22:25:38 2023 +0200

    Update matRad_calcIDD_pencil.m

commit 9a6a660cec64f1f5fbc26f7062b3ad51f98348fa
Author: Noa Homolka <[email protected]>
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 <[email protected]>
Date:   Thu Jun 15 21:09:14 2023 +0200

    merge testing and optimization changes from dev_varRBErobOpt

commit 7448b9312294e1d1c3f734e004dc4117d734fa32
Author: Noa Homolka <[email protected]>
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 <[email protected]>
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 <[email protected]>
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 <[email protected]>
Date:   Wed Jun 14 16:29:23 2023 +0200

    save numOfSamples in dose modulation

commit d1fd9af3de87c0937bc85d148bac3f8216e980d5
Author: Noa Homolka <[email protected]>
Date:   Wed Jun 14 16:28:53 2023 +0200

    update machine downsampling

    downsample first, and then truncate!

commit c484bca7e57cdfbc7a26149cb9a78460ba53ad16
Author: Noa Homolka <[email protected]>
Date:   Fri Jun 9 12:36:11 2023 +0200

    fix another bug in phaseSpace splitting pipeline

commit ca1644b828429d755abb9fddbe01c83188616ab6
Author: Noa Homolka <[email protected]>
Date:   Thu Jun 8 22:24:50 2023 +0200

    update genericTOPAS LET

commit 90932c312717913935923753d60b35e53bcafab3
Author: Noa Homolka <[email protected]>
Date:   Thu Jun 8 22:13:18 2023 +0200

    fixed typo in TOPAS phaseSpace

commit 1c6b5ca2efdde6c99a769a2f76532368802684be
Author: Noa Homolka <[email protected]>
Date:   Wed Jun 7 13:39:14 2023 +0200

    Fix for separated phaseSpace calculation (heterogeneity correction)

commit 56116e662a8851f40338fd5788f1d35de7fb80b0
Author: Noa Homolka <[email protected]>
Date:   Wed Jun 7 11:20:33 2023 +0200

    Update protons_generic_TOPAS_LET with updated sigma

commit f9cf6836f122ea143e9c63cc63c68b7c17ebed78
Author: Noa Homolka <[email protected]>
Date:   Tue Jun 6 21:56:41 2023 +0200

    Create protons_generic_TOPAS_newInitFocus.mat

commit 96082d4e9a8199bf4317370f25950ee4d7431ba4
Author: Noa Homolka <[email protected]>
Date:   Tue Jun 6 21:06:14 2023 +0200

    fix bug in emittanceBaseData

commit 02a2a11af396af2965bd445243843996038e172e
Author: Niklas Wahl <[email protected]>
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 <[email protected]>
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 <[email protected]>
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 <[email protected]>
Date:   Tue Jun 6 14:25:25 2023 +0200

    update machineData downsampling with gradual grid

commit 81276fc0e6b6e4ab511d91d970cf14d19f9bfab0
Author: Noa Homolka <[email protected]>
Date:   Tue Jun 6 14:19:15 2023 +0200

    update genericTOPAS with LET

commit ef068390531105e6a657428bda9c0750dcd85676
Author: Noa Homolka <[email protected]>
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 <[email protected]>
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 <[email protected]>
Date:   Wed May 31 12:51:21 2023 +0200

    set RBE for TOPAS as default

commit c47ef526381de7ca05119955b4894f6e47822fdb
Author: Noa Homolka <[email protected]>
Date:   Wed May 31 12:36:28 2023 +0200

    TopasConfig further automate phaseSpace splitting

commit 530fa40d2ac88750593ab49b576bcb00edc3e4ee
Author: Noa Homolka <[email protected]>
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 <[email protected]>
Date:   Wed May 31 12:32:49 2023 +0200

    Update matRad_example12_simpleParticleMonteCarlo.m

commit 01463de09c4def8580b02e71db66b52021745762
Author: Noa Homolka <[email protected]>
Date:   Thu May 25 12:35:31 2023 +0200

    actually name the base data set accordingly

commit 63ea625f779ac395f9c1dd702d9b5c4e3461e195
Author: Noa Homolka <[email protected]>
Date:   Thu May 25 12:34:28 2023 +0200

    Create protons_generic_TOPAS with fixed 3% energy spread

commit 48a09f433702f091364f24405f65ecdb66ec14d1
Author: Noa Homolka <[email protected]>
Date:   Thu May 25 12:33:23 2023 +0200

    Fix typo in calcParticleDoseMCtopas for phaseSpace

commit 5feb58a66d783e684109cd920b864c5adf4151d4
Author: Noa Homolka <[email protected]>
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 <[email protected]>
Date:   Thu May 25 12:32:12 2023 +0200

    Use rangeEnergy fit for protons based on NIST tables

commit 13d39263c2e2a9303cf852bd4a82f59bd2bf3951
Author: Noa Homolka <[email protected]>
Date:   Wed May 17 16:58:42 2023 +0200

    Fixed merge issue with bioModel

    commit 8ca3b98198321714bb4a88c183bc65d359f42f80
    Author: Noa Homolka <[email protected]>
    Date:   Mon May 15 14:58:52 2023 +0200

        Merge E0404/dev_varRBErobOpt >> dev_varRBErobOpt_Update

        commit 58362ac810fafea3ada04a93c9af319fd6d91a13
        Author: Niklas Wahl <[email protected]>
        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 <[email protected]>
        Date:   Tue Mar 7 01:50:55 2023 +0100

            remove phsp-header

        commit b85ec2c1d50cb67d5e0be75dcce21f61bf3701e4
        Author: Niklas Wahl <[email protected]>
        Date:   Wed Jan 25 23:04:36 2023 +0100

            Downwards compatibility of biological model

        commit 56638039c2d46e96c7de1ff0e8aaef0c3be247ab
        Author: Niklas Wahl <[email protected]>
        Date:   Wed Jan 25 18:11:35 2023 +0100

            fix missing extractBetween function in Octave

        commit 64ce14ca2b7337c8d141bcd1ca9dba5c2bf79a48
        Merge: d3625aad 4e875716
        Author: Niklas Wahl <[email protected]>
        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 <[email protected]>
        Date:   Thu Jan 19 13:41:47 2023 +0100

            Remove opengl software rendering query due to deprecation

        commit 3e427cfa7595986d32555beae70fe16178cd99a4
        Author: Niklas Wahl <[email protected]>
        Date:   Thu Jan 19 01:44:05 2023 +0100

            Avoid erroring on opengl in matRadGUI

        commit 894211de77e83de4cc586251ecd1eadf3c4e2793
        Author: Niklas Wahl <[email protected]>
        Date:   Wed Dec 21 18:34:02 2022 +0100

            improve dicom import handling for RTPlan and RTDose

    commit 7c2a36f29af48d66f9b9638ce48929a378ae9a97
    Author: Homolka <[email protected]>
    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 <[email protected]>
    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 <[email protected]>
    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 <[email protected]>
    Date:   Mon Feb 27 15:38:53 2023 +0100

        Add readme reagarding topas phasespace file

    commit b6c8e6477ba320a1d3d7efea84e3b87f9298e71d
    Author: Noa Homolka <[email protected]>
    Date:   Sun Feb 19 16:11:26 2023 +0100

        small additions and fixes to last merge

    commit 63e9e2dc3438da5a78fc0936dab9c80c51755278
    Author: Noa Homolka <[email protected]>
    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 <[email protected]>
    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 <[email protected]>
    Date:   Tue Dec 20 00:07:42 2022 +0100

        typo fix in MCsquare dose calculation

    commit aa9fb10200ba52d3fde335ad1c60831100302aae
    Merge: a5352d99 cbc78d07
    Author: Niklas Wahl <[email protected]>
    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 <[email protected]>
    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 <[email protected]>
    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 <[email protected]>
    Date:   Mon Dec 19 18:43:02 2022 +0100

        fix MU normalization

    commit cb16de9c1aea902d21241446cfeee13a8ac92ce4
    Merge: 675ebcb0 68724001
    Author: Niklas Wahl <[email protected]>
    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 <[email protected]>
    Date:   Mon Dec 19 18:41:45 2022 +0100

        range scenario fix and loop simplification for MC

    commit 0eb3d41b3418e8ec84cc062ac6ed279dafe59c9a
    Author: Noa Homolka <[email protected]>
    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 <[email protected]>
    Date:   Fri Dec 2 13:52:20 2022 +0100

        Update matRad_calcParticleDose.m

        Catch failure in drawing the waitbar

    commit 74f4f5d44401e77d8b7a14fa68dbce3f4ecf37dd
    Author: Noa Homolka <[email protected]>
    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 <[email protected]>
    Date:   Wed Nov 30 18:40:18 2022 +0100

        Delete protons_savedMatRadMachine.mat

    commit 3782e6c7fe2b125e3911b2537869b491e7024b22
    Author: Noa Homolka <[email protected]>
    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 <[email protected]>
    Date:   Tue Nov 29 20:32:15 2022 +0100

        Merge branch 'master' into dev_varRBErobOpt

        # Conflicts:
        #	README.md

    commit cb6b04a603533a5906617d489eb36e4a054eaa3a
    Author: Niklas Wahl <[email protected]>
    Date:   Tue Nov 29 20:26:59 2022 +0100

        Update README.md

        Update Cancer Aid Funding

    commit 538f08b63ee433e96c4b3f2fea2ac2253a9b60e6
    Author: Niklas Wahl <[email protected]>
    Date:   Tue Nov 29 20:23:17 2022 +0100

        Update README.md

        Add funding information

    commit f1e446a8d06eff73e8224a59498bbfde53bc4456
    Author: Noa Homolka <[email protected]>
    Date:   Wed Nov 23 18:28:10 2022 +0100

        minor MC workflow fixes

    commit 63bb149b191840e240e21e07f257f6172241f8f8
    Author: Niklas Wahl <[email protected]>
    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 <[email protected]>
    Date:   Tue Nov 22 16:48:04 2022 +0100

        remove weird slab file in scenarios folder

    commit d81012dd18badb6fcb74dacf5518c9fd267ef99c
    Author: Niklas Wahl <[email protected]>
    Date:   Tue Nov 22 13:43:40 2022 +0100

        make mex file compilation a static function

    commit 20626d1e4321e2b3d9e5887d4904c1f5c5f5f9b3
    Merge: fcc026f0 37d41298
    Author: Niklas Wahl <[email protected]>
    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 <[email protected]>
    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 <[email protected]>
    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 <[email protected]>
    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 <[email protected]>
    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 <[email protected]>
    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 <[email protected]>
    Date:   Fri Nov 18 16:42:07 2022 +0100

        Phase space file starts at end of colimator

    commit 16c9610a9b65ad45b1dabbea5ddd155e2019eb80
    Author: Hardt <[email protected]>
    Date:   Fri Nov 18 16:41:46 2022 +0100

        otherwise out and log file are the same file

    commit c8fd30297275590ef6f390239267c1f49f10d4a5
    Author: Noa Homolka <[email protected]>
    Date:   Fri Nov 18 16:06:14 2022 +0100

        Update matRad_calcPhotonDoseOmpMC.m

        Typo

    commit 704d2c08ae503705d87dafc8af8a65f223754ec6
    Author: Noa Homolka <[email protected]>
    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 <[email protected]>
    Date:   Fri Nov 18 10:32:02 2022 +0100

        Update .gitignore

    commit 147f0582bfc487378ea651bce4d2ff1e185698bb
    Author: Noa Homolka <[email protected]>
    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 <[email protected]>
    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 <[email protected]>
    Date:   Mon Nov 14 20:14:14 2022 +0100

        Update MatRad_TopasConfig.m

        Some more octave changes

    commit 2f0b541a6791c340b316a7f5db275e8a1304f913
    Author: Noa Homolka <[email protected]>
    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 <[email protected]>
    Date:   Fri Nov 11 18:05:52 2022 +0100

        add some compatibility functions to scenarioModel

    commit 2c576ab155599f00650d408fe9089cae999bde21
    Author: Niklas Wahl <[email protected]>
    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 <[email protected]>
    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 <[email protected]>
    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 <[email protected]>
    Date:   Fri Oct 28 14:43:47 2022 +0200

        some technical fixes

    commit ee58c3d155a7b33ac44c60753b35d48fcb409904
    Author: Niklas Wahl <[email protected]>
    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 <[email protected]>
    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 <[email protected]>
    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 <[email protected]>
    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 <[email protected]>
    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 <[email protected]>
    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 <[email protected]>
    Date:   Wed Oct 26 15:53:20 2022 +0200

        fix props in MatRad_Config

    commit 0c2094d33ba42566fb7a186b81975bdb93288105
    Author: Noa Homolka <[email protected]>
    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 <[email protected]>
    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 <[email protected]>
    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 <[email protected]>
    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 <[email protected]>
        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 <[email protected]>
        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 <[email protected]>
        Date:   Fri Sep 16 14:47:50 2022 +0200

            Reduced size of source, increased number of histories

        commit 9067aa9c7ea33be6c219b98ca260a35e1f6357d6
        Author: pia.stammer <[email protected]>
        Date:   Fri Sep 16 11:31:06 2022 +0200

            Add uniform source and rotate MLC

        commit e7031b191568979b54bdc2c89811d0248f59d5d2
        Author: Noa Homolka <[email protected]>
        Date:   Fri Sep 16 10:30:36 2022 +0200

            disabled tracking of MCrun folder

        commit 23b517aa56a9cb88b1e65d12c91cff6cbf1fa056
        Author: pia.stammer <[email protected]>
        Date:   Fri Sep 16 09:57:44 2022 +0200

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

        commit bd68b3b70aa41321ec69248f748f1c8696b3811d
        Author: pia.stammer <[email protected]>
        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 <[email protected]>
        Date:   Fri Apr 29 09:49:26 2022 +0200

            added basic photon infrastructure

        commit df91e40747d1e84ff8ef06e59513b7b6596d0340
        Merge: e0ffefeb ea37a851
        Author: Niklas Wahl <[email protected]>
        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 <[email protected]>
    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 <[email protected]>
    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 <[email protected]>
    Date:   Wed Oct 5 17:21:33 2022 +0200

        Merge branch 'master' into pr/536

        # Conflicts:
        #	README.md

    commit 19e22df3ba1553adb14b516fbe4d674ebd221b64
    Author: Niklas Wahl <[email protected]>
    Date:   Wed Oct 5 16:36:42 2022 +0200

        reset to old bixelwidth-dependent dij sampling

    commit 1ee132d5e2b85176681cdaf86ce06946164d0688
    Author: Noa Homolka <[email protected]>
    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 <[email protected]>
    Date:   Sat Sep 24 00:39:04 2022 +0200

        Update tests.yml

    commit d24dc5faa966e63a93643c0aacdab98379bd0f84
    Author: Niklas Wahl <[email protected]>
    Date:   Sat Sep 24 00:14:14 2022 +0200

        Update README.md

    commit 4a3e73a9cb4f825214478ebfc5ef43e60ca9cc42
    Author: Noa Homolka <[email protected]>
    Date:   Thu Sep 22 21:35:00 2022 +0200

        Update to emittanceBaseData energyspread handling

    commit 87bf5febf8bc02481a17c7c72de09ecafbb4622c
    Author: Niklas Wahl <[email protected]>
    Date:   Fri Sep 23 15:25:24 2022 +0200

        Fix indent

    commit 37d3c58f3ce42427ba3717002202b50cfa17335b
    Author: Noa Homolka <[email protected]>
    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 <[email protected]>
    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 <[email protected]>
    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 <[email protected]>
    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 <[email protected]>
    Date:   Sat Sep 17 01:33:39 2022 +0200

        Merge pull request #579 from wahln/master

        Create CITATION.cff

    commit f69a0076a11dfbcf4e3d642c8453f2ed94e2f553
    Author: Niklas Wahl <[email protected]>
    Date:   Sat Sep 17 01:28:31 2022 +0200

        Create CITATION.cff

    commit 9a431cdb86096f4776135ad8591077d1fa49312b
    Merge: 3ae8fc1e 54a6dfc6
    Author: Niklas Wahl <[email protected]>
    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 <[email protected]>
    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 <[email protected]>
    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 <[email protected]>
    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 <[email protected]>
    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 <[email protected]>
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 <[email protected]>
Date:   Mon May 15 15:08:41 2023 +0200

    Merge dev_varRBErobOpt_Update >> dev_varRBErobOpt_experimental

    commit 8ca3b98198321714bb4a88c183bc65d359f42f80
    Author: Noa Homolka <[email protected]>
    Date:   Mon May 15 14:58:52 2023 +0200

        Merge E0404/dev_varRBErobOpt >> dev_varRBErobOpt_Update

        commit 58362ac810fafea3ada04a93c9af319fd6d91a13
        Author: Niklas Wahl <[email protected]>
        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 <[email protected]>
        Date:   Tue Mar 7 01:50:55 2023 +0100

            remove phsp-header

        commit b85ec2c1d50cb67d5e0be75dcce21f61bf3701e4
        Author: Niklas Wahl <[email protected]>
        Date:   Wed Jan 25 23:04:36 2023 +0100

            Downwards compatibility of biological model

        commit 56638039c2d46e96c7de1ff0e8aaef0c3be247ab
        Author: Niklas Wahl <[email protected]>
        Date:   Wed Jan 25 18:11:35 2023 +0100

            fix missing extractBetween function in Octave

        commit 64ce14ca2b7337c8d141bcd1ca9dba5c2bf79a48
        Merge: d3625aad 4e875716
        Author: Niklas Wahl <[email protected]>
        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 <[email protected]>
        Date:   Thu Jan 19 13:41:47 2023 +0100

            Remove opengl software rendering query due to deprecation

        commit 3e427cfa7595986d32555beae70fe16178cd99a4
        Author: Niklas Wahl <[email protected]>
        Date:   Thu Jan 19 01:44:05 2023 +0100

            Avoid erroring on opengl in matRadGUI

        commit 894211de77e83de4cc586251ecd1eadf3c4e2793
        Author: Niklas Wahl <[email protected]>
        Date:   Wed Dec 21 18:34:02 2022 +0100

            improve dicom import handling for RTPlan and RTDose

    commit 7c2a36f29af48d66f9b9638ce48929a378ae9a97
    Author: Homolka <[email protected]>
    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 <[email protected]>
    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 <[email protected]>
    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 <[email protected]>
    Date:   Mon Feb 27 15:38:53 2023 +0100

        Add readme reagarding topas phasespace file

    commit b6c8e6477ba320a1d3d7efea84e3b87f9298e71d
    Author: Noa Homolka <[email protected]>
    Date:   Sun Feb 19 16:11:26 2023 +0100

        small additions and fixes to last merge

    commit 63e9e2dc3438da5a78fc0936dab9c80c51755278
    Author: Noa Homolka <[email protected]>
    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 <[email protected]>
    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 <[email protected]>
    Date:   Tue Dec 20 00:07:42 2022 +0100

        typo fix in MCsquare dose calculation

    commit aa9fb10200ba52d3fde335ad1c60831100302aae
    Merge: a5352d99 cbc78d07
    Author: Niklas Wahl <[email protected]>
    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 <[email protected]>
    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 <[email protected]>
    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 <[email protected]>
    Date:   Mon Dec 19 18:43:02 2022 +0100

        fix MU normalization

    commit cb16de9c1aea902d21241446cfeee13a8ac92ce4
    Merge: 675ebcb0 68724001
    Author: Niklas Wahl <[email protected]>
    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 <[email protected]>
    Date:   Mon Dec 19 18:41:45 2022 +0100

        range scenario fix and loop simplification for MC

    commit 0eb3d41b3418e8ec84cc062ac6ed279dafe59c9a
    Author: Noa Homolka <[email protected]>
    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 <[email protected]>
    Date:   Fri Dec 2 13:52:20 2022 +0100

        Update matRad_calcParticleDose.m

        Catch failure in drawing the waitbar

    commit 74f4f5d44401e77d8b7a14fa68dbce3f4ecf37dd
    Author: Noa Homolka <[email protected]>
    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 <[email protected]>
    Date:   Wed Nov 30 18:40:18 2022 +0100

        Delete protons_savedMatRadMachine.mat

    commit 3782e6c7fe2b125e3911b2537869b491e7024b22
    Author: Noa Homolka <[email protected]>
    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 <[email protected]>
    Date:   Tue Nov 29 20:32:15 2022 +0100

        Merge branch 'master' into dev_varRBErobOpt

        # Conflicts:
        #	README.md

    commit cb6b04a603533a5906617d489eb36e4a054eaa3a
    Author: Niklas Wahl <[email protected]>
    Date:   Tue Nov 29 20:26:59 2022 +0100

        Update README.md

        Update Cancer Aid Funding

    commit 538f08b63ee433e96c4b3f2fea2ac2253a9b60e6
    Author: Niklas Wahl <[email protected]>
    Date:   Tue Nov 29 20:23:17 2022 +0100

        Update README.md

        Add funding information

    commit f1e446a8d06eff73e8224a59498bbfde53bc4456
    Author: Noa Homolka <[email protected]>
    Date:   Wed Nov 23 18:28:10 2022 +0100

        minor MC workflow fixes

    commit 63bb149b191840e240e21e07f257f6172241f8f8
    Author: Niklas Wahl <[email protected]>
    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 <[email protected]>
    Date:   Tue Nov 22 16:48:04 2022 +0100

        remove weird slab file in scenarios folder

    commit d81012dd18badb6fcb74dacf5518c9fd267ef99c
    Author: Niklas Wahl <[email protected]>
    Date:   Tue Nov 22 13:43:40 2022 +0100

        make mex file compilation a static function

    commit 20626d1e4321e2b3d9e5887d4904c1f5c5f5f9b3
    Merge: fcc026f0 37d41298
    Author: Niklas Wahl <[email protected]>
    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 <[email protected]>
    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 <[email protected]>
    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 <[email protected]>
    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 <[email protected]>
    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 <[email protected]>
    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 <[email protected]>
    Date:   Fri Nov 18 16:42:07 2022 +0100

        Phase space file starts at end of colimator

    commit 16c9610a9b65ad45b1dabbea5ddd155e2019eb80
    Author: Hardt <[email protected]>
    Date:   Fri Nov 18 16:41:46 2022 +0100

        otherwise out and log file are the same file

    commit c8fd30297275590ef6f390239267c1f49f10d4a5
    Author: Noa Homolka <[email protected]>
    Date:   Fri Nov 18 16:06:14 2022 +0100

        Update matRad_calcPhotonDoseOmpMC.m

        Typo

    commit 704d2c08ae503705d87dafc8af8a65f223754ec6
    Author: Noa Homolka <[email protected]>
    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 <[email protected]>
    Date:   Fri Nov 18 10:32:02 2022 +0100

        Update .gitignore

    commit 147f0582bfc487378ea651bce4d2ff1e185698bb
    Author: Noa Homolka <[email protected]>
    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 <[email protected]>
    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 <[email protected]>
    Date:   Mon Nov 14 20:14:14 2022 +0100

        Update MatRad_TopasConfig.m

        Some more octave changes

    commit 2f0b541a6791c340b316a7f5db275e8a1304f913
    Author: Noa Homolka <[email protected]>
    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 <[email protected]>
    Date:   Fri Nov 11 18:05:52 2022 +0100

        add some compatibility functions to scenarioModel

    commit 2c576ab155599f00650d408fe9089cae999bde21
    Author: Niklas Wahl <[email protected]>
    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 <[email protected]>
    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 <[email protected]>
    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 <[email protected]>
    Date:   Fri Oct 28 14:43:47 2022 +0200

        some technical fixes

    commit ee58c3d155a7b33ac44c60753b35d48fcb409904
    Author: Niklas Wahl <[email protected]>
    Date:   Fri Oct 28 14:43:23 2022 +0200

        remove the MCsquare MU correction as it is no longer valid

    commit d0e…
HomolkaN added a commit to HomolkaN/matRad that referenced this pull request Sep 5, 2023
@HomolkaN
Merge dev_varRBErobOpt from dev -> update
f708b2f 
commit e915ed6
Merge: ce9179d 9cc05a8
Author: Niklas Wahl <[email protected]>
Date:   Fri Jul 21 16:59:52 2023 +0200

    Merge pull request e0404#650 from piastammer/dev_varRBErobOpt

    minor bug fix and small documentation changes

commit ce9179d
Merge: 32bff43 6ef2c24
Author: Niklas Wahl <[email protected]>
Date:   Fri Jul 21 16:57:40 2023 +0200

    Merge pull request e0404#649 from remocristoforetti/dev_varRBErobOpt_bugFix

    minor bug fix

commit 9cc05a8
Author: Pia Stammer <[email protected]>
Date:   Fri Jul 21 16:53:47 2023 +0200

    added warning and TODO for single bixel example

commit 6ef2c24
Author: remocristoforetti <[email protected]>
Date:   Fri Jul 21 16:44:19 2023 +0200

    minor change in generic photon machine
    machine.meta.name turned into machine.meta.machine

commit ad9f5f9
Author: remocristoforetti <[email protected]>
Date:   Fri Jul 21 16:34:06 2023 +0200

    error printout message fix in matRad_multScen

commit 32bff43
Merge: 87832ed a6f7004
Author: Niklas Wahl <[email protected]>
Date:   Fri Jul 21 15:09:43 2023 +0200

    Merge pull request e0404#624 from tobiasbecher/dev_Pareto

    Small changes to where penalties are applied

commit 42a4edc
Author: Pia Stammer <[email protected]>
Date:   Fri Jul 21 14:44:01 2023 +0200

    added TODOs to check commented lines

commit 59e3e43
Author: Pia Stammer <[email protected]>
Date:   Fri Jul 21 14:22:15 2023 +0200

    removed redundant copyright statements & added Todos for documenation

commit e400ee9
Author: Pia Stammer <[email protected]>
Date:   Fri Jul 21 13:56:22 2023 +0200

    Set default BAMStoIsoDist for topas machine file

commit 87832ed
Merge: acd73e7 2958dc4
Author: Niklas Wahl <[email protected]>
Date:   Thu Jul 20 11:07:55 2023 +0200

    Merge pull request e0404#610 from tobiasbecher/dev_varRBErobOptPhantomBuilder

    Phantom builder added

commit 2958dc4
Merge: 03ec1a0 acd73e7
Author: Niklas Wahl <[email protected]>
Date:   Thu Jul 20 10:01:53 2023 +0200

    Merge branch 'dev_varRBErobOpt' into pr/610

    # Conflicts:
    #	.gitignore

commit 03ec1a0
Author: Niklas Wahl <[email protected]>
Date:   Thu Jul 20 10:00:26 2023 +0200

    reorganization of builder files

commit acd73e7
Merge: c9acdc5 a83b691
Author: Niklas Wahl <[email protected]>
Date:   Wed Jul 19 17:15:39 2023 +0200

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

commit c9acdc5
Author: Niklas Wahl <[email protected]>
Date:   Wed Jul 19 17:15:33 2023 +0200

    Update of base data file for estimate of energy spectrum

commit 2f00898
Author: Tobias Becher <[email protected]>
Date:   Mon Jul 10 12:47:38 2023 +0200

    Final updates

    Final changes to the phantom builder

commit a83b691
Merge: d5bf94a f2e62b6
Author: Niklas Wahl <[email protected]>
Date:   Mon Jul 10 10:13:15 2023 +0200

    Merge pull request e0404#642 from JenHardt/dev_varRBErobOpt

    IsoCenterShift BugFix

commit f2e62b6
Author: JenHardt <[email protected]>
Date:   Fri Jul 7 13:56:16 2023 +0200

    IsoCenterShift BugFix

commit bca2260
Author: Tobias Becher <[email protected]>
Date:   Fri Jun 30 14:41:50 2023 +0200

    Update matRad_runTests.m

commit d474f09
Author: Tobias Becher <[email protected]>
Date:   Fri Jun 30 14:33:25 2023 +0200

    Removed indexing of VOI

    VOI are no longer assigned an index on initialization.
    -> No need to clear all at the start of  a script if rerunning

commit c12f5e8
Author: Tobias Becher <[email protected]>
Date:   Fri Jun 30 14:10:55 2023 +0200

    Fixed geometry issues

    Fixed issues with the coordinate system

commit a6f7004
Author: Tobias Becher <[email protected]>
Date:   Fri Jun 30 10:24:52 2023 +0200

    Slack parameter changes

    - Changed epsilon variable name to slackParameter
    - Now parameter of constraint
    - Removed objective funtion to turn into constraint

commit dedf147
Author: Tobias Becher <[email protected]>
Date:   Wed Jun 28 13:37:18 2023 +0200

    Some changes

    Some changes made for pull request. Commit also tests if server tests now run through.

commit d5bf94a
Author: Niklas Wahl <[email protected]>
Date:   Wed Jun 28 10:18:28 2023 +0200

    allows to compute the bixel dose when cutoff was not precomputed by setting the compensation factor to 1

commit 83fc8a6
Author: Niklas Wahl <[email protected]>
Date:   Wed Jun 28 10:17:45 2023 +0200

    emittance base data format now allows one emittance per focus

commit 5fda67e
Merge: 99eaa34 bffb834
Author: Niklas Wahl <[email protected]>
Date:   Wed Jun 21 10:56:08 2023 +0200

    Merge pull request e0404#637 from remocristoforetti/dev_varRBErobOpt_bugFix_MCemittanceBaseData

    bugFix in MCemittanceBaseData for negative distances

commit bffb834
Author: RemoCristoforetti <[email protected]>
Date:   Wed Jun 21 10:49:28 2023 +0200

    bugFix negative distance for spot size correction in air.

commit 99eaa34
Author: Niklas Wahl <[email protected]>
Date:   Wed Jun 21 10:10:19 2023 +0200

    Fix matRad_MCemittanceBaseData.m

    Replaced Inf with realmax so interpolation does not error

commit 3e7952a
Author: Niklas Wahl <[email protected]>
Date:   Wed Jun 7 13:19:31 2023 +0200

    AppendResultGUI now creates consistent fieldnames

commit c5dd9eb
Author: Niklas Wahl <[email protected]>
Date:   Tue Jun 6 18:32:40 2023 +0200

    appendresultgui now either overwrites or always appends the identifier

commit 1bab14d
Author: Niklas Wahl <[email protected]>
Date:   Tue Jun 6 18:32:21 2023 +0200

    fix for the spot size air MCS correction

commit 6a746ee
Author: Niklas Wahl <[email protected]>
Date:   Tue Jun 6 14:13:20 2023 +0200

    fix variable names in example 12

commit a7e72fa
Author: Niklas Wahl <[email protected]>
Date:   Tue Jun 6 14:13:01 2023 +0200

    add empirical correction for MCS in air when approximating beam model

commit 1a80ea9
Author: Tobias Becher <[email protected]>
Date:   Mon Jun 5 11:01:52 2023 +0200

    Name change for constraints

    Changed the name for created constraints in the optimization

commit 48ca910
Author: Niklas Wahl <[email protected]>
Date:   Tue May 30 16:35:22 2023 +0200

    revert explicit start of parpool in testing pipeline

commit 871e0b6
Merge: 153ba54 a531a2d
Author: Niklas Wahl <[email protected]>
Date:   Tue May 30 16:27:48 2023 +0200

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

commit 153ba54
Author: Niklas Wahl <[email protected]>
Date:   Tue May 30 16:25:33 2023 +0200

    explicit start of parallel pool in testing workflow

commit a531a2d
Author: Niklas Wahl <[email protected]>
Date:   Tue May 30 13:51:31 2023 +0200

    Fix wrong test folder in tests.yml

commit d2da6e4
Merge: 8f03510 d6ea09a
Author: Niklas Wahl <[email protected]>
Date:   Tue May 30 13:42:19 2023 +0200

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

    # Conflicts:
    #	.github/workflows/tests.yml
    #	MatRad_Config.m
    #	matRad_fluenceOptimization.m
    #	matRad_rc.m
    #	ompMC/matRad_compileOmpMCInterface.m
    #	optimization/optimizer/compile_ipopt_minGW_octave640.sh

commit d6ea09a
Merge: 689eabe beaee4e
Author: Niklas Wahl <[email protected]>
Date:   Tue May 30 13:27:32 2023 +0200

    Merge pull request e0404#628 from e0404/hotfix/fixTestEnvironment

    Hotfix to the test pipeline on the master branch

commit beaee4e
Merge: 2f42625 689eabe
Author: Niklas Wahl <[email protected]>
Date:   Fri May 26 19:14:53 2023 +0200

    Merge branch 'master' into hotfix/fixTestEnvironment

commit 2f42625
Author: Niklas Wahl <[email protected]>
Date:   Fri May 26 18:44:48 2023 +0200

    Update job name for octave

commit 0fe09aa
Author: Niklas Wahl <[email protected]>
Date:   Fri May 26 18:35:04 2023 +0200

    Update job name

commit 2397e3f
Author: Niklas Wahl <[email protected]>
Date:   Fri May 26 18:23:04 2023 +0200

    Add latest supported release options for tests to cover for release changes

commit fa26d01
Author: Tobias Becher <[email protected]>
Date:   Fri May 26 16:15:06 2023 +0200

    Small changes to where penalties are applied

    Moved the penalties from the objectives to the objective function. Also added an option for objective constraint.

commit 689eabe
Merge: f7bded9 46d5f2c
Author: Amit Bennan <[email protected]>
Date:   Fri May 26 11:35:38 2023 +0200

    Merge pull request e0404#608 from e0404/bug/606-matrad_plotvoicontourslice-tries-to-access-ct-as-cell-bug

    fix passes ct struct instead of ct.cubeHU to matRad_plotVoiContourSlice

commit 2bca404
Author: Tobias Becher <[email protected]>
Date:   Fri May 26 11:27:42 2023 +0200

    Compatibility with test script

    Added phantomBuilder example to test script and rounding added in BOX phantom assignment

commit 8f03510
Merge: 58362ac 82742b0
Author: Niklas Wahl <[email protected]>
Date:   Tue May 23 18:25:09 2023 +0200

    Merge pull request e0404#621 from tobiasbecher/dev_varRBErobOptGradient

    Bugfix for RBExD gradient calculation.

commit 82742b0
Author: Tobias Becher <[email protected]>
Date:   Tue May 16 10:27:55 2023 +0200

    Update .gitignore

commit 19799c8
Author: Tobias Becher <[email protected]>
Date:   Tue May 16 10:24:27 2023 +0200

    Fixed gradient Bug

commit 58362ac
Author: Niklas Wahl <[email protected]>
Date:   Wed May 10 12:08:26 2023 +0200

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

commit 380b740
Author: Tobias Becher <[email protected]>
Date:   Fri Apr 28 16:19:12 2023 +0200

    Update matRad_runTests.m

    Removing new example1 for now from unit tests

commit 497e036
Author: Tobias Becher <[email protected]>
Date:   Fri Apr 28 15:56:33 2023 +0200

    Final changes

    Renamed matRad_VOIVolume to matRad_PhantomVOIVolume and changed example files.

commit 46d5f2c
Merge: 539dc94 f7bded9
Author: Niklas Wahl <[email protected]>
Date:   Fri Apr 28 15:35:17 2023 +0200

    Merge branch 'master' into bug/606-matrad_plotvoicontourslice-tries-to-access-ct-as-cell-bug

commit f7bded9
Merge: 03cc52f 7456efc
Author: Niklas Wahl <[email protected]>
Date:   Fri Apr 28 15:34:40 2023 +0200

    Merge pull request e0404#607 from e0404/bug/605-bug-warning-and-error-messages-in-matrad_readnrrd-fail-string-concatenation-is-wrong-when-linecontent-is-an-empty-cell

    Error message rectified

commit 539dc94
Merge: 711dc58 03cc52f
Author: Amit Bennan <[email protected]>
Date:   Fri Apr 28 15:23:39 2023 +0200

    Merge branch 'master' into bug/606-matrad_plotvoicontourslice-tries-to-access-ct-as-cell-bug

commit 7456efc
Merge: 8fb0fb8 03cc52f
Author: Niklas Wahl <[email protected]>
Date:   Fri Apr 28 15:01:26 2023 +0200

    Merge branch 'master' into bug/605-bug-warning-and-error-messages-in-matrad_readnrrd-fail-string-concatenation-is-wrong-when-linecontent-is-an-empty-cell

commit 03cc52f
Merge: b2ce690 bb41c69
Author: Niklas Wahl <[email protected]>
Date:   Fri Apr 28 14:59:51 2023 +0200

    Merge pull request e0404#617 from SakuMyl/master

    Check installation of image processing toolbox in DICOM import

commit bb41c69
Author: Saku Myllymäki <[email protected]>
Date:   Fri Apr 28 14:23:24 2023 +0300

    check installation of image processing toolbox

commit 8fb0fb8
Author: Amit Bennan <[email protected]>
Date:   Thu Apr 20 15:21:47 2023 +0200

    displays parsed line in warning message

commit 711dc58
Merge: bcbc8b7 b2ce690
Author: Amit Bennan <[email protected]>
Date:   Tue Apr 11 11:41:53 2023 +0200

    Merge branch 'master' into bug/606-matrad_plotvoicontourslice-tries-to-access-ct-as-cell-bug

commit 85f7cda
Author: Niklas Wahl <[email protected]>
Date:   Thu Apr 6 17:06:51 2023 +0200

    fix problem with constant property containing filepath

commit d6238cd
Author: Niklas Wahl <[email protected]>
Date:   Wed Apr 5 14:59:25 2023 +0200

    Update tests.yml

    Update apt before octave install

commit eab8fc2
Merge: 375987a b2ce690
Author: Niklas Wahl <[email protected]>
Date:   Wed Apr 5 14:46:18 2023 +0200

    Merge branch 'master' into bug/605-bug-warning-and-error-messages-in-matrad_readnrrd-fail-string-concatenation-is-wrong-when-linecontent-is-an-empty-cell

commit b10d896
Author: Tobias Becher <[email protected]>
Date:   Tue Apr 4 11:46:17 2023 +0200

    Changed number of example file

commit 48786f3
Author: Tobias Becher <[email protected]>
Date:   Tue Apr 4 11:35:05 2023 +0200

    Updates to the phantom

    - Moved ct creation to phantom
      builder
    - ct and cst are now private and can be
      received by calling getctst
    - Added documentaion to phantom
      builder functions
    - Modified example file to incorporate
      changes

commit cf1e27b
Author: Tobias Becher <[email protected]>
Date:   Tue Apr 4 11:32:06 2023 +0200

    Updates to VOI related classes

    Renamed Cubic and Spherical VOI classes
    Added option to set HU for VOI

commit ba69a3b
Merge: 4d394f6 b85ec2c
Author: Niklas Wahl <[email protected]>
Date:   Mon Apr 3 11:45:22 2023 +0200

    Merge branch 'dev_varRBErobOpt' into dev_varRBErobOptPhantomBuilder

commit 4d394f6
Author: Tobias Becher <[email protected]>
Date:   Mon Apr 3 10:49:36 2023 +0200

    Delete matRad_createPhantomnew.m

commit 51deb77
Author: Tobias Becher <[email protected]>
Date:   Mon Apr 3 10:47:03 2023 +0200

    Added phantom builder

    Added folder for phantom builder and an example

commit ab666aa
Author: Tobias Becher <[email protected]>
Date:   Mon Apr 3 10:30:24 2023 +0200

    Update .gitignore

commit 0a03aee
Author: Niklas Wahl <[email protected]>
Date:   Mon Feb 6 02:17:51 2023 +0100

    fix path

    (cherry picked from commit ec57365)

commit fe61134
Author: Niklas Wahl <[email protected]>
Date:   Mon Feb 6 02:11:54 2023 +0100

    use preinstallex xvfb in linux test

    (cherry picked from commit cee9df6)

commit 5a8c7f9
Author: Niklas Wahl <[email protected]>
Date:   Sat Feb 4 15:48:06 2023 +0100

    Revert "adjust xvfb call in testing"

    This reverts commit 075402c.

    (cherry picked from commit 78c7b3d)

commit 99336e0
Author: Niklas Wahl <[email protected]>
Date:   Sat Feb 4 15:43:05 2023 +0100

    adjust xvfb call in testing

    (cherry picked from commit 075402c)

commit d4acb02
Author: Niklas Wahl <[email protected]>
Date:   Sat Feb 4 15:10:49 2023 +0100

    update scripts for github folder

    (cherry picked from commit ec4e8b2)

commit 4b9a2fa
Author: Niklas Wahl <[email protected]>
Date:   Sat Feb 4 15:06:49 2023 +0100

    move scripts used during testing to github folder

    (cherry picked from commit 735976d)

commit c3a673f
Author: Niklas Wahl <[email protected]>
Date:   Fri Feb 3 18:47:36 2023 +0100

    update workflow actions

    (cherry picked from commit bf5f4b9)

commit 7060a3a
Author: Niklas Wahl <[email protected]>
Date:   Fri Feb 3 16:27:44 2023 +0100

    include rehash of file directory after linking the optimizer and added availability check

    (cherry picked from commit c509e82)

commit ef95ac3
Author: Niklas Wahl <[email protected]>
Date:   Fri Feb 3 01:15:32 2023 +0100

    option to disable function plot in optimization

    (cherry picked from commit 46445b2)

commit 2c9b118
Author: Niklas Wahl <[email protected]>
Date:   Fri Feb 3 01:15:14 2023 +0100

    update compiled linux optimizer

    (cherry picked from commit ffced04)

commit 8e17c34
Author: Niklas Wahl <[email protected]>
Date:   Wed Feb 1 16:28:33 2023 +0100

    update compiled optimizers with static linking

    (cherry picked from commit 73d6097)

commit f0b7199
Author: Niklas Wahl <[email protected]>
Date:   Wed Feb 1 16:09:03 2023 +0100

    updated optimizer compilation scripts

    (cherry picked from commit 5eff06f)

commit c274d6d
Author: Niklas Wahl <[email protected]>
Date:   Wed Feb 1 14:39:05 2023 +0100

    Recompiled Octave 6.4.0 mex files for windows and linux, updated scripts and submodules

    (cherry picked from commit b353948)

commit 4f436df
Author: Niklas Wahl <[email protected]>
Date:   Mon Jan 30 18:00:41 2023 +0100

    ompMC interface and MCsquare interface - fix eval function for obtaining preconfigured compiler flags

    (cherry picked from commit 7d788f7)

commit add110e
Author: Niklas Wahl <[email protected]>
Date:   Sun Jan 29 20:07:06 2023 +0100

    Update tests.yml

    Switch to Ubuntu 22.04 and thus Octave 6 in test workflow

    (cherry picked from commit bdb95e9)

commit b2ce690
Merge: cb6b04a 091f78b
Author: Niklas Wahl <[email protected]>
Date:   Thu Mar 23 13:07:04 2023 +0100

    Merge pull request e0404#602 from e0404/bug/601-bug-using-minmaxmeandose-constraint-on-structure-with-only-1-voxel-failes

    Fix error when constraints are applied to volumes which have 0 or 1 voxel.

commit bcbc8b7
Author: Amit Bennan <[email protected]>
Date:   Thu Mar 23 12:00:26 2023 +0100

    fix passes ct struct instead of ct.cubeHU to matRad_plotVoiContourSlice

commit 375987a
Author: Amit Bennan <[email protected]>
Date:   Thu Mar 23 11:33:56 2023 +0100

    Error message rectified and all error and warning messages use matRad config messages

commit c0c8353
Author: Niklas Wahl <[email protected]>
Date:   Tue Mar 7 01:50:55 2023 +0100

    remove phsp-header

commit 091f78b
Author: Niklas Wahl <[email protected]>
Date:   Mon Feb 27 12:13:17 2023 +0100

    fixes wrong detection of constraint bounds and jacobian structure when respective volume has 0 or only 1 voxel.

commit b85ec2c
Author: Niklas Wahl <[email protected]>
Date:   Wed Jan 25 23:04:36 2023 +0100

    Downwards compatibility of biological model

commit 5663803
Author: Niklas Wahl <[email protected]>
Date:   Wed Jan 25 18:11:35 2023 +0100

    fix missing extractBetween function in Octave

commit 64ce14c
Merge: d3625aa 4e87571
Author: Niklas Wahl <[email protected]>
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 <[email protected]>
Date:   Thu Jan 19 13:41:47 2023 +0100

    Remove opengl software rendering query due to deprecation

commit 3e427cf
Author: Niklas Wahl <[email protected]>
Date:   Thu Jan 19 01:44:05 2023 +0100

    Avoid erroring on opengl in matRadGUI

commit 894211d
Author: Niklas Wahl <[email protected]>
Date:   Wed Dec 21 18:34:02 2022 +0100

    improve dicom import handling for RTPlan and RTDose
HomolkaN added a commit to HomolkaN/matRad that referenced this pull request Sep 6, 2023
@HomolkaN
Merge dev/dev_varRBErobOpt into varRBErobOpt/Update
f40d8b6 
commit 3215c95
Merge: ccc73dc 5263869
Author: Niklas Wahl <[email protected]>
Date:   Wed Sep 6 11:28:32 2023 +0200

    Merge branch 'dev' into dev_varRBErobOpt

commit ccc73dc
Merge: e915ed6 bdc7567
Author: Niklas Wahl <[email protected]>
Date:   Wed Sep 6 11:22:34 2023 +0200

    Merge pull request e0404#652 from amitantony/dev_varRBErobOpt_GUI

    class based GUI capabilities for the var RBE  plans

commit bdc7567
Author: amitantony <[email protected]>
Date:   Mon Sep 4 17:02:31 2023 +0200

    bugfix for mistaken function call in plotslicewrapper

commit 50b0805
Author: amitantony <[email protected]>
Date:   Fri Sep 1 11:42:25 2023 +0200

    Robustness functionality

commit 5263869
Author: Niklas Wahl <[email protected]>
Date:   Thu Aug 31 14:36:15 2023 +0200

    fix capital letter in MatRad_Config in CT dicom import

commit 0e76650
Author: Niklas Wahl <[email protected]>
Date:   Thu Aug 31 14:35:45 2023 +0200

    fix missing env switch in dicom import

commit 0040374
Merge: fe7fe40 51734ac
Author: Niklas Wahl <[email protected]>
Date:   Thu Aug 31 11:46:51 2023 +0200

    Merge branch 'dev_classGUI' of https://github.com/e0404/matRad into pr/652

    # Conflicts:
    #	dicom/matRad_importDicomRTPlan.m
    #	dicom/matRad_scanDicomImportFolder.m
    #	gui/widgets/matRad_OptimizationWidget.m
    #	gui/widgets/matRad_PlanWidget.m
    #	matRad.m

commit a5a8e62
Merge: 2ff9f09 51734ac
Author: Niklas Wahl <[email protected]>
Date:   Thu Aug 31 11:02:32 2023 +0200

    Merge pull request e0404#646 from e0404/dev_classGUI

    class GUI for dev

commit fe7fe40
Author: Amit Bennan <[email protected]>
Date:   Thu Aug 31 10:56:35 2023 +0200

    clean up code

commit 629f91d
Author: amitantony <[email protected]>
Date:   Tue Aug 29 16:53:38 2023 +0200

    Using Scenario based optimization for the gui

commit 51734ac
Merge: 33f3a1d 38a43ce
Author: Amit Bennan <[email protected]>
Date:   Fri Aug 4 13:04:06 2023 +0200

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

commit 33f3a1d
Author: Amit Bennan <[email protected]>
Date:   Fri Aug 4 13:03:07 2023 +0200

    Bug fix for Viewing widget and Viewer option updates on changes to pln or workflow options

commit 38a43ce
Author: Niklas Wahl <[email protected]>
Date:   Thu Aug 3 15:22:28 2023 -0700

    some more cleanup and default positioning of widgets

commit 27b01e8
Author: Niklas Wahl <[email protected]>
Date:   Thu Aug 3 14:59:34 2023 -0700

    fix for obtaining environment information

commit 68b8c3a
Author: Niklas Wahl <[email protected]>
Date:   Thu Aug 3 14:37:06 2023 -0700

    some cleanup

commit 43e086e
Author: Niklas Wahl <[email protected]>
Date:   Thu Aug 3 14:13:19 2023 -0700

    deprecate java warning

commit 37c0ff8
Author: Amit Bennan <[email protected]>
Date:   Thu Aug 3 18:57:09 2023 +0200

    1. matRad.m to original example setting, 2. MainGUI Documentation, 3. missing documentation

commit 6e03ecf
Merge: 0991137 92bc88d
Author: Amit Bennan <[email protected]>
Date:   Wed Aug 2 22:41:37 2023 +0200

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

commit 0991137
Author: Amit Bennan <[email protected]>
Date:   Wed Aug 2 22:41:03 2023 +0200

    'isOctave' checks replaced with 'matRad_Config object.isOctave'

commit 92bc88d
Author: amitantony <[email protected]>
Date:   Tue Aug 1 15:20:45 2023 +0200

    Documentation and TODO update

commit bfaf5f1
Author: amitantony <[email protected]>
Date:   Fri Jul 28 17:11:48 2023 +0200

    Comments and documentation corrections

commit aaec9ba
Merge: 41e2a65 5385ba4
Author: Niklas Wahl <[email protected]>
Date:   Tue Jul 25 16:10:29 2023 +0200

    Merge pull request e0404#653 from amitantony/dev_classGUI_feature

    Feature to autofill the couch angles

commit cf4fe0b
Author: amitantony <[email protected]>
Date:   Tue Jul 25 09:01:03 2023 +0200

    Default Values for BioParam

commit 5385ba4
Author: amitantony <[email protected]>
Date:   Tue Jul 25 08:44:39 2023 +0200

    Feature to autofill the couch angles to gantry angle size if single value of couch angle is entered

commit 78cd622
Author: amitantony <[email protected]>
Date:   Mon Jul 24 18:29:50 2023 +0200

    carbon pop up bug

commit 9c7a91d
Author: amitantony <[email protected]>
Date:   Mon Jul 24 18:26:51 2023 +0200

    pop up bug for bio model

commit 5b35787
Author: amitantony <[email protected]>
Date:   Mon Jul 24 17:53:51 2023 +0200

    Merge mistake Rectified

commit 322ca69
Merge: 522569c 41e2a65
Author: amitantony <[email protected]>
Date:   Mon Jul 24 17:37:43 2023 +0200

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

commit 522569c
Merge: f3ea5c8 e915ed6
Author: amitantony <[email protected]>
Date:   Mon Jul 24 13:19:42 2023 +0200

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

commit f3ea5c8
Merge: 87832ed ca479fe
Author: amitantony <[email protected]>
Date:   Mon Jul 24 13:18:41 2023 +0200

    Merge branch 'dev_classGUI' of https://github.com/e0404/matRad into dev_varRBErobOpt_GUI
    Runs Basic Var RBE plans in GUI

commit e915ed6
Merge: ce9179d 9cc05a8
Author: Niklas Wahl <[email protected]>
Date:   Fri Jul 21 16:59:52 2023 +0200

    Merge pull request e0404#650 from piastammer/dev_varRBErobOpt

    minor bug fix and small documentation changes

commit ce9179d
Merge: 32bff43 6ef2c24
Author: Niklas Wahl <[email protected]>
Date:   Fri Jul 21 16:57:40 2023 +0200

    Merge pull request e0404#649 from remocristoforetti/dev_varRBErobOpt_bugFix

    minor bug fix

commit 9cc05a8
Author: Pia Stammer <[email protected]>
Date:   Fri Jul 21 16:53:47 2023 +0200

    added warning and TODO for single bixel example

commit 6ef2c24
Author: remocristoforetti <[email protected]>
Date:   Fri Jul 21 16:44:19 2023 +0200

    minor change in generic photon machine
    machine.meta.name turned into machine.meta.machine

commit 41e2a65
Author: Amit Bennan <[email protected]>
Date:   Fri Jul 21 16:42:27 2023 +0200

    bugfix for error on loading first case

commit ad9f5f9
Author: remocristoforetti <[email protected]>
Date:   Fri Jul 21 16:34:06 2023 +0200

    error printout message fix in matRad_multScen

commit 32bff43
Merge: 87832ed a6f7004
Author: Niklas Wahl <[email protected]>
Date:   Fri Jul 21 15:09:43 2023 +0200

    Merge pull request e0404#624 from tobiasbecher/dev_Pareto

    Small changes to where penalties are applied

commit ca479fe
Author: Amit Bennan <[email protected]>
Date:   Fri Jul 21 14:45:33 2023 +0200

    set tissue warning

commit 42a4edc
Author: Pia Stammer <[email protected]>
Date:   Fri Jul 21 14:44:01 2023 +0200

    added TODOs to check commented lines

commit da50e91
Author: Amit Bennan <[email protected]>
Date:   Fri Jul 21 14:30:33 2023 +0200

     test if pln.propSeq exists ( bug from  example 1 with GUI)

commit 59e3e43
Author: Pia Stammer <[email protected]>
Date:   Fri Jul 21 14:22:15 2023 +0200

    removed redundant copyright statements & added Todos for documenation

commit e400ee9
Author: Pia Stammer <[email protected]>
Date:   Fri Jul 21 13:56:22 2023 +0200

    Set default BAMStoIsoDist for topas machine file

commit f497b16
Author: Amit Bennan <[email protected]>
Date:   Fri Jul 21 11:56:40 2023 +0200

    bugfix: 1. fixed reinitialization parameter changes, 2. fixed faulty overwrite of VOIPlotFlag that caused skipping contours

commit 87832ed
Merge: acd73e7 2958dc4
Author: Niklas Wahl <[email protected]>
Date:   Thu Jul 20 11:07:55 2023 +0200

    Merge pull request e0404#610 from tobiasbecher/dev_varRBErobOptPhantomBuilder

    Phantom builder added

commit 2958dc4
Merge: 03ec1a0 acd73e7
Author: Niklas Wahl <[email protected]>
Date:   Thu Jul 20 10:01:53 2023 +0200

    Merge branch 'dev_varRBErobOpt' into pr/610

    # Conflicts:
    #	.gitignore

commit 03ec1a0
Author: Niklas Wahl <[email protected]>
Date:   Thu Jul 20 10:00:26 2023 +0200

    reorganization of builder files

commit acd73e7
Merge: c9acdc5 a83b691
Author: Niklas Wahl <[email protected]>
Date:   Wed Jul 19 17:15:39 2023 +0200

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

commit c9acdc5
Author: Niklas Wahl <[email protected]>
Date:   Wed Jul 19 17:15:33 2023 +0200

    Update of base data file for estimate of energy spectrum

commit 2f00898
Author: Tobias Becher <[email protected]>
Date:   Mon Jul 10 12:47:38 2023 +0200

    Final updates

    Final changes to the phantom builder

commit a83b691
Merge: d5bf94a f2e62b6
Author: Niklas Wahl <[email protected]>
Date:   Mon Jul 10 10:13:15 2023 +0200

    Merge pull request e0404#642 from JenHardt/dev_varRBErobOpt

    IsoCenterShift BugFix

commit f2e62b6
Author: JenHardt <[email protected]>
Date:   Fri Jul 7 13:56:16 2023 +0200

    IsoCenterShift BugFix

commit bca2260
Author: Tobias Becher <[email protected]>
Date:   Fri Jun 30 14:41:50 2023 +0200

    Update matRad_runTests.m

commit d474f09
Author: Tobias Becher <[email protected]>
Date:   Fri Jun 30 14:33:25 2023 +0200

    Removed indexing of VOI

    VOI are no longer assigned an index on initialization.
    -> No need to clear all at the start of  a script if rerunning

commit c12f5e8
Author: Tobias Becher <[email protected]>
Date:   Fri Jun 30 14:10:55 2023 +0200

    Fixed geometry issues

    Fixed issues with the coordinate system

commit a6f7004
Author: Tobias Becher <[email protected]>
Date:   Fri Jun 30 10:24:52 2023 +0200

    Slack parameter changes

    - Changed epsilon variable name to slackParameter
    - Now parameter of constraint
    - Removed objective funtion to turn into constraint

commit c91799c
Merge: 94e701c 4177468
Author: amitantony <[email protected]>
Date:   Fri Jun 30 10:03:04 2023 +0200

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

commit dedf147
Author: Tobias Becher <[email protected]>
Date:   Wed Jun 28 13:37:18 2023 +0200

    Some changes

    Some changes made for pull request. Commit also tests if server tests now run through.

commit d5bf94a
Author: Niklas Wahl <[email protected]>
Date:   Wed Jun 28 10:18:28 2023 +0200

    allows to compute the bixel dose when cutoff was not precomputed by setting the compensation factor to 1

commit 83fc8a6
Author: Niklas Wahl <[email protected]>
Date:   Wed Jun 28 10:17:45 2023 +0200

    emittance base data format now allows one emittance per focus

commit 5fda67e
Merge: 99eaa34 bffb834
Author: Niklas Wahl <[email protected]>
Date:   Wed Jun 21 10:56:08 2023 +0200

    Merge pull request e0404#637 from remocristoforetti/dev_varRBErobOpt_bugFix_MCemittanceBaseData

    bugFix in MCemittanceBaseData for negative distances

commit bffb834
Author: RemoCristoforetti <[email protected]>
Date:   Wed Jun 21 10:49:28 2023 +0200

    bugFix negative distance for spot size correction in air.

commit 99eaa34
Author: Niklas Wahl <[email protected]>
Date:   Wed Jun 21 10:10:19 2023 +0200

    Fix matRad_MCemittanceBaseData.m

    Replaced Inf with realmax so interpolation does not error

commit 3e7952a
Author: Niklas Wahl <[email protected]>
Date:   Wed Jun 7 13:19:31 2023 +0200

    AppendResultGUI now creates consistent fieldnames

commit c5dd9eb
Author: Niklas Wahl <[email protected]>
Date:   Tue Jun 6 18:32:40 2023 +0200

    appendresultgui now either overwrites or always appends the identifier

commit 1bab14d
Author: Niklas Wahl <[email protected]>
Date:   Tue Jun 6 18:32:21 2023 +0200

    fix for the spot size air MCS correction

commit 6a746ee
Author: Niklas Wahl <[email protected]>
Date:   Tue Jun 6 14:13:20 2023 +0200

    fix variable names in example 12

commit a7e72fa
Author: Niklas Wahl <[email protected]>
Date:   Tue Jun 6 14:13:01 2023 +0200

    add empirical correction for MCS in air when approximating beam model

commit 1a80ea9
Author: Tobias Becher <[email protected]>
Date:   Mon Jun 5 11:01:52 2023 +0200

    Name change for constraints

    Changed the name for created constraints in the optimization

commit 94e701c
Author: amitantony <[email protected]>
Date:   Fri Jun 2 15:25:13 2023 +0200

    1. avoid sequencing warning everytime we optimize particles,  2. IGNORED as a tissue type, 3. fix for "ignoring legend entries" warning , 4. DVHStat naming bugfix

commit 4177468
Merge: 2273867 893f9b3
Author: Niklas Wahl <[email protected]>
Date:   Thu Jun 1 14:02:31 2023 +0200

    Merge pull request e0404#631 from amitantony/bug/DVHWidgetFix

    Bug/dvh widget fix

commit f59722c
Merge: 893f9b3 2273867
Author: amitantony <[email protected]>
Date:   Thu Jun 1 12:38:18 2023 +0200

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

commit 893f9b3
Author: amitantony <[email protected]>
Date:   Wed May 31 15:58:13 2023 +0200

    Consistant naming fix

commit ae58086
Author: amitantony <[email protected]>
Date:   Wed May 31 15:45:17 2023 +0200

    more compact application of recenter

commit 2273867
Merge: 37c2f02 602bae6
Author: Amit Bennan <[email protected]>
Date:   Wed May 31 15:36:47 2023 +0200

    Merge pull request e0404#626 from amitantony/dev_classGUI_matPatientLoadBug

    Dev class GUI .mat patient load bug

commit 8c2d20e
Author: amitantony <[email protected]>
Date:   Wed May 31 15:34:18 2023 +0200

    feature: Recentering to iso center button

commit 602bae6
Author: amitantony <[email protected]>
Date:   Tue May 30 18:01:48 2023 +0200

    fix for test failing in matRad.m

commit 48ca910
Author: Niklas Wahl <[email protected]>
Date:   Tue May 30 16:35:22 2023 +0200

    revert explicit start of parpool in testing pipeline

commit 871e0b6
Merge: 153ba54 a531a2d
Author: Niklas Wahl <[email protected]>
Date:   Tue May 30 16:27:48 2023 +0200

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

commit 153ba54
Author: Niklas Wahl <[email protected]>
Date:   Tue May 30 16:25:33 2023 +0200

    explicit start of parallel pool in testing workflow

commit 7561424
Merge: ec8fd78 37c2f02
Author: amitantony <[email protected]>
Date:   Tue May 30 15:07:11 2023 +0200

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

commit a531a2d
Author: Niklas Wahl <[email protected]>
Date:   Tue May 30 13:51:31 2023 +0200

    Fix wrong test folder in tests.yml

commit d2da6e4
Merge: 8f03510 d6ea09a
Author: Niklas Wahl <[email protected]>
Date:   Tue May 30 13:42:19 2023 +0200

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

    # Conflicts:
    #	.github/workflows/tests.yml
    #	MatRad_Config.m
    #	matRad_fluenceOptimization.m
    #	matRad_rc.m
    #	ompMC/matRad_compileOmpMCInterface.m
    #	optimization/optimizer/compile_ipopt_minGW_octave640.sh

commit d6ea09a
Merge: 689eabe beaee4e
Author: Niklas Wahl <[email protected]>
Date:   Tue May 30 13:27:32 2023 +0200

    Merge pull request e0404#628 from e0404/hotfix/fixTestEnvironment

    Hotfix to the test pipeline on the master branch

commit beaee4e
Merge: 2f42625 689eabe
Author: Niklas Wahl <[email protected]>
Date:   Fri May 26 19:14:53 2023 +0200

    Merge branch 'master' into hotfix/fixTestEnvironment

commit 37c2f02
Merge: 5984075 72d5d3c
Author: Niklas Wahl <[email protected]>
Date:   Fri May 26 18:58:18 2023 +0200

    Merge pull request e0404#625 from amitantony/dev_classGUI_a_DicomImportBug

    Dev class GUI a dicom import bug

commit 72d5d3c
Merge: ef55778 5984075
Author: Niklas Wahl <[email protected]>
Date:   Fri May 26 18:57:28 2023 +0200

    Merge branch 'dev_classGUI' into dev_classGUI_a_DicomImportBug

commit 5984075
Merge: 671baea 1f7bc74
Author: Niklas Wahl <[email protected]>
Date:   Fri May 26 18:55:48 2023 +0200

    Merge pull request e0404#627 from amitantony/dev_classGUI_IsoDoseBugFix

    BUGFIX: Iso dose contour not updated with changing selectedDisplayOption

commit 2f42625
Author: Niklas Wahl <[email protected]>
Date:   Fri May 26 18:44:48 2023 +0200

    Update job name for octave

commit 0fe09aa
Author: Niklas Wahl <[email protected]>
Date:   Fri May 26 18:35:04 2023 +0200

    Update job name

commit 2397e3f
Author: Niklas Wahl <[email protected]>
Date:   Fri May 26 18:23:04 2023 +0200

    Add latest supported release options for tests to cover for release changes

commit ef55778
Author: amitantony <[email protected]>
Date:   Fri May 26 16:15:48 2023 +0200

    Class GUI dicom import bugs resolve to return atleast 1 DICOM patient case

commit fa26d01
Author: Tobias Becher <[email protected]>
Date:   Fri May 26 16:15:06 2023 +0200

    Small changes to where penalties are applied

    Moved the penalties from the objectives to the objective function. Also added an option for objective constraint.

commit ec8fd78
Author: Amit Bennan <[email protected]>
Date:   Fri May 26 14:30:12 2023 +0200

    bug fix on first load of patient case

commit 689eabe
Merge: f7bded9 46d5f2c
Author: Amit Bennan <[email protected]>
Date:   Fri May 26 11:35:38 2023 +0200

    Merge pull request e0404#608 from e0404/bug/606-matrad_plotvoicontourslice-tries-to-access-ct-as-cell-bug

    fix passes ct struct instead of ct.cubeHU to matRad_plotVoiContourSlice

commit 2bca404
Author: Tobias Becher <[email protected]>
Date:   Fri May 26 11:27:42 2023 +0200

    Compatibility with test script

    Added phantomBuilder example to test script and rounding added in BOX phantom assignment

commit 1f7bc74
Author: amitantony <[email protected]>
Date:   Fri May 26 11:09:50 2023 +0200

    Bugfix for : Iso dose contour not updated with changing selectedDisplayOption

commit 8f03510
Merge: 58362ac 82742b0
Author: Niklas Wahl <[email protected]>
Date:   Tue May 23 18:25:09 2023 +0200

    Merge pull request e0404#621 from tobiasbecher/dev_varRBErobOptGradient

    Bugfix for RBExD gradient calculation.

commit 82742b0
Author: Tobias Becher <[email protected]>
Date:   Tue May 16 10:27:55 2023 +0200

    Update .gitignore

commit 19799c8
Author: Tobias Becher <[email protected]>
Date:   Tue May 16 10:24:27 2023 +0200

    Fixed gradient Bug

commit 58362ac
Author: Niklas Wahl <[email protected]>
Date:   Wed May 10 12:08:26 2023 +0200

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

commit 380b740
Author: Tobias Becher <[email protected]>
Date:   Fri Apr 28 16:19:12 2023 +0200

    Update matRad_runTests.m

    Removing new example1 for now from unit tests

commit 497e036
Author: Tobias Becher <[email protected]>
Date:   Fri Apr 28 15:56:33 2023 +0200

    Final changes

    Renamed matRad_VOIVolume to matRad_PhantomVOIVolume and changed example files.

commit 46d5f2c
Merge: 539dc94 f7bded9
Author: Niklas Wahl <[email protected]>
Date:   Fri Apr 28 15:35:17 2023 +0200

    Merge branch 'master' into bug/606-matrad_plotvoicontourslice-tries-to-access-ct-as-cell-bug

commit f7bded9
Merge: 03cc52f 7456efc
Author: Niklas Wahl <[email protected]>
Date:   Fri Apr 28 15:34:40 2023 +0200

    Merge pull request e0404#607 from e0404/bug/605-bug-warning-and-error-messages-in-matrad_readnrrd-fail-string-concatenation-is-wrong-when-linecontent-is-an-empty-cell

    Error message rectified

commit 539dc94
Merge: 711dc58 03cc52f
Author: Amit Bennan <[email protected]>
Date:   Fri Apr 28 15:23:39 2023 +0200

    Merge branch 'master' into bug/606-matrad_plotvoicontourslice-tries-to-access-ct-as-cell-bug

commit 7456efc
Merge: 8fb0fb8 03cc52f
Author: Niklas Wahl <[email protected]>
Date:   Fri Apr 28 15:01:26 2023 +0200

    Merge branch 'master' into bug/605-bug-warning-and-error-messages-in-matrad_readnrrd-fail-string-concatenation-is-wrong-when-linecontent-is-an-empty-cell

commit 03cc52f
Merge: b2ce690 bb41c69
Author: Niklas Wahl <[email protected]>
Date:   Fri Apr 28 14:59:51 2023 +0200

    Merge pull request e0404#617 from SakuMyl/master

    Check installation of image processing toolbox in DICOM import

commit bb41c69
Author: Saku Myllymäki <[email protected]>
Date:   Fri Apr 28 14:23:24 2023 +0300

    check installation of image processing toolbox

commit 8fb0fb8
Author: Amit Bennan <[email protected]>
Date:   Thu Apr 20 15:21:47 2023 +0200

    displays parsed line in warning message

commit 711dc58
Merge: bcbc8b7 b2ce690
Author: Amit Bennan <[email protected]>
Date:   Tue Apr 11 11:41:53 2023 +0200

    Merge branch 'master' into bug/606-matrad_plotvoicontourslice-tries-to-access-ct-as-cell-bug

commit 85f7cda
Author: Niklas Wahl <[email protected]>
Date:   Thu Apr 6 17:06:51 2023 +0200

    fix problem with constant property containing filepath

commit d6238cd
Author: Niklas Wahl <[email protected]>
Date:   Wed Apr 5 14:59:25 2023 +0200

    Update tests.yml

    Update apt before octave install

commit eab8fc2
Merge: 375987a b2ce690
Author: Niklas Wahl <[email protected]>
Date:   Wed Apr 5 14:46:18 2023 +0200

    Merge branch 'master' into bug/605-bug-warning-and-error-messages-in-matrad_readnrrd-fail-string-concatenation-is-wrong-when-linecontent-is-an-empty-cell

commit b10d896
Author: Tobias Becher <[email protected]>
Date:   Tue Apr 4 11:46:17 2023 +0200

    Changed number of example file

commit 48786f3
Author: Tobias Becher <[email protected]>
Date:   Tue Apr 4 11:35:05 2023 +0200

    Updates to the phantom

    - Moved ct creation to phantom
      builder
    - ct and cst are now private and can be
      received by calling getctst
    - Added documentaion to phantom
      builder functions
    - Modified example file to incorporate
      changes

commit cf1e27b
Author: Tobias Becher <[email protected]>
Date:   Tue Apr 4 11:32:06 2023 +0200

    Updates to VOI related classes

    Renamed Cubic and Spherical VOI classes
    Added option to set HU for VOI

commit ba69a3b
Merge: 4d394f6 b85ec2c
Author: Niklas Wahl <[email protected]>
Date:   Mon Apr 3 11:45:22 2023 +0200

    Merge branch 'dev_varRBErobOpt' into dev_varRBErobOptPhantomBuilder

commit 4d394f6
Author: Tobias Becher <[email protected]>
Date:   Mon Apr 3 10:49:36 2023 +0200

    Delete matRad_createPhantomnew.m

commit 51deb77
Author: Tobias Becher <[email protected]>
Date:   Mon Apr 3 10:47:03 2023 +0200

    Added phantom builder

    Added folder for phantom builder and an example

commit ab666aa
Author: Tobias Becher <[email protected]>
Date:   Mon Apr 3 10:30:24 2023 +0200

    Update .gitignore

commit 0a03aee
Author: Niklas Wahl <[email protected]>
Date:   Mon Feb 6 02:17:51 2023 +0100

    fix path

    (cherry picked from commit ec57365)

commit fe61134
Author: Niklas Wahl <[email protected]>
Date:   Mon Feb 6 02:11:54 2023 +0100

    use preinstallex xvfb in linux test

    (cherry picked from commit cee9df6)

commit 5a8c7f9
Author: Niklas Wahl <[email protected]>
Date:   Sat Feb 4 15:48:06 2023 +0100

    Revert "adjust xvfb call in testing"

    This reverts commit 075402c.

    (cherry picked from commit 78c7b3d)

commit 99336e0
Author: Niklas Wahl <[email protected]>
Date:   Sat Feb 4 15:43:05 2023 +0100

    adjust xvfb call in testing

    (cherry picked from commit 075402c)

commit d4acb02
Author: Niklas Wahl <[email protected]>
Date:   Sat Feb 4 15:10:49 2023 +0100

    update scripts for github folder

    (cherry picked from commit ec4e8b2)

commit 4b9a2fa
Author: Niklas Wahl <[email protected]>
Date:   Sat Feb 4 15:06:49 2023 +0100

    move scripts used during testing to github folder

    (cherry picked from commit 735976d)

commit c3a673f
Author: Niklas Wahl <[email protected]>
Date:   Fri Feb 3 18:47:36 2023 +0100

    update workflow actions

    (cherry picked from commit bf5f4b9)

commit 7060a3a
Author: Niklas Wahl <[email protected]>
Date:   Fri Feb 3 16:27:44 2023 +0100

    include rehash of file directory after linking the optimizer and added availability check

    (cherry picked from commit c509e82)

commit ef95ac3
Author: Niklas Wahl <[email protected]>
Date:   Fri Feb 3 01:15:32 2023 +0100

    option to disable function plot in optimization

    (cherry picked from commit 46445b2)

commit 2c9b118
Author: Niklas Wahl <[email protected]>
Date:   Fri Feb 3 01:15:14 2023 +0100

    update compiled linux optimizer

    (cherry picked from commit ffced04)

commit 8e17c34
Author: Niklas Wahl <[email protected]>
Date:   Wed Feb 1 16:28:33 2023 +0100

    update compiled optimizers with static linking

    (cherry picked from commit 73d6097)

commit f0b7199
Author: Niklas Wahl <[email protected]>
Date:   Wed Feb 1 16:09:03 2023 +0100

    updated optimizer compilation scripts

    (cherry picked from commit 5eff06f)

commit c274d6d
Author: Niklas Wahl <[email protected]>
Date:   Wed Feb 1 14:39:05 2023 +0100

    Recompiled Octave 6.4.0 mex files for windows and linux, updated scripts and submodules

    (cherry picked from commit b353948)

commit 4f436df
Author: Niklas Wahl <[email protected]>
Date:   Mon Jan 30 18:00:41 2023 +0100

    ompMC interface and MCsquare interface - fix eval function for obtaining preconfigured compiler flags

    (cherry picked from commit 7d788f7)

commit add110e
Author: Niklas Wahl <[email protected]>
Date:   Sun Jan 29 20:07:06 2023 +0100

    Update tests.yml

    Switch to Ubuntu 22.04 and thus Octave 6 in test workflow

    (cherry picked from commit bdb95e9)

commit b2ce690
Merge: cb6b04a 091f78b
Author: Niklas Wahl <[email protected]>
Date:   Thu Mar 23 13:07:04 2023 +0100

    Merge pull request e0404#602 from e0404/bug/601-bug-using-minmaxmeandose-constraint-on-structure-with-only-1-voxel-failes

    Fix error when constraints are applied to volumes which have 0 or 1 voxel.

commit bcbc8b7
Author: Amit Bennan <[email protected]>
Date:   Thu Mar 23 12:00:26 2023 +0100

    fix passes ct struct instead of ct.cubeHU to matRad_plotVoiContourSlice

commit 375987a
Author: Amit Bennan <[email protected]>
Date:   Thu Mar 23 11:33:56 2023 +0100

    Error message rectified and all error and warning messages use matRad config messages

commit c0c8353
Author: Niklas Wahl <[email protected]>
Date:   Tue Mar 7 01:50:55 2023 +0100

    remove phsp-header

commit 091f78b
Author: Niklas Wahl <[email protected]>
Date:   Mon Feb 27 12:13:17 2023 +0100

    fixes wrong detection of constraint bounds and jacobian structure when respective volume has 0 or only 1 voxel.

commit 2ff9f09
Merge: 27ad9ff aab03e9
Author: Niklas Wahl <[email protected]>
Date:   Fri Feb 24 15:16:09 2023 +0100

    Merge pull request e0404#599 from JenHardt/dev

    BUG: ssd calculation should use actual ray distance instead of SAD

commit aab03e9
Merge: 9f4af93 27ad9ff
Author: Hardt <[email protected]>
Date:   Tue Feb 7 15:47:12 2023 +0100

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

commit 9f4af93
Author: Hardt <[email protected]>
Date:   Tue Feb 7 15:46:27 2023 +0100

    small Bugfix

commit 5084863
Author: Amit Bennan <[email protected]>
Date:   Fri Jan 27 10:32:23 2023 +0100

    Code style comments addressed  (MB review)

commit b85ec2c
Author: Niklas Wahl <[email protected]>
Date:   Wed Jan 25 23:04:36 2023 +0100

    Downwards compatibility of biological model

commit 5663803
Author: Niklas Wahl <[email protected]>
Date:   Wed Jan 25 18:11:35 2023 +0100

    fix missing extractBetween function in Octave

commit 64ce14c
Merge: d3625aa 4e87571
Author: Niklas Wahl <[email protected]>
Date:   Tue Jan 24 15:55:11 2023 +0100

    Merge pull request e0404#536 from HomolkaN/dev_varRBErobOpt_Update

    Extensive TOPAS workflow update:

commit 260bd66
Merge: a1c8743 ecc6e0c
Author: Amit Bennan <[email protected]>
Date:   Fri Jan 20 14:03:37 2023 +0100

    Merge branch 'dev_classGUI_a' of https://github.com/amitantony/matRad into dev_classGUI

commit d3625aa
Author: Niklas Wahl <[email protected]>
Date:   Thu Jan 19 13:41:47 2023 +0100

    Remove opengl software rendering query due to deprecation

commit 3e427cf
Author: Niklas Wahl <[email protected]>
Date:   Thu Jan 19 01:44:05 2023 +0100

    Avoid erroring on opengl in matRadGUI

commit ecc6e0c
Merge: 8c9f8ee 671baea
Author: Amit Bennan <[email protected]>
Date:   Wed Jan 4 13:03:51 2023 +0100

    Merge branch 'dev_classGUI' into dev_classGUI_a

commit 894211d
Author: Niklas Wahl <[email protected]>
Date:   Wed Dec 21 18:34:02 2022 +0100

    improve dicom import handling for RTPlan and RTDose

commit 671baea
Merge: 91cbc12 27ad9ff
Author: Amit Bennan <[email protected]>
Date:   Tue Dec 20 13:31:01 2022 +0100

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

commit 27ad9ff
Merge: 3b781b6 cb6b04a
Author: Niklas Wahl <[email protected]>
Date:   Tue Nov 29 20:29:38 2022 +0100

    Merge branch 'master' into dev

commit 8c9f8ee
Author: amitantony <[email protected]>
Date:   Thu Nov 10 14:51:40 2022 +0100

    documentation

commit c711bdc
Author: amitantony <[email protected]>
Date:   Fri Nov 4 19:19:26 2022 +0100

    first working prototype

commit 3fe5660
Author: amitantony <[email protected]>
Date:   Thu Oct 27 11:39:54 2022 +0200

    Gamma Widget skeleton

commit a1c8743
Author: Amit Bennan <[email protected]>
Date:   Thu Oct 27 11:38:59 2022 +0200

    DVHStatswidget object stored in main gui

commit 2d41f12
Author: Amit Bennan <[email protected]>
Date:   Mon Oct 24 13:36:12 2022 +0200

    1. Documentation for newer widget functions
    2. clean up of code
    3. fully update DVH solution

commit 3b781b6
Author: Niklas Wahl <[email protected]>
Date:   Thu Oct 20 00:01:08 2022 +0200

    Update matRad_calcCubes.m

    Correct MU vector calculation

commit 6db771e
Merge: fea82a8 1b13404
Author: Niklas Wahl <[email protected]>
Date:   Wed Oct 5 17:04:51 2022 +0200

    Merge branch 'master' into dev

commit b80323c
Merge: e4ad063 d8c58e0
Author: Amit Bennan <[email protected]>
Date:   Fri Jul 29 16:06:11 2022 +0200

    Merge branch 'dev_classGUI_a' of https://github.com/amitantony/matRad into dev_classGUI_a

commit e4ad063
Merge: a216bd1 c0a9f08
Author: Amit Bennan <[email protected]>
Date:   Fri Jul 29 16:05:59 2022 +0200

    Merge branch 'dev_clean' into dev_classGUI_a : runs basic examples

commit d8c58e0
Author: amitantony <[email protected]>
Date:   Fri Jul 29 14:26:47 2022 +0200

    [bugfix] errors while running the basic matrad script

commit a216bd1
Author: Amit Bennan <[email protected]>
Date:   Fri Jul 29 10:17:00 2022 +0200

    [bug fix] DVH updates with the selected cube for display

commit 657ef2b
Merge: 13d35e0 d17ecb2
Author: amitLT <[email protected]>
Date:   Thu Jun 9 14:09:42 2022 +0200

    Merge branch 'dev_classGUI_a' of https://github.com/amitantony/matRad into dev_classGUI_a

commit d17ecb2
Author: amitantony <[email protected]>
Date:   Fri Apr 29 17:40:54 2022 +0200

    Input Parser for DVH and statistics widget

commit eae4a47
Author: amitantony <[email protected]>
Date:   Wed Apr 27 11:59:30 2022 +0200

    bug fix :  iso line update problem for "Saved Results" of ResultGUI in viewing widget

commit 13d35e0
Author: amitLT <[email protected]>
Date:   Fri Apr 22 17:07:26 2022 +0200

    encoding to UTF8

commit baa9182
Author: amitLT <[email protected]>
Date:   Thu Apr 21 13:02:15 2022 +0200

    bug fix : enabling and disabling sequencing options

commit 7204af4
Author: amitLT <[email protected]>
Date:   Mon Apr 4 18:05:02 2022 +0200

    Added sequencing drop down menu  to the GUI

commit 16beca5
Author: amitLT <[email protected]>
Date:   Tue Mar 29 14:23:18 2022 +0200

    update of new referencing to sequencing in matRad and example scripts

commit 5f4da57
Author: amitLT <[email protected]>
Date:   Tue Mar 29 14:06:10 2022 +0200

    Sequencing wrapper function that accepts highlevel matRad structures

commit cb5a94c
Author: amitLT <[email protected]>
Date:   Thu Mar 24 09:43:13 2022 +0100

    Fixes for couch angle update, (cst,ct ) loaded message, CBTplanning

commit 91cbc12
Author: Niklas Wahl <[email protected]>
Date:   Fri Dec 10 16:15:17 2021 +0100

    some fixes in the class-based GUI

commit b3cd841
Merge: 5137fcc f725b01
Author: Niklas Wahl <[email protected]>
Date:   Mon Feb 8 15:01:31 2021 +0100

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

commit f725b01
Merge: 6b50cf5 51f8428
Author: Niklas Wahl <[email protected]>
Date:   Mon Feb 8 14:34:26 2021 +0100

    Merge pull request e0404#486 from palkma/dev_classGUI

    added tooltips to GUI elements

commit 51f8428
Author: Palkowitsch <[email protected]>
Date:   Tue Feb 2 16:19:11 2021 +0100

    added tooltips

commit 5137fcc
Merge: 1996919 d930c3e
Author: Niklas Wahl <[email protected]>
Date:   Thu Dec 24 13:39:51 2020 +0100

    Merge remote-tracking branch 'origin/master' into dev_classGUI

    # Conflicts:
    #	MatRad_Config.m
    #	dicom/@matRad_DicomExporter/matRad_DicomExporter.m
    #	dicom/matRad_scanDicomImportFolder.m
    #	matRadGUI.m
    #	matRad_showDVH.m
    #	plotting/matRad_plotIsoDoseLines.m

commit 1996919
Merge: 6b50cf5 4399711
Author: Niklas Wahl <[email protected]>
Date:   Mon Oct 5 11:17:34 2020 +0200

    Merge branch 'dev_classGUI' of https://github.com/nellyabbani/matRad into dev_classGUI

commit 4399711
Author: nelly.abbani <[email protected]>
Date:   Fri Aug 28 10:40:18 2020 +0200

    uiwrapper function

commit 6b50cf5
Author: Niklas Wahl <[email protected]>
Date:   Fri Aug 21 17:02:38 2020 +0200

    fix tests

commit 434422d
Merge: b4c7783 1463811
Author: Niklas Wahl <[email protected]>
Date:   Fri Aug 21 16:26:46 2020 +0200

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

commit b4c7783
Author: Niklas Wahl <[email protected]>
Date:   Fri Aug 21 16:26:10 2020 +0200

    changes to gui calls

commit 38c7131
Author: Niklas Wahl <[email protected]>
Date:   Fri Aug 21 15:46:46 2020 +0200

    more old files removal

commit b5d48cf
Author: Niklas Wahl <[email protected]>
Date:   Fri Aug 21 15:44:51 2020 +0200

    removal of old logo files

commit 736b2f2
Author: Niklas Wahl <[email protected]>
Date:   Fri Aug 21 15:43:39 2020 +0200

    gui fixes and removal of old files

commit a3ba0c2
Author: Niklas Wahl <[email protected]>
Date:   Thu Aug 20 18:38:18 2020 +0200

    More consistency and compatability updates

commit dfd8e9a
Author: Niklas Wahl <[email protected]>
Date:   Wed Aug 19 18:43:47 2020 +0200

    modifications to Widget structure and layout, consistent colors, etc

commit adac165
Author: Niklas Wahl <[email protected]>
Date:   Wed Aug 19 10:26:50 2020 +0200

    tweaks to the gui widgets, new EventData-based class to explicitly state changed workspace variables

commit 6e19dfa
Author: Niklas Wahl <[email protected]>
Date:   Wed Aug 19 10:25:09 2020 +0200

    crop logo a little

commit 15e4cd8
Author: Niklas Wahl <[email protected]>
Date:   Wed Aug 19 10:24:37 2020 +0200

    remove some old gui functions

commit 9bf703f
Author: Niklas Wahl <[email protected]>
Date:   Fri Aug 7 12:12:58 2020 +0200

    Move matRadGUI to main folder again

commit f271346
Author: Niklas Wahl <[email protected]>
Date:   Fri Aug 7 12:12:21 2020 +0200

    fix createLayout for dicom import

commit 52e8fe2
Author: Niklas Wahl <[email protected]>
Date:   Thu Jul 30 14:21:50 2020 +0200

    Fix paths and maximize matRadGUI

commit d0885c4
Merge: 36a149d ca4044b
Author: Niklas Wahl <[email protected]>
Date:   Thu Jul 30 11:59:33 2020 +0200

    Merge branch 'dev_classGUI' of https://github.com/nellyabbani/matRad into dev_classGUI

    # Conflicts:
    #	gui/matRadGUI.m

commit ca4044b
Author: nellyabbani <[email protected]>
Date:   Wed Jul 29 20:33:14 2020 +0200

    Split DVH widget into 2 widgets.
    Add exportDicom widget.
    +other small fixes

commit 36a149d
Author: Niklas Wahl <[email protected]>
Date:   Wed Jul 29 17:44:10 2020 +0200

    changes to avoid crash in Octave

commit 5694ffd
Author: nellyabbani <[email protected]>
Date:   Tue Jun 30 10:31:45 2020 +0200

    Further improvements to the GUI widgets

commit 4f69fa4
Author: nellyabbani <[email protected]>
Date:   Mon Jun 15 13:11:40 2020 +0200

    Small fixes on the GUI widgets

commit fe2abdc
Author: nellyabbani <[email protected]>
Date:   Fri Jun 12 17:15:08 2020 +0200

    Merge dev_classGUI with master class

commit a89edfe
Merge: 5620dbe c22da7d
Author: nellyabbani <[email protected]>
Date:   Fri Jun 12 15:59:35 2020 +0200

    Merge branch 'master' into dev_classGUI

    # Conflicts:
    #	dicom/@matRad_importDicomWidget/createLayout.m
    #	dicom/@matRad_importDicomWidget/matRad_importDicomWidget.m
    #	dicom/DKFZ_Logo.png
    #	dicom/gui/matRad_importDicomGUI_LayoutFcn.m
    #	dicom/gui/matRad_importDicomGUI_gui_mainFcn.m
    #	dicom/matRad_checkEnvDicomRequirements.m
    #	dicom/matRad_createCst.m
    #	dicom/matRad_importDicomGUI.fig.bak
    #	dicom/matrad_logo.png
    #	dicomImport/DKFZ_Logo.png
    #	dicomImport/matrad_logo.png
    #	gfx/DKFZ_Logo.png
    #	gfx/matrad_logo.png
    #	matRadGUI.m
    #	matRad_fluenceOptimization.m
    #	matRad_showQualityIndicators.m

commit 5620dbe
Author: nellyabbani <[email protected]>
Date:   Fri Jun 12 13:54:32 2020 +0200

    Update to refresh the GUI widgets when clicked + implementation of notify and listeners concepts in octave

commit 71e397e
Author: nellyabbani <[email protected]>
Date:   Mon Jun 8 09:27:35 2020 +0200

    Functioning version of all the GUI widgets

commit 4abd14e
Author: nellyabbani <[email protected]>
Date:   Fri May 1 13:06:35 2020 +0200

    Scripted GUI widgets

commit 3501e99
Author: nellyabbani <[email protected]>
Date:   Thu Apr 2 18:03:56 2020 +0200

    Scripted GUI workflow, plan, and optimization widgets

commit 986dbb6
Merge: 4045a4b 833e582
Author: nellyabbani <[email protected]>
Date:   Tue Mar 3 16:18:17 2020 +0100

    Merge remote-tracking branch 'origin/dev_classGUI' into dev_classGUI

    # Conflicts:
    #	gui/matRad_PlanWidget.m
    #	gui/matRad_WorkflowWidget.m

commit 4045a4b
Author: nellyabbani <[email protected]>
Date:   Tue Mar 3 16:13:38 2020 +0100

    Initial fix to the widgets

commit 833e582
Author: Nabe Al Hasnawi <[email protected]>
Date:   Fri Feb 28 13:43:55 2020 +0100

    Widget Default Values and Names

commit 0db80e1
Author: Nabe Al Hasnawi <[email protected]>
Date:   Tue Feb 25 12:07:10 2020 +0100

    matRad gui icons as mat file

commit 922c349
Author: Nabe Al Hasnawi <[email protected]>
Date:   Tue Feb 25 12:04:09 2020 +0100

    First developments on independent GUI widgets

commit b926ed9
Author: Nabe <[email protected]>
Date:   Tue Dec 10 11:27:12 2019 +0100

    Class based Widgets for import & export with shared import/export GUI

commit f55a46a
Merge: 6df1b0f d66cf32
Author: Niklas Wahl <[email protected]>
Date:   Fri Aug 16 16:13:11 2019 +0200

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

commit 6df1b0f
Author: Niklas Wahl <[email protected]>
Date:   Fri Aug 16 16:12:22 2019 +0200

    Exported the IO gui's and added the dicom external GUI files

commit b07c70c
Author: Niklas Wahl <[email protected]>
Date:   Tue Aug 13 12:42:03 2019 +0200

    fix for missing mat File containing GUI parmeters (is exported from guide).

commit 1ae350a
Merge: 7ee4580 81e4545
Author: Niklas Wahl <[email protected]>
Date:   Fri Aug 9 20:13:02 2019 +0200

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

commit 7ee4580
Merge: ecbcbc1 81332ae
Author: Niklas Wahl <[email protected]>
Date:   Fri Aug 9 20:09:15 2019 +0200

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

    # Conflicts:
    #	matRadGUI_export.m
    #	tools/matRad_fixExportedGUI.m

commit 81332ae
Author: Niklas Wahl <[email protected]>
Date:   Fri Aug 9 19:00:03 2019 +0200

    new figure files and backup

commit e8da6d6
Author: Niklas Wahl <[email protected]>
Date:   Fri Aug 9 18:56:34 2019 +0200

    fix for the dicom import

commit 78fd927
Author: Niklas Wahl <[email protected]>
Date:   Fri Aug 9 18:38:16 2019 +0200

    changes to the GUI so that exported main and layout fcn are used

commit fa937ee
Author: Niklas Wahl <[email protected]>
Date:   Fri Aug 9 14:04:03 2019 +0200

    improves matRadGUI compability and fixes display of the new obejctive table

commit df2ca61
Author: Niklas Wahl <[email protected]>
Date:   Thu Aug 8 12:10:56 2019 +0200

    octave compatible dicom import

commit ecbcbc1
Author: Niklas Wahl <[email protected]>
Date:   Wed Jun 12 23:28:26 2019 +0200

    fides to the exported GUI

commit 65a91ca
Author: Niklas Wahl <[email protected]>
Date:   Tue Jun 4 12:50:54 2019 +0200

    script to remove unnecessary options for graphics options

commit 2d7b739
Author: Niklas Wahl <[email protected]>
Date:   Fri May 24 21:08:39 2019 +0200

    initial export with line fix
HomolkaN added a commit to HomolkaN/matRad that referenced this pull request Sep 6, 2023
@HomolkaN
Merge dev/dev_varRBErobOpt into varRBErobOpt/Update
f52da89 
commit 3215c95
Merge: ccc73dc 5263869
Author: Niklas Wahl <[email protected]>
Date:   Wed Sep 6 11:28:32 2023 +0200

    Merge branch 'dev' into dev_varRBErobOpt

commit ccc73dc
Merge: e915ed6 bdc7567
Author: Niklas Wahl <[email protected]>
Date:   Wed Sep 6 11:22:34 2023 +0200

    Merge pull request e0404#652 from amitantony/dev_varRBErobOpt_GUI

    class based GUI capabilities for the var RBE  plans

commit bdc7567
Author: amitantony <[email protected]>
Date:   Mon Sep 4 17:02:31 2023 +0200

    bugfix for mistaken function call in plotslicewrapper

commit 50b0805
Author: amitantony <[email protected]>
Date:   Fri Sep 1 11:42:25 2023 +0200

    Robustness functionality

commit 5263869
Author: Niklas Wahl <[email protected]>
Date:   Thu Aug 31 14:36:15 2023 +0200

    fix capital letter in MatRad_Config in CT dicom import

commit 0e76650
Author: Niklas Wahl <[email protected]>
Date:   Thu Aug 31 14:35:45 2023 +0200

    fix missing env switch in dicom import

commit 0040374
Merge: fe7fe40 51734ac
Author: Niklas Wahl <[email protected]>
Date:   Thu Aug 31 11:46:51 2023 +0200

    Merge branch 'dev_classGUI' of https://github.com/e0404/matRad into pr/652

    # Conflicts:
    #	dicom/matRad_importDicomRTPlan.m
    #	dicom/matRad_scanDicomImportFolder.m
    #	gui/widgets/matRad_OptimizationWidget.m
    #	gui/widgets/matRad_PlanWidget.m
    #	matRad.m

commit a5a8e62
Merge: 2ff9f09 51734ac
Author: Niklas Wahl <[email protected]>
Date:   Thu Aug 31 11:02:32 2023 +0200

    Merge pull request e0404#646 from e0404/dev_classGUI

    class GUI for dev

commit fe7fe40
Author: Amit Bennan <[email protected]>
Date:   Thu Aug 31 10:56:35 2023 +0200

    clean up code

commit 629f91d
Author: amitantony <[email protected]>
Date:   Tue Aug 29 16:53:38 2023 +0200

    Using Scenario based optimization for the gui

commit 51734ac
Merge: 33f3a1d 38a43ce
Author: Amit Bennan <[email protected]>
Date:   Fri Aug 4 13:04:06 2023 +0200

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

commit 33f3a1d
Author: Amit Bennan <[email protected]>
Date:   Fri Aug 4 13:03:07 2023 +0200

    Bug fix for Viewing widget and Viewer option updates on changes to pln or workflow options

commit 38a43ce
Author: Niklas Wahl <[email protected]>
Date:   Thu Aug 3 15:22:28 2023 -0700

    some more cleanup and default positioning of widgets

commit 27b01e8
Author: Niklas Wahl <[email protected]>
Date:   Thu Aug 3 14:59:34 2023 -0700

    fix for obtaining environment information

commit 68b8c3a
Author: Niklas Wahl <[email protected]>
Date:   Thu Aug 3 14:37:06 2023 -0700

    some cleanup

commit 43e086e
Author: Niklas Wahl <[email protected]>
Date:   Thu Aug 3 14:13:19 2023 -0700

    deprecate java warning

commit 37c0ff8
Author: Amit Bennan <[email protected]>
Date:   Thu Aug 3 18:57:09 2023 +0200

    1. matRad.m to original example setting, 2. MainGUI Documentation, 3. missing documentation

commit 6e03ecf
Merge: 0991137 92bc88d
Author: Amit Bennan <[email protected]>
Date:   Wed Aug 2 22:41:37 2023 +0200

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

commit 0991137
Author: Amit Bennan <[email protected]>
Date:   Wed Aug 2 22:41:03 2023 +0200

    'isOctave' checks replaced with 'matRad_Config object.isOctave'

commit 92bc88d
Author: amitantony <[email protected]>
Date:   Tue Aug 1 15:20:45 2023 +0200

    Documentation and TODO update

commit bfaf5f1
Author: amitantony <[email protected]>
Date:   Fri Jul 28 17:11:48 2023 +0200

    Comments and documentation corrections

commit aaec9ba
Merge: 41e2a65 5385ba4
Author: Niklas Wahl <[email protected]>
Date:   Tue Jul 25 16:10:29 2023 +0200

    Merge pull request e0404#653 from amitantony/dev_classGUI_feature

    Feature to autofill the couch angles

commit cf4fe0b
Author: amitantony <[email protected]>
Date:   Tue Jul 25 09:01:03 2023 +0200

    Default Values for BioParam

commit 5385ba4
Author: amitantony <[email protected]>
Date:   Tue Jul 25 08:44:39 2023 +0200

    Feature to autofill the couch angles to gantry angle size if single value of couch angle is entered

commit 78cd622
Author: amitantony <[email protected]>
Date:   Mon Jul 24 18:29:50 2023 +0200

    carbon pop up bug

commit 9c7a91d
Author: amitantony <[email protected]>
Date:   Mon Jul 24 18:26:51 2023 +0200

    pop up bug for bio model

commit 5b35787
Author: amitantony <[email protected]>
Date:   Mon Jul 24 17:53:51 2023 +0200

    Merge mistake Rectified

commit 322ca69
Merge: 522569c 41e2a65
Author: amitantony <[email protected]>
Date:   Mon Jul 24 17:37:43 2023 +0200

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

commit 522569c
Merge: f3ea5c8 e915ed6
Author: amitantony <[email protected]>
Date:   Mon Jul 24 13:19:42 2023 +0200

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

commit f3ea5c8
Merge: 87832ed ca479fe
Author: amitantony <[email protected]>
Date:   Mon Jul 24 13:18:41 2023 +0200

    Merge branch 'dev_classGUI' of https://github.com/e0404/matRad into dev_varRBErobOpt_GUI
    Runs Basic Var RBE plans in GUI

commit e915ed6
Merge: ce9179d 9cc05a8
Author: Niklas Wahl <[email protected]>
Date:   Fri Jul 21 16:59:52 2023 +0200

    Merge pull request e0404#650 from piastammer/dev_varRBErobOpt

    minor bug fix and small documentation changes

commit ce9179d
Merge: 32bff43 6ef2c24
Author: Niklas Wahl <[email protected]>
Date:   Fri Jul 21 16:57:40 2023 +0200

    Merge pull request e0404#649 from remocristoforetti/dev_varRBErobOpt_bugFix

    minor bug fix

commit 9cc05a8
Author: Pia Stammer <[email protected]>
Date:   Fri Jul 21 16:53:47 2023 +0200

    added warning and TODO for single bixel example

commit 6ef2c24
Author: remocristoforetti <[email protected]>
Date:   Fri Jul 21 16:44:19 2023 +0200

    minor change in generic photon machine
    machine.meta.name turned into machine.meta.machine

commit 41e2a65
Author: Amit Bennan <[email protected]>
Date:   Fri Jul 21 16:42:27 2023 +0200

    bugfix for error on loading first case

commit ad9f5f9
Author: remocristoforetti <[email protected]>
Date:   Fri Jul 21 16:34:06 2023 +0200

    error printout message fix in matRad_multScen

commit 32bff43
Merge: 87832ed a6f7004
Author: Niklas Wahl <[email protected]>
Date:   Fri Jul 21 15:09:43 2023 +0200

    Merge pull request e0404#624 from tobiasbecher/dev_Pareto

    Small changes to where penalties are applied

commit ca479fe
Author: Amit Bennan <[email protected]>
Date:   Fri Jul 21 14:45:33 2023 +0200

    set tissue warning

commit 42a4edc
Author: Pia Stammer <[email protected]>
Date:   Fri Jul 21 14:44:01 2023 +0200

    added TODOs to check commented lines

commit da50e91
Author: Amit Bennan <[email protected]>
Date:   Fri Jul 21 14:30:33 2023 +0200

     test if pln.propSeq exists ( bug from  example 1 with GUI)

commit 59e3e43
Author: Pia Stammer <[email protected]>
Date:   Fri Jul 21 14:22:15 2023 +0200

    removed redundant copyright statements & added Todos for documenation

commit e400ee9
Author: Pia Stammer <[email protected]>
Date:   Fri Jul 21 13:56:22 2023 +0200

    Set default BAMStoIsoDist for topas machine file

commit f497b16
Author: Amit Bennan <[email protected]>
Date:   Fri Jul 21 11:56:40 2023 +0200

    bugfix: 1. fixed reinitialization parameter changes, 2. fixed faulty overwrite of VOIPlotFlag that caused skipping contours

commit 87832ed
Merge: acd73e7 2958dc4
Author: Niklas Wahl <[email protected]>
Date:   Thu Jul 20 11:07:55 2023 +0200

    Merge pull request e0404#610 from tobiasbecher/dev_varRBErobOptPhantomBuilder

    Phantom builder added

commit 2958dc4
Merge: 03ec1a0 acd73e7
Author: Niklas Wahl <[email protected]>
Date:   Thu Jul 20 10:01:53 2023 +0200

    Merge branch 'dev_varRBErobOpt' into pr/610

    # Conflicts:
    #	.gitignore

commit 03ec1a0
Author: Niklas Wahl <[email protected]>
Date:   Thu Jul 20 10:00:26 2023 +0200

    reorganization of builder files

commit acd73e7
Merge: c9acdc5 a83b691
Author: Niklas Wahl <[email protected]>
Date:   Wed Jul 19 17:15:39 2023 +0200

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

commit c9acdc5
Author: Niklas Wahl <[email protected]>
Date:   Wed Jul 19 17:15:33 2023 +0200

    Update of base data file for estimate of energy spectrum

commit 2f00898
Author: Tobias Becher <[email protected]>
Date:   Mon Jul 10 12:47:38 2023 +0200

    Final updates

    Final changes to the phantom builder

commit a83b691
Merge: d5bf94a f2e62b6
Author: Niklas Wahl <[email protected]>
Date:   Mon Jul 10 10:13:15 2023 +0200

    Merge pull request e0404#642 from JenHardt/dev_varRBErobOpt

    IsoCenterShift BugFix

commit f2e62b6
Author: JenHardt <[email protected]>
Date:   Fri Jul 7 13:56:16 2023 +0200

    IsoCenterShift BugFix

commit bca2260
Author: Tobias Becher <[email protected]>
Date:   Fri Jun 30 14:41:50 2023 +0200

    Update matRad_runTests.m

commit d474f09
Author: Tobias Becher <[email protected]>
Date:   Fri Jun 30 14:33:25 2023 +0200

    Removed indexing of VOI

    VOI are no longer assigned an index on initialization.
    -> No need to clear all at the start of  a script if rerunning

commit c12f5e8
Author: Tobias Becher <[email protected]>
Date:   Fri Jun 30 14:10:55 2023 +0200

    Fixed geometry issues

    Fixed issues with the coordinate system

commit a6f7004
Author: Tobias Becher <[email protected]>
Date:   Fri Jun 30 10:24:52 2023 +0200

    Slack parameter changes

    - Changed epsilon variable name to slackParameter
    - Now parameter of constraint
    - Removed objective funtion to turn into constraint

commit c91799c
Merge: 94e701c 4177468
Author: amitantony <[email protected]>
Date:   Fri Jun 30 10:03:04 2023 +0200

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

commit dedf147
Author: Tobias Becher <[email protected]>
Date:   Wed Jun 28 13:37:18 2023 +0200

    Some changes

    Some changes made for pull request. Commit also tests if server tests now run through.

commit d5bf94a
Author: Niklas Wahl <[email protected]>
Date:   Wed Jun 28 10:18:28 2023 +0200

    allows to compute the bixel dose when cutoff was not precomputed by setting the compensation factor to 1

commit 83fc8a6
Author: Niklas Wahl <[email protected]>
Date:   Wed Jun 28 10:17:45 2023 +0200

    emittance base data format now allows one emittance per focus

commit 5fda67e
Merge: 99eaa34 bffb834
Author: Niklas Wahl <[email protected]>
Date:   Wed Jun 21 10:56:08 2023 +0200

    Merge pull request e0404#637 from remocristoforetti/dev_varRBErobOpt_bugFix_MCemittanceBaseData

    bugFix in MCemittanceBaseData for negative distances

commit bffb834
Author: RemoCristoforetti <[email protected]>
Date:   Wed Jun 21 10:49:28 2023 +0200

    bugFix negative distance for spot size correction in air.

commit 99eaa34
Author: Niklas Wahl <[email protected]>
Date:   Wed Jun 21 10:10:19 2023 +0200

    Fix matRad_MCemittanceBaseData.m

    Replaced Inf with realmax so interpolation does not error

commit 3e7952a
Author: Niklas Wahl <[email protected]>
Date:   Wed Jun 7 13:19:31 2023 +0200

    AppendResultGUI now creates consistent fieldnames

commit c5dd9eb
Author: Niklas Wahl <[email protected]>
Date:   Tue Jun 6 18:32:40 2023 +0200

    appendresultgui now either overwrites or always appends the identifier

commit 1bab14d
Author: Niklas Wahl <[email protected]>
Date:   Tue Jun 6 18:32:21 2023 +0200

    fix for the spot size air MCS correction

commit 6a746ee
Author: Niklas Wahl <[email protected]>
Date:   Tue Jun 6 14:13:20 2023 +0200

    fix variable names in example 12

commit a7e72fa
Author: Niklas Wahl <[email protected]>
Date:   Tue Jun 6 14:13:01 2023 +0200

    add empirical correction for MCS in air when approximating beam model

commit 1a80ea9
Author: Tobias Becher <[email protected]>
Date:   Mon Jun 5 11:01:52 2023 +0200

    Name change for constraints

    Changed the name for created constraints in the optimization

commit 94e701c
Author: amitantony <[email protected]>
Date:   Fri Jun 2 15:25:13 2023 +0200

    1. avoid sequencing warning everytime we optimize particles,  2. IGNORED as a tissue type, 3. fix for "ignoring legend entries" warning , 4. DVHStat naming bugfix

commit 4177468
Merge: 2273867 893f9b3
Author: Niklas Wahl <[email protected]>
Date:   Thu Jun 1 14:02:31 2023 +0200

    Merge pull request e0404#631 from amitantony/bug/DVHWidgetFix

    Bug/dvh widget fix

commit f59722c
Merge: 893f9b3 2273867
Author: amitantony <[email protected]>
Date:   Thu Jun 1 12:38:18 2023 +0200

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

commit 893f9b3
Author: amitantony <[email protected]>
Date:   Wed May 31 15:58:13 2023 +0200

    Consistant naming fix

commit ae58086
Author: amitantony <[email protected]>
Date:   Wed May 31 15:45:17 2023 +0200

    more compact application of recenter

commit 2273867
Merge: 37c2f02 602bae6
Author: Amit Bennan <[email protected]>
Date:   Wed May 31 15:36:47 2023 +0200

    Merge pull request e0404#626 from amitantony/dev_classGUI_matPatientLoadBug

    Dev class GUI .mat patient load bug

commit 8c2d20e
Author: amitantony <[email protected]>
Date:   Wed May 31 15:34:18 2023 +0200

    feature: Recentering to iso center button

commit 602bae6
Author: amitantony <[email protected]>
Date:   Tue May 30 18:01:48 2023 +0200

    fix for test failing in matRad.m

commit 48ca910
Author: Niklas Wahl <[email protected]>
Date:   Tue May 30 16:35:22 2023 +0200

    revert explicit start of parpool in testing pipeline

commit 871e0b6
Merge: 153ba54 a531a2d
Author: Niklas Wahl <[email protected]>
Date:   Tue May 30 16:27:48 2023 +0200

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

commit 153ba54
Author: Niklas Wahl <[email protected]>
Date:   Tue May 30 16:25:33 2023 +0200

    explicit start of parallel pool in testing workflow

commit 7561424
Merge: ec8fd78 37c2f02
Author: amitantony <[email protected]>
Date:   Tue May 30 15:07:11 2023 +0200

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

commit a531a2d
Author: Niklas Wahl <[email protected]>
Date:   Tue May 30 13:51:31 2023 +0200

    Fix wrong test folder in tests.yml

commit d2da6e4
Merge: 8f03510 d6ea09a
Author: Niklas Wahl <[email protected]>
Date:   Tue May 30 13:42:19 2023 +0200

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

    # Conflicts:
    #	.github/workflows/tests.yml
    #	MatRad_Config.m
    #	matRad_fluenceOptimization.m
    #	matRad_rc.m
    #	ompMC/matRad_compileOmpMCInterface.m
    #	optimization/optimizer/compile_ipopt_minGW_octave640.sh

commit d6ea09a
Merge: 689eabe beaee4e
Author: Niklas Wahl <[email protected]>
Date:   Tue May 30 13:27:32 2023 +0200

    Merge pull request e0404#628 from e0404/hotfix/fixTestEnvironment

    Hotfix to the test pipeline on the master branch

commit beaee4e
Merge: 2f42625 689eabe
Author: Niklas Wahl <[email protected]>
Date:   Fri May 26 19:14:53 2023 +0200

    Merge branch 'master' into hotfix/fixTestEnvironment

commit 37c2f02
Merge: 5984075 72d5d3c
Author: Niklas Wahl <[email protected]>
Date:   Fri May 26 18:58:18 2023 +0200

    Merge pull request e0404#625 from amitantony/dev_classGUI_a_DicomImportBug

    Dev class GUI a dicom import bug

commit 72d5d3c
Merge: ef55778 5984075
Author: Niklas Wahl <[email protected]>
Date:   Fri May 26 18:57:28 2023 +0200

    Merge branch 'dev_classGUI' into dev_classGUI_a_DicomImportBug

commit 5984075
Merge: 671baea 1f7bc74
Author: Niklas Wahl <[email protected]>
Date:   Fri May 26 18:55:48 2023 +0200

    Merge pull request e0404#627 from amitantony/dev_classGUI_IsoDoseBugFix

    BUGFIX: Iso dose contour not updated with changing selectedDisplayOption

commit 2f42625
Author: Niklas Wahl <[email protected]>
Date:   Fri May 26 18:44:48 2023 +0200

    Update job name for octave

commit 0fe09aa
Author: Niklas Wahl <[email protected]>
Date:   Fri May 26 18:35:04 2023 +0200

    Update job name

commit 2397e3f
Author: Niklas Wahl <[email protected]>
Date:   Fri May 26 18:23:04 2023 +0200

    Add latest supported release options for tests to cover for release changes

commit ef55778
Author: amitantony <[email protected]>
Date:   Fri May 26 16:15:48 2023 +0200

    Class GUI dicom import bugs resolve to return atleast 1 DICOM patient case

commit fa26d01
Author: Tobias Becher <[email protected]>
Date:   Fri May 26 16:15:06 2023 +0200

    Small changes to where penalties are applied

    Moved the penalties from the objectives to the objective function. Also added an option for objective constraint.

commit ec8fd78
Author: Amit Bennan <[email protected]>
Date:   Fri May 26 14:30:12 2023 +0200

    bug fix on first load of patient case

commit 689eabe
Merge: f7bded9 46d5f2c
Author: Amit Bennan <[email protected]>
Date:   Fri May 26 11:35:38 2023 +0200

    Merge pull request e0404#608 from e0404/bug/606-matrad_plotvoicontourslice-tries-to-access-ct-as-cell-bug

    fix passes ct struct instead of ct.cubeHU to matRad_plotVoiContourSlice

commit 2bca404
Author: Tobias Becher <[email protected]>
Date:   Fri May 26 11:27:42 2023 +0200

    Compatibility with test script

    Added phantomBuilder example to test script and rounding added in BOX phantom assignment

commit 1f7bc74
Author: amitantony <[email protected]>
Date:   Fri May 26 11:09:50 2023 +0200

    Bugfix for : Iso dose contour not updated with changing selectedDisplayOption

commit 8f03510
Merge: 58362ac 82742b0
Author: Niklas Wahl <[email protected]>
Date:   Tue May 23 18:25:09 2023 +0200

    Merge pull request e0404#621 from tobiasbecher/dev_varRBErobOptGradient

    Bugfix for RBExD gradient calculation.

commit 82742b0
Author: Tobias Becher <[email protected]>
Date:   Tue May 16 10:27:55 2023 +0200

    Update .gitignore

commit 19799c8
Author: Tobias Becher <[email protected]>
Date:   Tue May 16 10:24:27 2023 +0200

    Fixed gradient Bug

commit 58362ac
Author: Niklas Wahl <[email protected]>
Date:   Wed May 10 12:08:26 2023 +0200

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

commit 380b740
Author: Tobias Becher <[email protected]>
Date:   Fri Apr 28 16:19:12 2023 +0200

    Update matRad_runTests.m

    Removing new example1 for now from unit tests

commit 497e036
Author: Tobias Becher <[email protected]>
Date:   Fri Apr 28 15:56:33 2023 +0200

    Final changes

    Renamed matRad_VOIVolume to matRad_PhantomVOIVolume and changed example files.

commit 46d5f2c
Merge: 539dc94 f7bded9
Author: Niklas Wahl <[email protected]>
Date:   Fri Apr 28 15:35:17 2023 +0200

    Merge branch 'master' into bug/606-matrad_plotvoicontourslice-tries-to-access-ct-as-cell-bug

commit f7bded9
Merge: 03cc52f 7456efc
Author: Niklas Wahl <[email protected]>
Date:   Fri Apr 28 15:34:40 2023 +0200

    Merge pull request e0404#607 from e0404/bug/605-bug-warning-and-error-messages-in-matrad_readnrrd-fail-string-concatenation-is-wrong-when-linecontent-is-an-empty-cell

    Error message rectified

commit 539dc94
Merge: 711dc58 03cc52f
Author: Amit Bennan <[email protected]>
Date:   Fri Apr 28 15:23:39 2023 +0200

    Merge branch 'master' into bug/606-matrad_plotvoicontourslice-tries-to-access-ct-as-cell-bug

commit 7456efc
Merge: 8fb0fb8 03cc52f
Author: Niklas Wahl <[email protected]>
Date:   Fri Apr 28 15:01:26 2023 +0200

    Merge branch 'master' into bug/605-bug-warning-and-error-messages-in-matrad_readnrrd-fail-string-concatenation-is-wrong-when-linecontent-is-an-empty-cell

commit 03cc52f
Merge: b2ce690 bb41c69
Author: Niklas Wahl <[email protected]>
Date:   Fri Apr 28 14:59:51 2023 +0200

    Merge pull request e0404#617 from SakuMyl/master

    Check installation of image processing toolbox in DICOM import

commit bb41c69
Author: Saku Myllymäki <[email protected]>
Date:   Fri Apr 28 14:23:24 2023 +0300

    check installation of image processing toolbox

commit 8fb0fb8
Author: Amit Bennan <[email protected]>
Date:   Thu Apr 20 15:21:47 2023 +0200

    displays parsed line in warning message

commit 711dc58
Merge: bcbc8b7 b2ce690
Author: Amit Bennan <[email protected]>
Date:   Tue Apr 11 11:41:53 2023 +0200

    Merge branch 'master' into bug/606-matrad_plotvoicontourslice-tries-to-access-ct-as-cell-bug

commit 85f7cda
Author: Niklas Wahl <[email protected]>
Date:   Thu Apr 6 17:06:51 2023 +0200

    fix problem with constant property containing filepath

commit d6238cd
Author: Niklas Wahl <[email protected]>
Date:   Wed Apr 5 14:59:25 2023 +0200

    Update tests.yml

    Update apt before octave install

commit eab8fc2
Merge: 375987a b2ce690
Author: Niklas Wahl <[email protected]>
Date:   Wed Apr 5 14:46:18 2023 +0200

    Merge branch 'master' into bug/605-bug-warning-and-error-messages-in-matrad_readnrrd-fail-string-concatenation-is-wrong-when-linecontent-is-an-empty-cell

commit b10d896
Author: Tobias Becher <[email protected]>
Date:   Tue Apr 4 11:46:17 2023 +0200

    Changed number of example file

commit 48786f3
Author: Tobias Becher <[email protected]>
Date:   Tue Apr 4 11:35:05 2023 +0200

    Updates to the phantom

    - Moved ct creation to phantom
      builder
    - ct and cst are now private and can be
      received by calling getctst
    - Added documentaion to phantom
      builder functions
    - Modified example file to incorporate
      changes

commit cf1e27b
Author: Tobias Becher <[email protected]>
Date:   Tue Apr 4 11:32:06 2023 +0200

    Updates to VOI related classes

    Renamed Cubic and Spherical VOI classes
    Added option to set HU for VOI

commit ba69a3b
Merge: 4d394f6 b85ec2c
Author: Niklas Wahl <[email protected]>
Date:   Mon Apr 3 11:45:22 2023 +0200

    Merge branch 'dev_varRBErobOpt' into dev_varRBErobOptPhantomBuilder

commit 4d394f6
Author: Tobias Becher <[email protected]>
Date:   Mon Apr 3 10:49:36 2023 +0200

    Delete matRad_createPhantomnew.m

commit 51deb77
Author: Tobias Becher <[email protected]>
Date:   Mon Apr 3 10:47:03 2023 +0200

    Added phantom builder

    Added folder for phantom builder and an example

commit ab666aa
Author: Tobias Becher <[email protected]>
Date:   Mon Apr 3 10:30:24 2023 +0200

    Update .gitignore

commit 0a03aee
Author: Niklas Wahl <[email protected]>
Date:   Mon Feb 6 02:17:51 2023 +0100

    fix path

    (cherry picked from commit ec57365)

commit fe61134
Author: Niklas Wahl <[email protected]>
Date:   Mon Feb 6 02:11:54 2023 +0100

    use preinstallex xvfb in linux test

    (cherry picked from commit cee9df6)

commit 5a8c7f9
Author: Niklas Wahl <[email protected]>
Date:   Sat Feb 4 15:48:06 2023 +0100

    Revert "adjust xvfb call in testing"

    This reverts commit 075402c.

    (cherry picked from commit 78c7b3d)

commit 99336e0
Author: Niklas Wahl <[email protected]>
Date:   Sat Feb 4 15:43:05 2023 +0100

    adjust xvfb call in testing

    (cherry picked from commit 075402c)

commit d4acb02
Author: Niklas Wahl <[email protected]>
Date:   Sat Feb 4 15:10:49 2023 +0100

    update scripts for github folder

    (cherry picked from commit ec4e8b2)

commit 4b9a2fa
Author: Niklas Wahl <[email protected]>
Date:   Sat Feb 4 15:06:49 2023 +0100

    move scripts used during testing to github folder

    (cherry picked from commit 735976d)

commit c3a673f
Author: Niklas Wahl <[email protected]>
Date:   Fri Feb 3 18:47:36 2023 +0100

    update workflow actions

    (cherry picked from commit bf5f4b9)

commit 7060a3a
Author: Niklas Wahl <[email protected]>
Date:   Fri Feb 3 16:27:44 2023 +0100

    include rehash of file directory after linking the optimizer and added availability check

    (cherry picked from commit c509e82)

commit ef95ac3
Author: Niklas Wahl <[email protected]>
Date:   Fri Feb 3 01:15:32 2023 +0100

    option to disable function plot in optimization

    (cherry picked from commit 46445b2)

commit 2c9b118
Author: Niklas Wahl <[email protected]>
Date:   Fri Feb 3 01:15:14 2023 +0100

    update compiled linux optimizer

    (cherry picked from commit ffced04)

commit 8e17c34
Author: Niklas Wahl <[email protected]>
Date:   Wed Feb 1 16:28:33 2023 +0100

    update compiled optimizers with static linking

    (cherry picked from commit 73d6097)

commit f0b7199
Author: Niklas Wahl <[email protected]>
Date:   Wed Feb 1 16:09:03 2023 +0100

    updated optimizer compilation scripts

    (cherry picked from commit 5eff06f)

commit c274d6d
Author: Niklas Wahl <[email protected]>
Date:   Wed Feb 1 14:39:05 2023 +0100

    Recompiled Octave 6.4.0 mex files for windows and linux, updated scripts and submodules

    (cherry picked from commit b353948)

commit 4f436df
Author: Niklas Wahl <[email protected]>
Date:   Mon Jan 30 18:00:41 2023 +0100

    ompMC interface and MCsquare interface - fix eval function for obtaining preconfigured compiler flags

    (cherry picked from commit 7d788f7)

commit add110e
Author: Niklas Wahl <[email protected]>
Date:   Sun Jan 29 20:07:06 2023 +0100

    Update tests.yml

    Switch to Ubuntu 22.04 and thus Octave 6 in test workflow

    (cherry picked from commit bdb95e9)

commit b2ce690
Merge: cb6b04a 091f78b
Author: Niklas Wahl <[email protected]>
Date:   Thu Mar 23 13:07:04 2023 +0100

    Merge pull request e0404#602 from e0404/bug/601-bug-using-minmaxmeandose-constraint-on-structure-with-only-1-voxel-failes

    Fix error when constraints are applied to volumes which have 0 or 1 voxel.

commit bcbc8b7
Author: Amit Bennan <[email protected]>
Date:   Thu Mar 23 12:00:26 2023 +0100

    fix passes ct struct instead of ct.cubeHU to matRad_plotVoiContourSlice

commit 375987a
Author: Amit Bennan <[email protected]>
Date:   Thu Mar 23 11:33:56 2023 +0100

    Error message rectified and all error and warning messages use matRad config messages

commit c0c8353
Author: Niklas Wahl <[email protected]>
Date:   Tue Mar 7 01:50:55 2023 +0100

    remove phsp-header

commit 091f78b
Author: Niklas Wahl <[email protected]>
Date:   Mon Feb 27 12:13:17 2023 +0100

    fixes wrong detection of constraint bounds and jacobian structure when respective volume has 0 or only 1 voxel.

commit 2ff9f09
Merge: 27ad9ff aab03e9
Author: Niklas Wahl <[email protected]>
Date:   Fri Feb 24 15:16:09 2023 +0100

    Merge pull request e0404#599 from JenHardt/dev

    BUG: ssd calculation should use actual ray distance instead of SAD

commit aab03e9
Merge: 9f4af93 27ad9ff
Author: Hardt <[email protected]>
Date:   Tue Feb 7 15:47:12 2023 +0100

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

commit 9f4af93
Author: Hardt <[email protected]>
Date:   Tue Feb 7 15:46:27 2023 +0100

    small Bugfix

commit 5084863
Author: Amit Bennan <[email protected]>
Date:   Fri Jan 27 10:32:23 2023 +0100

    Code style comments addressed  (MB review)

commit b85ec2c
Author: Niklas Wahl <[email protected]>
Date:   Wed Jan 25 23:04:36 2023 +0100

    Downwards compatibility of biological model

commit 5663803
Author: Niklas Wahl <[email protected]>
Date:   Wed Jan 25 18:11:35 2023 +0100

    fix missing extractBetween function in Octave

commit 64ce14c
Merge: d3625aa 4e87571
Author: Niklas Wahl <[email protected]>
Date:   Tue Jan 24 15:55:11 2023 +0100

    Merge pull request e0404#536 from HomolkaN/dev_varRBErobOpt_Update

    Extensive TOPAS workflow update:

commit 260bd66
Merge: a1c8743 ecc6e0c
Author: Amit Bennan <[email protected]>
Date:   Fri Jan 20 14:03:37 2023 +0100

    Merge branch 'dev_classGUI_a' of https://github.com/amitantony/matRad into dev_classGUI

commit d3625aa
Author: Niklas Wahl <[email protected]>
Date:   Thu Jan 19 13:41:47 2023 +0100

    Remove opengl software rendering query due to deprecation

commit 3e427cf
Author: Niklas Wahl <[email protected]>
Date:   Thu Jan 19 01:44:05 2023 +0100

    Avoid erroring on opengl in matRadGUI

commit ecc6e0c
Merge: 8c9f8ee 671baea
Author: Amit Bennan <[email protected]>
Date:   Wed Jan 4 13:03:51 2023 +0100

    Merge branch 'dev_classGUI' into dev_classGUI_a

commit 894211d
Author: Niklas Wahl <[email protected]>
Date:   Wed Dec 21 18:34:02 2022 +0100

    improve dicom import handling for RTPlan and RTDose

commit 671baea
Merge: 91cbc12 27ad9ff
Author: Amit Bennan <[email protected]>
Date:   Tue Dec 20 13:31:01 2022 +0100

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

commit 27ad9ff
Merge: 3b781b6 cb6b04a
Author: Niklas Wahl <[email protected]>
Date:   Tue Nov 29 20:29:38 2022 +0100

    Merge branch 'master' into dev

commit 8c9f8ee
Author: amitantony <[email protected]>
Date:   Thu Nov 10 14:51:40 2022 +0100

    documentation

commit c711bdc
Author: amitantony <[email protected]>
Date:   Fri Nov 4 19:19:26 2022 +0100

    first working prototype

commit 3fe5660
Author: amitantony <[email protected]>
Date:   Thu Oct 27 11:39:54 2022 +0200

    Gamma Widget skeleton

commit a1c8743
Author: Amit Bennan <[email protected]>
Date:   Thu Oct 27 11:38:59 2022 +0200

    DVHStatswidget object stored in main gui

commit 2d41f12
Author: Amit Bennan <[email protected]>
Date:   Mon Oct 24 13:36:12 2022 +0200

    1. Documentation for newer widget functions
    2. clean up of code
    3. fully update DVH solution

commit 3b781b6
Author: Niklas Wahl <[email protected]>
Date:   Thu Oct 20 00:01:08 2022 +0200

    Update matRad_calcCubes.m

    Correct MU vector calculation

commit 6db771e
Merge: fea82a8 1b13404
Author: Niklas Wahl <[email protected]>
Date:   Wed Oct 5 17:04:51 2022 +0200

    Merge branch 'master' into dev

commit b80323c
Merge: e4ad063 d8c58e0
Author: Amit Bennan <[email protected]>
Date:   Fri Jul 29 16:06:11 2022 +0200

    Merge branch 'dev_classGUI_a' of https://github.com/amitantony/matRad into dev_classGUI_a

commit e4ad063
Merge: a216bd1 c0a9f08
Author: Amit Bennan <[email protected]>
Date:   Fri Jul 29 16:05:59 2022 +0200

    Merge branch 'dev_clean' into dev_classGUI_a : runs basic examples

commit d8c58e0
Author: amitantony <[email protected]>
Date:   Fri Jul 29 14:26:47 2022 +0200

    [bugfix] errors while running the basic matrad script

commit a216bd1
Author: Amit Bennan <[email protected]>
Date:   Fri Jul 29 10:17:00 2022 +0200

    [bug fix] DVH updates with the selected cube for display

commit 657ef2b
Merge: 13d35e0 d17ecb2
Author: amitLT <[email protected]>
Date:   Thu Jun 9 14:09:42 2022 +0200

    Merge branch 'dev_classGUI_a' of https://github.com/amitantony/matRad into dev_classGUI_a

commit d17ecb2
Author: amitantony <[email protected]>
Date:   Fri Apr 29 17:40:54 2022 +0200

    Input Parser for DVH and statistics widget

commit eae4a47
Author: amitantony <[email protected]>
Date:   Wed Apr 27 11:59:30 2022 +0200

    bug fix :  iso line update problem for "Saved Results" of ResultGUI in viewing widget

commit 13d35e0
Author: amitLT <[email protected]>
Date:   Fri Apr 22 17:07:26 2022 +0200

    encoding to UTF8

commit baa9182
Author: amitLT <[email protected]>
Date:   Thu Apr 21 13:02:15 2022 +0200

    bug fix : enabling and disabling sequencing options

commit 7204af4
Author: amitLT <[email protected]>
Date:   Mon Apr 4 18:05:02 2022 +0200

    Added sequencing drop down menu  to the GUI

commit 16beca5
Author: amitLT <[email protected]>
Date:   Tue Mar 29 14:23:18 2022 +0200

    update of new referencing to sequencing in matRad and example scripts

commit 5f4da57
Author: amitLT <[email protected]>
Date:   Tue Mar 29 14:06:10 2022 +0200

    Sequencing wrapper function that accepts highlevel matRad structures

commit cb5a94c
Author: amitLT <[email protected]>
Date:   Thu Mar 24 09:43:13 2022 +0100

    Fixes for couch angle update, (cst,ct ) loaded message, CBTplanning

commit 91cbc12
Author: Niklas Wahl <[email protected]>
Date:   Fri Dec 10 16:15:17 2021 +0100

    some fixes in the class-based GUI

commit b3cd841
Merge: 5137fcc f725b01
Author: Niklas Wahl <[email protected]>
Date:   Mon Feb 8 15:01:31 2021 +0100

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

commit f725b01
Merge: 6b50cf5 51f8428
Author: Niklas Wahl <[email protected]>
Date:   Mon Feb 8 14:34:26 2021 +0100

    Merge pull request e0404#486 from palkma/dev_classGUI

    added tooltips to GUI elements

commit 51f8428
Author: Palkowitsch <[email protected]>
Date:   Tue Feb 2 16:19:11 2021 +0100

    added tooltips

commit 5137fcc
Merge: 1996919 d930c3e
Author: Niklas Wahl <[email protected]>
Date:   Thu Dec 24 13:39:51 2020 +0100

    Merge remote-tracking branch 'origin/master' into dev_classGUI

    # Conflicts:
    #	MatRad_Config.m
    #	dicom/@matRad_DicomExporter/matRad_DicomExporter.m
    #	dicom/matRad_scanDicomImportFolder.m
    #	matRadGUI.m
    #	matRad_showDVH.m
    #	plotting/matRad_plotIsoDoseLines.m

commit 1996919
Merge: 6b50cf5 4399711
Author: Niklas Wahl <[email protected]>
Date:   Mon Oct 5 11:17:34 2020 +0200

    Merge branch 'dev_classGUI' of https://github.com/nellyabbani/matRad into dev_classGUI

commit 4399711
Author: nelly.abbani <[email protected]>
Date:   Fri Aug 28 10:40:18 2020 +0200

    uiwrapper function

commit 6b50cf5
Author: Niklas Wahl <[email protected]>
Date:   Fri Aug 21 17:02:38 2020 +0200

    fix tests

commit 434422d
Merge: b4c7783 1463811
Author: Niklas Wahl <[email protected]>
Date:   Fri Aug 21 16:26:46 2020 +0200

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

commit b4c7783
Author: Niklas Wahl <[email protected]>
Date:   Fri Aug 21 16:26:10 2020 +0200

    changes to gui calls

commit 38c7131
Author: Niklas Wahl <[email protected]>
Date:   Fri Aug 21 15:46:46 2020 +0200

    more old files removal

commit b5d48cf
Author: Niklas Wahl <[email protected]>
Date:   Fri Aug 21 15:44:51 2020 +0200

    removal of old logo files

commit 736b2f2
Author: Niklas Wahl <[email protected]>
Date:   Fri Aug 21 15:43:39 2020 +0200

    gui fixes and removal of old files

commit a3ba0c2
Author: Niklas Wahl <[email protected]>
Date:   Thu Aug 20 18:38:18 2020 +0200

    More consistency and compatability updates

commit dfd8e9a
Author: Niklas Wahl <[email protected]>
Date:   Wed Aug 19 18:43:47 2020 +0200

    modifications to Widget structure and layout, consistent colors, etc

commit adac165
Author: Niklas Wahl <[email protected]>
Date:   Wed Aug 19 10:26:50 2020 +0200

    tweaks to the gui widgets, new EventData-based class to explicitly state changed workspace variables

commit 6e19dfa
Author: Niklas Wahl <[email protected]>
Date:   Wed Aug 19 10:25:09 2020 +0200

    crop logo a little

commit 15e4cd8
Author: Niklas Wahl <[email protected]>
Date:   Wed Aug 19 10:24:37 2020 +0200

    remove some old gui functions

commit 9bf703f
Author: Niklas Wahl <[email protected]>
Date:   Fri Aug 7 12:12:58 2020 +0200

    Move matRadGUI to main folder again

commit f271346
Author: Niklas Wahl <[email protected]>
Date:   Fri Aug 7 12:12:21 2020 +0200

    fix createLayout for dicom import

commit 52e8fe2
Author: Niklas Wahl <[email protected]>
Date:   Thu Jul 30 14:21:50 2020 +0200

    Fix paths and maximize matRadGUI

commit d0885c4
Merge: 36a149d ca4044b
Author: Niklas Wahl <[email protected]>
Date:   Thu Jul 30 11:59:33 2020 +0200

    Merge branch 'dev_classGUI' of https://github.com/nellyabbani/matRad into dev_classGUI

    # Conflicts:
    #	gui/matRadGUI.m

commit ca4044b
Author: nellyabbani <[email protected]>
Date:   Wed Jul 29 20:33:14 2020 +0200

    Split DVH widget into 2 widgets.
    Add exportDicom widget.
    +other small fixes

commit 36a149d
Author: Niklas Wahl <[email protected]>
Date:   Wed Jul 29 17:44:10 2020 +0200

    changes to avoid crash in Octave

commit 5694ffd
Author: nellyabbani <[email protected]>
Date:   Tue Jun 30 10:31:45 2020 +0200

    Further improvements to the GUI widgets

commit 4f69fa4
Author: nellyabbani <[email protected]>
Date:   Mon Jun 15 13:11:40 2020 +0200

    Small fixes on the GUI widgets

commit fe2abdc
Author: nellyabbani <[email protected]>
Date:   Fri Jun 12 17:15:08 2020 +0200

    Merge dev_classGUI with master class

commit a89edfe
Merge: 5620dbe c22da7d
Author: nellyabbani <[email protected]>
Date:   Fri Jun 12 15:59:35 2020 +0200

    Merge branch 'master' into dev_classGUI

    # Conflicts:
    #	dicom/@matRad_importDicomWidget/createLayout.m
    #	dicom/@matRad_importDicomWidget/matRad_importDicomWidget.m
    #	dicom/DKFZ_Logo.png
    #	dicom/gui/matRad_importDicomGUI_LayoutFcn.m
    #	dicom/gui/matRad_importDicomGUI_gui_mainFcn.m
    #	dicom/matRad_checkEnvDicomRequirements.m
    #	dicom/matRad_createCst.m
    #	dicom/matRad_importDicomGUI.fig.bak
    #	dicom/matrad_logo.png
    #	dicomImport/DKFZ_Logo.png
    #	dicomImport/matrad_logo.png
    #	gfx/DKFZ_Logo.png
    #	gfx/matrad_logo.png
    #	matRadGUI.m
    #	matRad_fluenceOptimization.m
    #	matRad_showQualityIndicators.m

commit 5620dbe
Author: nellyabbani <[email protected]>
Date:   Fri Jun 12 13:54:32 2020 +0200

    Update to refresh the GUI widgets when clicked + implementation of notify and listeners concepts in octave

commit 71e397e
Author: nellyabbani <[email protected]>
Date:   Mon Jun 8 09:27:35 2020 +0200

    Functioning version of all the GUI widgets

commit 4abd14e
Author: nellyabbani <[email protected]>
Date:   Fri May 1 13:06:35 2020 +0200

    Scripted GUI widgets

commit 3501e99
Author: nellyabbani <[email protected]>
Date:   Thu Apr 2 18:03:56 2020 +0200

    Scripted GUI workflow, plan, and optimization widgets

commit 986dbb6
Merge: 4045a4b 833e582
Author: nellyabbani <[email protected]>
Date:   Tue Mar 3 16:18:17 2020 +0100

    Merge remote-tracking branch 'origin/dev_classGUI' into dev_classGUI

    # Conflicts:
    #	gui/matRad_PlanWidget.m
    #	gui/matRad_WorkflowWidget.m

commit 4045a4b
Author: nellyabbani <[email protected]>
Date:   Tue Mar 3 16:13:38 2020 +0100

    Initial fix to the widgets

commit 833e582
Author: Nabe Al Hasnawi <[email protected]>
Date:   Fri Feb 28 13:43:55 2020 +0100

    Widget Default Values and Names

commit 0db80e1
Author: Nabe Al Hasnawi <[email protected]>
Date:   Tue Feb 25 12:07:10 2020 +0100

    matRad gui icons as mat file

commit 922c349
Author: Nabe Al Hasnawi <[email protected]>
Date:   Tue Feb 25 12:04:09 2020 +0100

    First developments on independent GUI widgets

commit b926ed9
Author: Nabe <[email protected]>
Date:   Tue Dec 10 11:27:12 2019 +0100

    Class based Widgets for import & export with shared import/export GUI

commit f55a46a
Merge: 6df1b0f d66cf32
Author: Niklas Wahl <[email protected]>
Date:   Fri Aug 16 16:13:11 2019 +0200

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

commit 6df1b0f
Author: Niklas Wahl <[email protected]>
Date:   Fri Aug 16 16:12:22 2019 +0200

    Exported the IO gui's and added the dicom external GUI files

commit b07c70c
Author: Niklas Wahl <[email protected]>
Date:   Tue Aug 13 12:42:03 2019 +0200

    fix for missing mat File containing GUI parmeters (is exported from guide).

commit 1ae350a
Merge: 7ee4580 81e4545
Author: Niklas Wahl <[email protected]>
Date:   Fri Aug 9 20:13:02 2019 +0200

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

commit 7ee4580
Merge: ecbcbc1 81332ae
Author: Niklas Wahl <[email protected]>
Date:   Fri Aug 9 20:09:15 2019 +0200

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

    # Conflicts:
    #	matRadGUI_export.m
    #	tools/matRad_fixExportedGUI.m

commit 81332ae
Author: Niklas Wahl <[email protected]>
Date:   Fri Aug 9 19:00:03 2019 +0200

    new figure files and backup

commit e8da6d6
Author: Niklas Wahl <[email protected]>
Date:   Fri Aug 9 18:56:34 2019 +0200

    fix for the dicom import

commit 78fd927
Author: Niklas Wahl <[email protected]>
Date:   Fri Aug 9 18:38:16 2019 +0200

    changes to the GUI so that exported main and layout fcn are used

commit fa937ee
Author: Niklas Wahl <[email protected]>
Date:   Fri Aug 9 14:04:03 2019 +0200

    improves matRadGUI compability and fixes display of the new obejctive table

commit df2ca61
Author: Niklas Wahl <[email protected]>
Date:   Thu Aug 8 12:10:56 2019 +0200

    octave compatible dicom import

commit ecbcbc1
Author: Niklas Wahl <[email protected]>
Date:   Wed Jun 12 23:28:26 2019 +0200

    fides to the exported GUI

commit 65a91ca
Author: Niklas Wahl <[email protected]>
Date:   Tue Jun 4 12:50:54 2019 +0200

    script to remove unnecessary options for graphics options

commit 2d7b739
Author: Niklas Wahl <[email protected]>
Date:   Fri May 24 21:08:39 2019 +0200

    initial export with line fix
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3 participants
@HomolkaN @wahln @JenHardt