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Adapt dose engine concept to dev_varRBErobOpt #684

Merged
merged 226 commits into from
May 10, 2024
Merged

Adapt dose engine concept to dev_varRBErobOpt #684

merged 226 commits into from
May 10, 2024

Commits on Jun 10, 2021

  1. First commit, init dose calc engines (+ branch goal explanation) 

    First (real) commit into the refactorDoseCalc branch. Includes all up till now created dose calc engines for the refactoring of the dose calculation in MatRad.

The goal of this refactoring is, to leave the full script-file based dose calculation (which is used right now) and use a modular class based  dose calculation. This should provide a modifiable and modular engine class for each major calculation method. Those engines can then be expanded and specified by inheritance. This solution should also add a factory like overview, over possible engines for a given treatment planning.
    @NathanKunz
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Commits on Jun 29, 2021

  1. Merge pull request #1 from e0404/master 

    Merge new master changes into dev_refactorDoseCalc
    @NathanKunz
    NathanKunz authored Jun 29, 2021
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Commits on Jul 7, 2021

  1. Edited engine names annd some internal logic

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  2. Create matRad_calcDose funktion 

    matRad_calcDose funktion should supersede the funktion of the other matRad_... calc funktions by creating the fitting engine and call the dose calc method.
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Commits on Aug 2, 2021

  1. Small changes to matRad_calcDose

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  2. Added documentation to the dose engines

    @NathanKunz
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Commits on Aug 9, 2021

  1. Changed calcDose and moved getAvailable dose from Engine to separate … 

    …file
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  2. Minor changes to engines manly because bugs in example runs

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  3. Comments cleanup and fix of some typos

    @NathanKunz
    NathanKunz committed Aug 9, 2021
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  4. Moved dijSampling method to PencilBeam Superclass

    @NathanKunz
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  5. Removed depricated functions 

    Removed the content of deprecated functions and replaced their content with the creation and call of a fitting doseCalcEngine. The functions can still be called exactly like before in order to assure downwards compatibility.
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Commits on Aug 11, 2021

  1. Added default engines to MatRad_Config

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  2. Move or removed functions which are either used in the dose calculati… 

    …on or are now implemented inside the engines
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  3. Merge pull request #2 from e0404/master 

    Merge e0404/master branch into dev_refactorDoseCalc
    @NathanKunz
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  4. Moved the last files to the doseCalc folder

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  5. Merge branch 'dev' into dev_refactorDoseCalc

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Commits on Nov 17, 2021

  1. Merge branch 'dev' into pr/519 

    # Conflicts:
#	AUTHORS.txt
#	MatRad_Config.m
#	matRad_calcDoseInit.m
#	matRad_calcPhotonDose.m
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  2. fix kernel convolution with interpn for octave

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Commits on Nov 19, 2021

  1. Merge branch 'dev' of https://github.com/e0404/matRad into pr/519 

    # Conflicts:
#	matRad_calcPhotonDose.m
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Commits on Dec 1, 2021

  1. some restructuring of the photon engine

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Commits on Jan 20, 2022

  1. doc change

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Commits on Feb 1, 2022

  1. Changes to engine properties

    @NathanKunz
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  2. Turn off visualization for Lateral Cut Off (octave fix) 

    Forgot to turn off the visualization for the lateral cut off inside the physical dose calculation, which resulted in an octave error
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Commits on Mar 10, 2022

  1. Merge branch 'dev' into pr/519 

    # Conflicts:
#	matRad_calcParticleDose.m
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  2. Merge branch 'dev' of https://github.com/e0404/matRad into pr/519 

    # Conflicts:
#	matRad_calcParticleDose.m
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  3. Merge branch 'dev_refactorDoseCalc' of https://github.com/NathanKunz/… 

    …matRad into pr/519
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Commits on Aug 2, 2022

  1. Merge branch 'dev' of https://github.com/e0404/matRad into pr/519 

    # Conflicts:
#	matRad_calcParticleDose.m
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  2. Merge branch 'dev' of https://github.com/e0404/matRad into pr/519 

    # Conflicts:
#	matRad_calcParticleDose.m
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  3. Merge branch 'dev_refactorDoseCalc' of https://github.com/NathanKunz/… 

    …matRad into pr/519
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Commits on Aug 3, 2022

  1. Update on dose engine variable naming and function structure

    @wahln
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  2. fix function name

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Commits on Aug 4, 2022

  1. fix for class folders

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Commits on Aug 10, 2022

  1. some cleanup of the dose calculation function

    @wahln
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  2. add helper function to find subclasses in folders / packages

    @wahln
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  3. streamlined available machine check and loading

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  4. some streamlining and name changes

    @wahln
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  5. fix missing new load machine file

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  6. fix in class availability check

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Commits on Aug 11, 2022

  1. Extended availability check by call to isAvailable function

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Commits on Aug 12, 2022

  1. Octave Fix for calling availability function

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Commits on Sep 15, 2022

  1. Update interfaces and property assignment in dose engines

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Commits on Oct 5, 2022

  1. Merge branch 'master' into pr/519

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  2. update to dij sampling (only photons), slightly adapt sampling radius

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  3. Merge branch 'dev' into pr/519

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Commits on Oct 21, 2022

  1. Merge branch 'dev_DVHcolor' into pr/519

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  2. changes to SSD computation so the propDoseCalc value is set in the en… 

    …gine
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  3. stf now contains machine as well

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Commits on Jan 24, 2023

  1. some parameter checking and using in dose engine initialization

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Commits on Jan 27, 2023

  1. remove pln requirement from dose calculation initialization

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Commits on Jan 28, 2023

  1. fix radialogical depth interpolation

    @wahln
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  2. fix anisotropic dose grid check for MCsquare

    @wahln
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  3. pln cleanup in dose engine constructors

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  4. further fixes for pln argument management, offset fix, superclass cal… 

    …ling fix in pencil-beam engine
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Commits on Jan 29, 2023

  1. defaults setter and addition of the struct assignment to constructor

    @wahln
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  2. Update tests.yml 

    Switch to Ubuntu 22.04 and thus Octave 6 in test workflow
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Commits on Jan 30, 2023

  1. ompMC interface and MCsquare interface - fix eval function for obtain… 

    …ing preconfigured compiler flags
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Commits on Feb 1, 2023

  1. Recompiled Octave 6.4.0 mex files for windows and linux, updated scri… 

    …pts and submodules
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  2. updated optimizer compilation scripts

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  3. update compiled optimizers with static linking

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Commits on Feb 3, 2023

  1. update compiled linux optimizer

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  2. option to disable function plot in optimization

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  3. include rehash of file directory after linking the optimizer and adde… 

    …d availability check
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  4. Merge branch 'dev_refactorDoseCalc' of https://github.com/NathanKunz/… 

    …matRad into pr/519
    @wahln
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  5. update workflow actions

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Commits on Feb 4, 2023

  1. move scripts used during testing to github folder

    @wahln
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  2. update scripts for github folder

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  3. adjust xvfb call in testing

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  4. Revert "adjust xvfb call in testing" 

    This reverts commit 075402c.
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Commits on Feb 6, 2023

  1. use preinstallex xvfb in linux test

    @wahln
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  2. fix path

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Commits on Feb 24, 2023

  1. incorperate multiple weighted Latteral Gaussian Profiles

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  2. Update matRad_DoseEngineParticlePB.m

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Commits on Apr 3, 2023

  1. Update matRad_DoseEngineParticlePB.m

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Commits on Jun 30, 2023

  1. Implementation of the analytical dose engine with the Bragg peak from… 

    … the Bortfeld paper (1997)
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Commits on Aug 17, 2023

  1. Update README.md

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Commits on Sep 1, 2023

  1. Create matRad_example15_photonMC_MLC.m

    @JenHardt
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  2. small bug fix

    @JenHardt
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  3. Update matRad_calcPhotonDoseMCtopas.m 

    small bug fix, and read in of MLC weights and energy for TOPAS simulation
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  4. MLC updates 

    Changed Positioning of MLC so that is SCD away,
Made MLC bigger to prevent photons flying past it
 Initilise Time Features. and us to weight different MLC shapes
Cchanged Material of MLC to thungsten
To Do: Check out multiple Photon Fields, Improve histories per run for the different shapes - do it like it is done for the particle bixels
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  5. Update matRad_example15_photonMC_MLC.m

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  6. Update matRad_TopasConfig.m

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Commits on Sep 4, 2023

  1. small bugfix

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  2. Update matRad_TopasConfig.m

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Commits on Sep 6, 2023

  1. Update matRad_TopasConfig.m

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Commits on Oct 20, 2023

  1. Preliminary Separation of Subsampling and Standard pencil-beam dose c… 

    …alculation
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  2. Additional modularization (move preparations into calcDoseInit

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  3. Merge branch 'dev' of https://github.com/e0404/matRad into pr/519 

    # Conflicts:
#	MatRad_Config.m
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Commits on Oct 23, 2023

  1. change of the naming scheme

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  2. refine documentation

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Commits on Oct 26, 2023

  1. Small Update in Dose Engine management

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Commits on Oct 27, 2023

  1. Fix Availability Checks

    @wahln
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  2. fix function arguments

    @wahln
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  3. add missing function

    @wahln
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  4. Changes to the engine selection logic and fixing of compatibility wit… 

    …h calcDoseDirect functions
    @wahln
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  5. Update matRad_DoseEngineAnalytical.m

    @SimonaFa
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  6. enable selection of Dose Engine in GUI

    @wahln
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  7. update 

    extension to multiple field, corrected leaf position to be at collimator not as isocenter
    @JenHardt
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  8. Make sure default engines are prioritized

    @wahln
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  9. Merge branch 'refactor/doseEngines' into pr/640

    @wahln
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  10. adapt to chagnes in dose engine logic

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Commits on Oct 30, 2023

  1. Merge branch 'dev' of https://github.com/e0404/matRad into pr/519

    @wahln
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  2. improve reusability of code in dose engine structure

    @wahln
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  3. Update matRad_TopasConfig.m

    @JenHardt
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  4. streamline DIJ filling for pencil-beam algorithms

    @wahln
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  5. available classes now given as row vector

    @wahln
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  6. unified progress initialization and finalization

    @wahln
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  7. streamline progress update

    @wahln
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Commits on Oct 31, 2023

  1. small fix / cosmetic change in indexing

    @wahln
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  2. rename ray initialization

    @wahln
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Commits on Nov 10, 2023

  1. improve separation of engines and fix fine-sampling engine

    @wahln
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  2. Merge branch 'pr/519' into pr/640

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Commits on Nov 14, 2023

  1. Merge pull request #640 from SimonaFa/refactor/AnalyticalDoseEngines 

    Implementation of the analytical dose engine
    @wahln
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  2. clean-up of the bortfeld engine

    @wahln
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  3. fix missing check in the Widget

    @wahln
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  4. optimize geometric distance calculation part I

    @wahln
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  5. name change calcDoseInitBeam to initBeam for consistency

    @wahln
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  6. update all names to call calcDose, and some trivial reoranization in … 

    …beam geometry
    @wahln
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  7. Fix new Analytical Bortfeld Engine

    @wahln
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  8. Catch the if statement if cutOff is only one value

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Commits on Nov 15, 2023

  1. Merge branch 'refactor/doseEngines' into pr/600 

    # Conflicts:
#	doseCalc/+DoseEngines/matRad_DoseEngineParticlePB.m
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  2. Merge pull request #600 from JenHardt/refactor/doseEngines 

    Incorperate multiple weighted lateral Gaussian Profiles
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Commits on Nov 17, 2023

  1. cosmetics on DoseEngineBase

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  2. Merge branch 'dev' of https://github.com/e0404/matRad into pr/519

    @wahln
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  3. fix photon dose influence calculation if stored primary fluence is used

    @wahln
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  4. remove warning and restructure some code

    @wahln
    wahln committed Nov 17, 2023
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  5. Streamlining of the MainGUI call

    @wahln
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  6. Missing units in axes definition

    @wahln
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  7. Handle border color and units of panels explicitly

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Commits on Nov 20, 2023

  1. Merge branch 'dev' of https://github.com/e0404/matRad into pr/519

    @wahln
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  2. clearer workflow for pln-stf, stf-dij consistancy checks

    @amitantony
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  3. cleaner update conditions for viewing widget using changedWorkspace f… 

    …ramework
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Commits on Nov 21, 2023

  1. Loading plans from the ETHOS device enabled

    @g-stanic
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  2. Update matRad_calcDoseDirectMC.m

    @g-stanic
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  3. Merge pull request #676 from amitantony/dev_structureAvailability 

    bugfixes for matRadstructure consistancy checks and update conditions for matRad_ViewingWidget
    @wahln
    wahln authored Nov 21, 2023
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  4. Add option to construct dose engines without pln

    @wahln
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  5. name change

    @wahln
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Commits on Nov 22, 2023

  1. initalization call for GUI

    @amitantony
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  2. initDoseCalc does no longer change matRad's data structures implicitl… 

    …y for cleaner management of data
    @wahln
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  3. name change for dose finalization function

    @wahln
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  4. update on index management

    @wahln
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Commits on Nov 23, 2023

  1. Import DICOM with HFP/FFP orientation Update 

    flip orientation of x,y,z vectors if ct.cube orientation is also flipped during interpolation
    @JenHardt
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  2. Dose Engines now have shortNames for better identification and creati… 

    …on by string
    @wahln
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  3. name change matRad_calcDose to matRad_calcDoseInfluence

    @wahln
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  4. Adapt warning in old dose calculation functions

    @wahln
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  5. now clear differentiation between matRad_calcDoseInlfuence and matRad… 

    …_calcDoseDirect
    @wahln
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  6. fix for lock setting of the viewing widget

    @amitantony
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  7. Merge branch 'dev_structureAvailability' of https://github.com/amitan… 

    …tony/matRad into dev_diffmap
    @amitantony
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  8. Merge pull request #519 from NathanKunz/dev_refactorDoseCalc 

    Refactor the dose calculation into object oriented dose engines
    @wahln
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  9. Merge pull request #677 from g-stanic/dev/ETHOSfix 

    Loading plans from the ETHOS device enabled
    @wahln
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  10. Merge pull request #678 from amitantony/dev_structureAvailability 

    initalization call for ViewingWidget
    @wahln
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  11. Merge pull request #679 from JenHardt/dev_DicomImportOrientation 

    Import DICOM with HFP/FFP orientation Update
    @wahln
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Commits on Nov 28, 2023

  1. bugfix for cutoff values that affect difference map and gamma index d… 

    …isplays
    @amitantony
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Commits on Nov 29, 2023

  1. bug fixes from incomplete changes from recent PRs (1) dvh update func… 

    …tion renamed (2) updating the optimization widget with the listener setup
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Commits on Dec 4, 2023

  1. Merge branch 'dev' into dev_varRBErobOpt 

    # Conflicts:
#	.github/workflows/tests.yml
#	MatRad_Config.m
#	dicom/matRad_calcWaterEqD.m
#	doseCalc/matRad_interpRadDepth.m
#	examples/matRad_example5_protons.m
#	examples/matRad_example6_protonsNoise.m
#	gui/widgets/matRad_PlanWidget.m
#	matRad.m
#	matRad_calcDoseDirect.m
#	matRad_calcDoseDirectMC.m
#	matRad_calcDoseFillDij.m
#	matRad_calcDoseInit.m
#	matRad_calcDoseInitBeam.m
#	matRad_calcLateralParticleCutOff.m
#	matRad_calcParticleDose.m
#	matRad_calcParticleDoseBixel.m
#	matRad_calcParticleDoseMC.m
#	matRad_calcPhotonDose.m
#	matRad_calcPhotonDoseMC.m
#	matRad_generateStf.m
#	ompMC/matRad_compileOmpMCInterface.m
#	optimization/optimizer/compile_ipopt_minGW_octave640.sh
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  2. Merge pull request #680 from amitantony/dev_diffDisplay 

    bugfix for cutoff values that affect difference map and gamma index display
    @wahln
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Commits on Dec 9, 2023

  1. fix stf typo in pencilBeamEngine

    @wahln
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  2. streamline matrix preallocation in pencilbeamengine abstract 

    More sustainable as scenario iteration is no longer explicit (could add future scenario dimensions)
    @wahln
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  3. we now keep radDepthCubes for all ct scenarios

    @wahln
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Commits on Dec 15, 2023

  1. Change example 8 to use the phantom builder

    @wahln
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  2. Pencil beam engine now correctly calculates robustness scenarios

    @wahln
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Commits on Dec 20, 2023

  1. Merge branch 'refactor/doseEngines' of https://github.com/e0404/matRad … 

    …into refactor/doseEnginesRobOpt

# Conflicts:
#	doseCalc/+DoseEngines/matRad_ParticlePencilBeamEngineAbstract.m
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  2. fix bug in showWarning of widgets

    @wahln
    wahln committed Dec 20, 2023
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  3. fix repeated warning regarding AutoAffectLimits

    @wahln
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  4. Merge branch 'dev' of https://github.com/e0404/matRad into refactor/d… 

    …oseEnginesRobOpt
    @wahln
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  5. Merge branch 'refactor/doseEnginesRobOpt' of https://github.com/e0404… 

    …/matRad into refactor/doseEnginesRobOpt
    @wahln
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Commits on Dec 25, 2023

  1. fix missing instantiation of matRad_cfg

    @wahln
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  2. geometric data now also cell array of ct scenarios

    @wahln
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  3. make sure geoDepths are also selected from scenario

    @wahln
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Commits on Dec 26, 2023

  1. Scenario models now include management of 4D phase scenarios as well.

    @wahln
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  2. remove calculation of geometric depths when not needed for particle e… 

    …ngines
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Commits on Jan 25, 2024

  1. bug that triggers "number of beam mismatch" warning

    @amitantony
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Commits on Jan 26, 2024

  1. use other phase space file and adjustments to that

    @JenHardt
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Commits on Jan 28, 2024

  1. move some scenario logic to ScenarioModel

    @wahln
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  2. only get geoDepths when needed

    @wahln
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  3. fix example 8 (robust proton opt)

    @wahln
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  4. fix negative radDepths with negative absolute range error in photon c… 

    …alculation
    @wahln
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  5. adaptation of biological model calculation

    @wahln
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Commits on Jan 29, 2024

  1. fix bug in sagittal coronal plot slice title 

    add author name
    @ferdymercury
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Commits on Jan 31, 2024

  1. Update Strucutre Visibility in uifigure

    @wahln
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  2. Compatibility of StructureVisibilityWidget with uifigure (to allow us… 

    …age of the new desktop)
    @wahln
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  3. fix for matRad_cfg check in structurevisibility widget

    @wahln
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Commits on Feb 1, 2024

  1. small changes

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Commits on Feb 6, 2024

  1. Small fix to structure visibility widget to show correct color and no… 

    …t open a second listbox when new uifigure-based desktop is used
    @wahln
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  2. Merge pull request #693 from ferdymercury/plotlabels 

    fix bug in sagittal coronal plot slice title
    @wahln
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Commits on Feb 7, 2024

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

    # Conflicts:
#	.github/workflows/tests.yml
#	AUTHORS.txt
#	MatRad_Config.m
#	dicom/matRad_scanDicomImportFolder.m
#	matRad_calcDoseDirectMC.m
#	matRad_rc.m
#	tools/matRad_plotSliceWrapper.m
    @wahln
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  2. Merge branch 'dev' into refactor/doseEnginesRobOpt 

    # Conflicts:
#	.github/workflows/tests.yml
#	MatRad_Config.m
#	tools/matRad_plotSliceWrapper.m
    @wahln
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  3. fix ignoreOutsideDensities switch writing only into temporary ct vari… 

    …able
    @wahln
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  4. Merge branch 'dev_varRBErobOpt' of https://github.com/e0404/matRad in… 

    …to refactor/doseEnginesRobOpt
    @wahln
    wahln committed Feb 7, 2024
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Commits on Feb 16, 2024

  1. Fix typo in DoseEngineBase

    @wahln
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  2. Merge branch 'dev_varRBErobOpt' of https://github.com/e0404/matRad in… 

    …to refactor/doseEnginesRobOpt
    @wahln
    wahln committed Feb 16, 2024
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  3. fix VdoseGrid in LET calculation and LET file name in config

    @wahln
    wahln committed Feb 16, 2024
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Commits on Feb 20, 2024

  1. fix size of vAlphaX and vBetaX in particle PB dose engine

    @wahln
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  2. clarify name of Hong engine

    @wahln
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  3. RBExD naming fix in Widget

    @wahln
    wahln committed Feb 20, 2024
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Commits on Feb 28, 2024

  1. Update matRad_TopasConfig.m

    @JenHardt
    JenHardt committed Feb 28, 2024
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Commits on Mar 1, 2024

  1. Merge branch 'refactor/doseEnginesRobOpt' into dev_varRBErobOpt_photo… 

    …nmlc
    @JenHardt
    JenHardt committed Mar 1, 2024
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  2. Addjust example to merge

    @JenHardt
    JenHardt committed Mar 1, 2024
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  3. pln is no longer a variable, in the writeStfField adjust for that

    @JenHardt
    JenHardt committed Mar 1, 2024
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  4. The TOPAS engine was not correctly initalized

    @JenHardt
    JenHardt committed Mar 1, 2024
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  5. Update matRad_TopasMCEngine.m

    @JenHardt
    JenHardt committed Mar 1, 2024
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  6. Update matRad_TopasMCEngine.m

    @JenHardt
    JenHardt committed Mar 1, 2024
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Commits on Mar 27, 2024

  1. Update to externalCalculation 

    Changed output of TopasMCEngine to be empty not a 0 struct, this way, we dont need the check for externalCalculation in the MonteCarlo DoseEngine, and the resultGUI is still returned as empty in the calc cubes
    @JenHardt
    JenHardt committed Mar 27, 2024
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Commits on Apr 4, 2024

  1. Merge pull request #701 from JenHardt/dev_varRBErobOpt_photonmlc 

    Update to Photon calculation with TOPAS (new engine concept)
    @wahln
    wahln authored Apr 4, 2024
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Commits on Apr 12, 2024

  1. fix TOPAS engine and base data

    @wahln
    wahln committed Apr 12, 2024
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Commits on Apr 18, 2024

  1. 4D update to dose engines. Also changes optimization

    @wahln
    wahln committed Apr 18, 2024
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Commits on Apr 19, 2024

  1. 4D Update to scenario handling with carbon

    @JenHardt
    JenHardt committed Apr 19, 2024
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  2. clean up

    @JenHardt
    JenHardt committed Apr 19, 2024
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Commits on Apr 20, 2024

  1. Merge pull request #710 from JenHardt/refactor/doseEnginesRobOpt 

    4D Update to scenario handling with carbon
    @wahln
    wahln authored Apr 20, 2024
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Commits on Apr 24, 2024

  1. Merge remote-tracking branch 'origin/dev_varRBErobOpt' into refactor/… 

    …doseEnginesRobOpt
    @wahln
    wahln committed Apr 24, 2024
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Commits on Apr 26, 2024

  1. Remove transpose from matRad_interp3 for octave

    @wahln
    wahln committed Apr 26, 2024
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Commits on Apr 27, 2024

  1. minor documentation edit

    @wahln
    wahln committed Apr 27, 2024
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  2. update tests

    @wahln
    wahln committed Apr 27, 2024
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  3. small fixes in dose engines

    @wahln
    wahln committed Apr 27, 2024
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  4. fix tests

    @wahln
    wahln committed Apr 27, 2024
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  5. fix dose engine base exception assertion test

    @wahln
    wahln committed Apr 27, 2024
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Commits on May 8, 2024

  1. avoid deletion of temporary files to avoid coverage errors

    @wahln
    wahln committed May 8, 2024
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Commits on May 10, 2024

  1. Rearrange ThirdParty (parfor progress / pu)

    @wahln
    wahln committed May 10, 2024
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  2. auto update GUI on matRadGUI call.

    @wahln
    wahln committed May 10, 2024
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  3. optimizer fixes and added basic tests

    @wahln
    wahln committed May 10, 2024
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  4. Merge branch 'refactor/doseEnginesRobOpt' of https://github.com/e0404… 

    …/matRad into refactor/doseEnginesRobOpt
    @wahln
    wahln committed May 10, 2024
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  5. modularize extraction of single scenario in pencil beam engines

    @wahln
    wahln committed May 10, 2024
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  6. Add Optimization Toolbox to test fmincon

    @wahln
    wahln committed May 10, 2024
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  7. fix scenario selection in PB engines

    @wahln
    wahln committed May 10, 2024
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  8. fmincon optimizer compatibility switch to avoid diagnostics bug

    @wahln
    wahln committed May 10, 2024
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  9. bigger lbfgs history for better convergence

    @wahln
    wahln committed May 10, 2024
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  10. Fix cleanup of failed example tests.

    @wahln
    wahln committed May 10, 2024
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