…tion

Dev varRBE robopt world coordinate system

# Conflicts:
#	matRad/planAnalysis/matRad_compareDose.m

Dev constraints tests

Bug fixing

Cutoff method

Small update to dev

* Change release candidate version

* rename changelog file to make it markdown

* Update dose engine base for class based bio model. Add new properties and assignBioParam function for selection of biological model

* add functions for looping through subclasses and struct fields.

* minor change in findSubclasses

* Update particle ParticlePencilBeamAbstract for class based bio model

* Update HongPB engine for class based bio model

* Update initDoseCalc of Base engine for class based bio model

* Update fluence optimization for class based bio model

* Deprecate old Biological Model functions and classes

* Main Biological Model class

* LET based and RBEminMax models

* Kernel based models (LEM)

* Tabulated RBE models

* Added documentation and function description

* minor updates in tabulated model for RBEtable path search ande avoid storage of bixel.energies

* chage kernel interpolation from radDepth to radDepth(:), used for 2D kernel interpolation for fine samplng engine

* Update fine sampling engine to allow for 2D kernels with mutliple subBixels

* iterate fix version

* move bioModel from propDoseCalc to separate field in pln, adapt engines

* adapt fluence optimmization, move bioModel from propDoseCalc

* machine check moved to BiologicalModel

* Adapt tabulated models and constRBE to latest changes

* Adapt matRad_bioModel to new class structure

* Iterate patch version and update changelog

* Add brachy as radiation modality to model matRad_None

* Add example for biological parameter setup

* Update to dev branch and minor bug fixes

* minor bug fix

* Update bio model testing, initial tests

* renaming of none model

* Test modified validation function for folders input in matRad_findSubclasses

* Test modified validation function for folders input in matRad_findSubclasses

* change split to strsplit for octave compatibility

* Another test for matRad_findSubclasses

* Another test for matRad_findSubclasses

* Revert changes to validation function for input folders in matRad_findSubclasses

* Changes for error handling and octave compatibility

* Update validate function for folders input matRad_findSubclasses

* Explicit Abstractc defintion for class matRad_LQKernelBasedModel

* Changes in input validation matRad_findSubclasses

* Chages in validation input for matRad_findSubclasses

* test

* test

* test: more info for debugging

* test: more info for debugging

* test: more info for debugging

* bioParam to bioModel name changing for pln properties

* Add quantityOpt and quantityVis as depreccated quantities

* quantityVis handling

* folder definition and validation in matRad_findSubclasses

* Updates of bioParam naming

* Update of bioModel naming for matRad.m

* Update test for bioModelling, brachy and Topas

* Update tests and example for bioModel compatibility

* Update test_biologicalModels testing

* change isProp to matRad_ispropCompat

* some file reorganization and streamlining of the bioModel function to create a model

* New Generic base data for protons, including MC simulated kernels and Fluence/Energy deposition spectra

* GUI update for bioModels

* Renaming Wedenberg model

* correct Generic machine file upload

* Replace remaining instances of bioParam to bioModel and do some gui fixes

* fix filling of bio model in Plan Widget

* static functions to obtain available models and create a model from string / struct

* adapt bioModel in new stf generators

* some model streamlining using constant properties

* consistent naming of constant property to check radiation modes

* update base data

* fixes to differences in how machine names are requested

* fix in machine creator string

* new focus spot spacing Lookup name

* fixed weights for some energies

* some improvements for availability checks

* fix some issues regarding optimization with unusual model choices (i.e. none for carbon)

* fix some issues in model selection

* remove unused and unecessary getSubfolders function

* remove commented code from dose engine

* changed validation of model to check if engine can compute the quantity from the machine

* calcBioCheckConsistency has been moved

* some adaptations to dose calculation and display and availability functions

(cherry picked from commit 8c6d010840801e3c86dd9be9155a325307de5736)

* example cleanup to respect new bioModel and multScen nomenclature

* revert version change

* some type fixes and quantityOpt fixes

* some more fixing for passing the tests

* Apply constant properties in TabluatedSpectralKernel

* some code cleanup and fixes

* small update to example script and standard setting for lateral model in dose calculation

* update changelog

* manage updates of machine / engine / model combination

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Co-authored-by: Niklas Wahl <[email protected]>

* Bug fix for matRad_plotAxisLabel, cube indexing for viualization

* Bug fix for GUI, visQuantity warning popup

…fectJacobianFix

constrained efect optimization, jacobian bug fix in sqrtBetaDose

* Minor bug, update cube dimension in writeMHD to make dimension permeutation effective

* Minor bug fix, misisng matRad_cfg

* Modify use of cube permutation and transformation matrix

* Add permutation to vtk writer

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Co-authored-by: Niklas Wahl <[email protected]>

Fixed bug: The iso center value must not match any specific point on the axis. It should lie within the minimum and maximum values but not be equal to either of them.

fixed bug with indices

fixed small bug, pln.radiationMode is defined as a property of object