JSON settings for ROE (models) - cerr/CERR GitHub Wiki
The functional forms of several dosimetric models are distributed with CERR. Associated model parameters are specified through JSON format files. This includes parameters required for bio-normalization of planned doses, i.e., the fraction number or fraction size used in developing the model.
JSON fields
General
- Name : Name of the model
- Type : May be "TCP", "BED" , or "NTCP".
For fractionation correction
- fractionCorrect: "Yes" or "No"
- correctionType: "fsize" or "nfrx"
- fractionSize: Fraction size of modelled dataset (required for correctionType: fsize)
- stdNumFractions: No. fractions of modelled dataset (required for correctionType: nfrx)
- abRatio: Radiosensitivity (α/β) in Gy
Functional form
- function: Function name defining model form.
Model forms distributed with CERR are detailed here. Custom implementations should follow the established function signature:
outcome = functionName(paramS, doseBinsV, volBinsV)
Model parameters
Each parameter is specified through 4 fields
-
val: Parameter value or function name to evaluate. Set t 1 for constant parameters.
-
weight : Coefficient. Set to fixed value for constant parameters.
-
type : An array of values specifying data types of value & weight inputs, respectively.
May be "string", "bin"(for binary) or "cont" (for numeric inputs). -
cteg: Specify supported values (e.g.: cteg =[0,1]) for binary type variables.
-
desc: Map labels to descriptions (e.g.: desc =["No","Yes"]) for binary type variables only.
-
Syntax for structure-specific parameters
"structure":{
"structName1": {
"param1":{
"val": val
"weight": weight
"type": [val_type, weight_type]
"cteg": [cteg1, cteg2]
}
}
Example
JSON settings for models distributed with ROE are available here.
E.g. Esophagitis model [1]
{
"name": "Esophagitis (Huang)",
"type": "NTCP",
"stdNumFractions": 35,
"fractionCorrect": "Yes",
"correctionType": "nfrx",
"abRatio": 10,
"parameters": {
"concurrentChemo": {
"val": 1,
"weight": 1.5,
"type": ["bin", "cont"],
"cteg": [0,1],
"desc": ["No", "Yes"]
},
"structures": {
"Esophagus":{
"meanDose": {
"val": "calc_meanDose",
"weight": 0.0688,
"type": ["string", "cont"],
"cteg": ["calc_meanDose","calc_meanDose"]
}
}
},
"constant": {
"val": 1,
"weight": -3.13,
"type": ["cont", "cont"],
"cteg": [0, 1]
}
},
"function": "logitFn"
}
References
- Huang, E. X., Hope, A. J., Lindsay, P. E., Trovo, M., El Naqa, I., Deasy, J. O., & Bradley, J. D. (2011). Heart irradiation as a risk factor for radiation pneumonitis. Acta Oncologica, 50(1), 51-60.