opentps.core.processing package
Subpackages
- opentps.core.processing.C_libraries package
- opentps.core.processing.deformableDataAugmentationToolBox package- Submodules
- opentps.core.processing.deformableDataAugmentationToolBox.BreathingSignalGeneration module
- opentps.core.processing.deformableDataAugmentationToolBox.generateDynamicSequencesFromModel module
- opentps.core.processing.deformableDataAugmentationToolBox.generateRandomSamplesFromModel module
- opentps.core.processing.deformableDataAugmentationToolBox.interFractionChanges module
- opentps.core.processing.deformableDataAugmentationToolBox.modelManipFunctions module
- opentps.core.processing.deformableDataAugmentationToolBox.multiProcSpawnMethods module
- opentps.core.processing.deformableDataAugmentationToolBox.weightMaps module
- Module contents
 
- opentps.core.processing.doseCalculation namespace- Subpackages
- Submodules
- opentps.core.processing.doseCalculation.abstractDoseCalculator module
- opentps.core.processing.doseCalculation.abstractDoseInfluenceCalculator module
- opentps.core.processing.doseCalculation.abstractMCDoseCalculator module
- opentps.core.processing.doseCalculation.doseCalculationConfig module
- opentps.core.processing.doseCalculation.geant4DoseCalculator module
- opentps.core.processing.doseCalculation.mcsquareDoseCalculator module- MCsquareDoseCalculator- MCsquareDoseCalculator.beamModel
- MCsquareDoseCalculator.computeBeamlets()
- MCsquareDoseCalculator.computeBeamletsAndLET()
- MCsquareDoseCalculator.computeDose()
- MCsquareDoseCalculator.computeDoseAndLET()
- MCsquareDoseCalculator.computeRobustScenario()
- MCsquareDoseCalculator.computeRobustScenarioBeamlets()
- MCsquareDoseCalculator.ct
- MCsquareDoseCalculator.ctCalibration
- MCsquareDoseCalculator.getSimulationProgress()
- MCsquareDoseCalculator.independentScoringGrid
- MCsquareDoseCalculator.kill()
- MCsquareDoseCalculator.nbPrimaries
- MCsquareDoseCalculator.optimizeBeamletFree()
- MCsquareDoseCalculator.scoringGridSize
- MCsquareDoseCalculator.scoringOrigin
- MCsquareDoseCalculator.scoringVoxelSpacing
- MCsquareDoseCalculator.setScoringParameters()
- MCsquareDoseCalculator.simulationDirectory
- MCsquareDoseCalculator.simulationFolderName
- MCsquareDoseCalculator.statUncertainty
 
 
 
- opentps.core.processing.imageProcessing package- Submodules
- opentps.core.processing.imageProcessing.crop2D module
- opentps.core.processing.imageProcessing.cupyImageProcessing module
- opentps.core.processing.imageProcessing.filter3D module
- opentps.core.processing.imageProcessing.image2DManip module
- opentps.core.processing.imageProcessing.imageTransform3D module- applyTransform3D()
- dicomCoordinate2iecGantry()
- dicomToIECGantry()
- extendAll()
- getTtransformMatrixInPixels()
- getVoxelIndexFromPosition()
- iecGantryCoordinatetoDicom()
- iecGantryToDicom()
- parseRotCenter()
- rotateData()
- rotateVectorsInPlace()
- transform3DMatrixFromTranslationAndRotationsVectors()
- translateData()
- translateDataByChangingOrigin()
 
- opentps.core.processing.imageProcessing.resampler3D module
- opentps.core.processing.imageProcessing.sitkImageProcessing module- applyTransform3D()
- applyTransform3DToImage3D()
- applyTransform3DToPoint()
- applyTransform3DToVectorField3D()
- connectComponents()
- dilateMask()
- extremePoints()
- extremePointsAfterTransform()
- image2DToSITK()
- image3DToSITK()
- imageToSITK()
- register()
- resize()
- rotateData()
- sitkImageToImage2D()
- sitkImageToImage3D()
- translateData()
 
- opentps.core.processing.imageProcessing.syntheticDeformation module
- Module contents
 
- opentps.core.processing.imageSimulation package
- opentps.core.processing.planDeliverySimulation package
- opentps.core.processing.planEvaluation package
- opentps.core.processing.planOptimization package- Subpackages- opentps.core.processing.planOptimization.acceleration package- Submodules
- opentps.core.processing.planOptimization.acceleration.backtracking module
- opentps.core.processing.planOptimization.acceleration.baseAccel module
- opentps.core.processing.planOptimization.acceleration.fistaAccel module
- opentps.core.processing.planOptimization.acceleration.linesearch module
- Module contents
 
- opentps.core.processing.planOptimization.objectives package- Submodules
- opentps.core.processing.planOptimization.objectives.baseFunction module
- opentps.core.processing.planOptimization.objectives.doseFidelity module
- opentps.core.processing.planOptimization.objectives.energySequencing module
- opentps.core.processing.planOptimization.objectives.logBarrier module
- opentps.core.processing.planOptimization.objectives.norms module
- opentps.core.processing.planOptimization.objectives.projections module
- Module contents
 
- opentps.core.processing.planOptimization.solvers package- Submodules
- opentps.core.processing.planOptimization.solvers.beamletFree module
- opentps.core.processing.planOptimization.solvers.bfgs module
- opentps.core.processing.planOptimization.solvers.fista module
- opentps.core.processing.planOptimization.solvers.gradientDescent module
- opentps.core.processing.planOptimization.solvers.localSearch module
- opentps.core.processing.planOptimization.solvers.lp module
- opentps.core.processing.planOptimization.solvers.mip module
- opentps.core.processing.planOptimization.solvers.solver module
- opentps.core.processing.planOptimization.solvers.sparcling module
- Module contents
 
 
- opentps.core.processing.planOptimization.acceleration package
- Submodules
- opentps.core.processing.planOptimization.optimizationWorkflows module
- opentps.core.processing.planOptimization.planInitializer module
- opentps.core.processing.planOptimization.planOptimization module
- opentps.core.processing.planOptimization.planOptimizationConfig module
- opentps.core.processing.planOptimization.planPreprocessing module
- opentps.core.processing.planOptimization.tools module- WeightStructure- WeightStructure.computeELSparsity()
- WeightStructure.computeIrradiationTime()
- WeightStructure.computeNOfLayers()
- WeightStructure.getBeamStructure()
- WeightStructure.getEnergyStructure()
- WeightStructure.getListOfActiveEnergies()
- WeightStructure.getListOfActiveLayersInBeams()
- WeightStructure.getMUPerBeam()
- WeightStructure.getMUPerLayer()
- WeightStructure.getSpotIndex()
- WeightStructure.getWeightsStruct()
- WeightStructure.groupSol()
- WeightStructure.groupSpots()
- WeightStructure.isActivated()
- WeightStructure.loadSolution()
- WeightStructure.ungroupSol()
 
- evaluateClinical()
- getEnergyWeights()
 
- Module contents
 
- Subpackages
- opentps.core.processing.registration package- Submodules
- opentps.core.processing.registration.midPosition module
- opentps.core.processing.registration.registration module
- opentps.core.processing.registration.registrationDemons module
- opentps.core.processing.registration.registrationMorphons module
- opentps.core.processing.registration.registrationQuick module
- opentps.core.processing.registration.registrationRigid module
- opentps.core.processing.registration.registrationTranslation module
- Module contents
 
- opentps.core.processing.segmentation package
- opentps.core.processing.trackingToolBox package
Submodules
opentps.core.processing.rangeEnergy module
- energyToRange(energy: float | ndarray) float | ndarray
- This function converts a proton beam energy (in MeV) to a water equivalent range (defined as r80, i.e., the position of the 80% dose in the distal falloff, in cm). - The formula comes from Loic Grevillot et al. [1, 2], from a fitting to the NIST/ICRU database. - [1] L. Grevillot, et al. “A Monte Carlo pencil beam scanning model for proton treatment plan simulation using GATE/GEANT4.” Phys Med Biol, 56(16):5203–5219, Aug 2011. [2] L. Grevillot, et al. “Optimization of geant4 settings for proton pencil beam scanning simulations using gate”. Nuclear Instruments and Methods in Physics Research Section B: Beam Interactions with Materials and Atoms, 268(20):3295 – 3305, 2010. - Parameters:
- energy (float) – Energy in MeV. 
- Returns:
- r80 – r80 in cm. 
- Return type:
- float 
 
- energyToRangeMM(energy: float | ndarray) float | ndarray
- This function converts a proton beam energy (in MeV) to a water equivalent range (defined as r80, i.e., the position of the 80% dose in the distal falloff, in mm). - It uses the function energyToRange, but converts the input and output to mm. - Parameters:
- energy (float) – Energy in MeV. 
- Returns:
- r80 – r80 in mm. 
- Return type:
- float 
 
- rangeMMToEnergy(r80: float | ndarray) float | ndarray
- This function converts the water equivalent range (defined as r80, i.e., the position of the 80% dose in the distal falloff, in mm) to incident energy of the proton beam (in MeV). - It uses the function rangeToEnergy, but converts the input and output to mm. - Parameters:
- r80 (float) – r80 in mm. 
- Returns:
- energy – Energy in MeV. 
- Return type:
- float 
 
- rangeToEnergy(r80: float | ndarray) float | ndarray
- This function converts the water equivalent range (defined as r80, i.e., the position of the 80% dose in the distal falloff, in cm) to incident energy of the proton beam (in MeV). - The formula comes from Loic Grevillot et al. [1, 2], from a fitting to the NIST/ICRU database. - [1] L. Grevillot, et al. “A Monte Carlo pencil beam scanning model for proton treatment plan simulation using GATE/GEANT4.” Phys Med Biol, 56(16):5203–5219, Aug 2011. [2] L. Grevillot, et al. “Optimization of geant4 settings for proton pencil beam scanning simulations using gate”. Nuclear Instruments and Methods in Physics Research Section B: Beam Interactions with Materials and Atoms, 268(20):3295 – 3305, 2010. - Parameters:
- r80 (float) – r80 in cm. 
- Returns:
- energy – Energy in MeV. 
- Return type:
- float