bioModels
Biological effect models for computing radiobiological quantities such as LET, RBE, and survival fractions.
- class matRad_BiologicalModel
Bases:
handle- matRad_BiologicalModel
This is an abstract interface class to define Biological Models for use in dose calculation and plan optimization. Subclasses should at least implement the methods:
calcBiologicalQuantitiesForBixel() to implement the specific model calculation algorithm
Additional methods that can be implemented are:
getTissueInformation() to collect meta information about the tissue defintion and paramters assignBioModelPropertiesFromEngine() to translate user defined paramters directly to the biological model subclass
All subclasses should also declare the properties:
‘possibleRadiationModes’ to specify the radiation modalities to which the model validity is limited ‘requiredQuantities’ to check the availability of information stored in the provided machine file
- constructor (Abstract)
matRad_BiologicalModel()
Copyright 2023-2026 the matRad development team.
This file is part of the matRad project. It is subject to the license terms in the LICENSE file found in the top-level directory of this distribution and at https://github.com/e0404/matRad/LICENSE.md. No part of the matRad project, including this file, may be copied, modified, propagated, or distributed except according to the terms contained in the LICENSE file.
The type of the None singleton.
- Property Summary
- model
- requiredQuantities
kernels in base data needed for the alpha/beta calculation
- possibleRadiationModes
radiation modalitites compatible with the model
- defaultReportQuantity
default suggested quantity to use for display and planning
- Method Summary
- calcBiologicalQuantitiesForBixel(this)
the actual calculation method wich calculates biological quantities for individual beamlets Needs to be implemented in non abstract subclasses.
- getTissueInformation(this, ~, ~, ~, vAlphaX, ~, ~, ~)
This is the default, should be masked by the specific model subclass if needed
- isAvailable(this, radiationMode, providedQuantities)
- static getAvailableModels(radiationMode, providedQuantities)
Get available models (optionally for radiationMode / machine combination)
- static create(modelMetadata)
- static validate(model, radiationMode, providedQuantities)
Make sure model is a validly created instance
- static getAvailableTissueParameters(pln)
empty values in standard implementation, needs to be overwritten in subclasses
- matRad_getPhotonLQMParameters(cst, numVoxel, VdoseGrid)
matRad function to receive the photon LQM reference parameter
call
[ax,bx] = matRad_getPhotonLQMParameters(cst,numVoxel,ctScen,VdoseGrid)
- Input:
cst – matRad cst struct
numVoxel – number of voxels of the dose cube
VdoseGrid – optional linear index vector that allows to specify subindices for which ax and bx will be computed
- Output:
ax – vector containing for each linear voxel index alpha_x
bx – vector containing for each linear voxel index beta_x
- References
Copyright 2018-2026 the matRad development team.
This file is part of the matRad project. It is subject to the license terms in the LICENSE file found in the top-level directory of this distribution and at https://github.com/e0404/matRad/LICENSE.md. No part of the matRad project, including this file, may be copied, modified, propagated, or distributed except according to the terms contained in the LICENSE file.
- class matRad_EmptyBiologicalModel
Bases:
matRad_BiologicalModel- matRad_None
Class to implement the None model
Copyright 2023-2026 the matRad development team.
This file is part of the matRad project. It is subject to the license terms in the LICENSE file found in the top-level directory of this distribution and at https://github.com/e0404/matRad/LICENSE.md. No part of the matRad project, including this file, may be copied, modified, propagated, or distributed except according to the terms contained in the LICENSE file.
- class matRad_ConstantRBE
Bases:
matRad_BiologicalModel- matRad_ConstantRBE
Class to implement the constantRBE model
Copyright 2023-2026 the matRad development team.
This file is part of the matRad project. It is subject to the license terms in the LICENSE file found in the top-level directory of this distribution and at https://github.com/e0404/matRad/LICENSE.md. No part of the matRad project, including this file, may be copied, modified, propagated, or distributed except according to the terms contained in the LICENSE file.
- matRad_bioModel(radiationMode, model, providedQuantities)
This is a helper function to instantiate a matRad_BiologicalModel. This function currently exists for downwards compatability, as the new Biological Models will follow a polymorphic software architecture
call
matRad_bioModel(radiationMode, model)
e.g. pln.bioModel = matRad_bioModel(‘protons’,’MCN’)
- Input:
radiationMode – radiation modality ‘photons’ ‘protons’ ‘helium’ ‘carbon’ ‘brachy’
model – string to denote which biological model is used ‘none’: for photons, protons, carbon ‘constRBE’: constant RBE for photons and protons ‘MCN’: McNamara-variable RBE model for protons ‘WED’: Wedenberg-variable RBE model for protons ‘LEM’: Local Effect Model for carbon ions
providedQuantities – optional cell string of provided quantities to check if the model can be evaluated
- Output:
model – instance of a biological model
LQ-based Models
Linear-quadratic based biological models.
- class matRad_LQBasedModel
Bases:
matRad_BiologicalModel- This is an Abstract class implementing Linear Quadratic based biological
models. These include all biological models exploiting the variable alpha/beta formalism.
Copyright 2023-2026 the matRad development team.
This file is part of the matRad project. It is subject to the license terms in the LICENSE file found in the top-level directory of this distribution and at https://github.com/e0404/matRad/LICENSE.md. No part of the matRad project, including this file, may be copied, modified, propagated, or distributed except according to the terms contained in the LICENSE file.