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class based biological models #756

Merged
merged 107 commits into from
Oct 16, 2024
Merged

class based biological models #756

merged 107 commits into from
Oct 16, 2024

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remocristoforetti
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Class based structure for biological modelling.

wahln and others added 29 commits July 9, 2024 16:07
@wahln
Change release candidate version
5ea1657
@wahln
rename changelog file to make it markdown
2d10d0c
@remocristoforetti
Update dose engine base for class based bio model. Add new properties…
8148f1b 
… and assignBioParam function for selection of biological model
@remocristoforetti
add functions for looping through subclasses and struct fields.
d988193
@remocristoforetti
minor change in findSubclasses
34c219d
@remocristoforetti
Update particle ParticlePencilBeamAbstract for class based bio model
49ab64b
@remocristoforetti
Update HongPB engine for class based bio model
69a8c40
@remocristoforetti
Update initDoseCalc of Base engine for class based bio model
25e4aa8
@remocristoforetti
Update fluence optimization for class based bio model
efb4f47
@remocristoforetti
Deprecate old Biological Model functions and classes
ab3a52e
@remocristoforetti
Main Biological Model class
abd1d60
@remocristoforetti
LET based and RBEminMax models
35fa4a8
@remocristoforetti
Kernel based models (LEM)
6236a4c
@remocristoforetti
Tabulated RBE models
94e2e4d
@remocristoforetti
Added documentation and function description
05ebf47
@remocristoforetti
minor updates in tabulated model for RBEtable path search ande avoid …
48a2e24 
…storage of bixel.energies
@remocristoforetti
chage kernel interpolation from radDepth to radDepth(:), used for 2D …
94f2a4e 
…kernel interpolation for fine samplng engine
@remocristoforetti
Update fine sampling engine to allow for 2D kernels with mutliple sub…
5040cf8 
…Bixels
@wahln
Merge branch 'dev' into rc/v3
65e3a88
@wahln
iterate fix version
52940e6
@remocristoforetti
move bioModel from propDoseCalc to separate field in pln, adapt engines
15cc3ee
@remocristoforetti
adapt fluence optimmization, move bioModel from propDoseCalc
9fbf68d
@remocristoforetti
machine check moved to BiologicalModel
5ca545e
@remocristoforetti
Adapt tabulated models and constRBE to latest changes
105b805
@remocristoforetti
Adapt matRad_bioModel to new class structure
8cf3c80
@wahln
Merge branch 'dev' into rc/v3
ecd3087
@wahln
Iterate patch version and update changelog
69abc7b
@remocristoforetti
Add brachy as radiation modality to model matRad_None
9aaf5c7
@remocristoforetti
Add example for biological parameter setup
b5a51e6
@remocristoforetti remocristoforetti marked this pull request as ready for review August 9, 2024 13:53
wahln and others added 3 commits October 10, 2024 00:33
@wahln
Merge branch 'dev' of https://github.com/e0404/matRad into pr/756
001a022 
# Conflicts:
#	matRad/dicom/@matRad_DicomImporter/matRad_importDicomRTPlan.m
#	matRad/gui/widgets/matRad_PlanWidget.m
@wahln
fix some issues regarding optimization with unusual model choices (i.…
6142ecc 
…e. none for carbon)
@wahln
fix some issues in model selection
0ba8f54
wahln
wahln requested changes Oct 10, 2024
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Preliminary review for now while this is still under construction

matRad/bioModels/LQbasedModels/RBEtabulatedModels/matRad_LQRBETabulatedModel.m Outdated Show resolved Hide resolved
matRad/bioModels/LQbasedModels/RBEtabulatedModels/matRad_TabulatedSpecralKernelBasedModel.m Outdated Show resolved Hide resolved
matRad/gui/widgets/matRad_ViewingWidget.m Show resolved Hide resolved
matRad/matRad_version.m Outdated Show resolved Hide resolved
matRad/util/matRad_getStructFieldsAndSubfields.m Outdated Show resolved Hide resolved
matRad/util/matRad_getSubfolders.m Outdated Show resolved Hide resolved
matRad/util/matRad_getSubfolders.m Outdated Show resolved Hide resolved
wahln and others added 15 commits October 10, 2024 13:46
@wahln
Merge branch 'dev' into dev_bioModelMerging
0a8cd80
@wahln
remove unused and unecessary getSubfolders function
1521df6
@wahln
remove commented code from dose engine
fe7b870
@wahln
changed validation of model to check if engine can compute the quanti…
b2b9588 
…ty from the machine
@wahln
calcBioCheckConsistency has been moved
eae959b
@wahln
Merge branch 'dev_bioModelMerging' of https://github.com/remocristofo…
fda7b89 
…retti/matRad into pr/756
@wahln
some adaptations to dose calculation and display and availability fun…
d9488e3 
…ctions

(cherry picked from commit 8c6d010840801e3c86dd9be9155a325307de5736)
@wahln
example cleanup to respect new bioModel and multScen nomenclature
ece65c7
@wahln
revert version change
aaca6c2
@wahln
some type fixes and quantityOpt fixes
533975e
@wahln
some more fixing for passing the tests
e5c9ac2
@wahln
Merge branch 'dev' into pr/756
e49807e
@wahln
Apply constant properties in TabluatedSpectralKernel
fb4d850
@wahln
Merge branch 'dev' into pr/756
d714fde
@wahln
some code cleanup and fixes
8fa1308
@wahln wahln marked this pull request as ready for review October 12, 2024 23:38
@wahln wahln mentioned this pull request Oct 15, 2024
Closed
@wahln wahln merged commit 3d98409 into e0404:dev Oct 16, 2024
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@amitantony amitantony amitantony left review comments

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@remocristoforetti @wahln @amitantony