Index

A

ABSOLUTE_DIFFERENCE (DoseComparisonImageProvider.Metric attribute) AbstractApplicationConfig (class in opentps.core.utils.applicationConfig) AbstractCTCalibration (class in opentps.core.data.CTCalibrations) AbstractDoseCalculator (class in opentps.core.processing.doseCalculation.abstractDoseCalculator) AbstractDoseInfluenceCalculator (class in opentps.core.processing.doseCalculation.abstractDoseInfluenceCalculator) AbstractMCDoseCalculator (class in opentps.core.processing.doseCalculation.abstractMCDoseCalculator) Accel (class in opentps.core.processing.planOptimization.acceleration.baseAccel) acceptFunct() (BreathingSignalPanel method) ActiveExtensions (class in opentps.gui.programSettingEditor) activePatient (ViewController property) activePatients (ViewController property) add_new_beam() (PlanDesignPanel method) addDynamicButtons() (ViewerToolbar method) addDynamicViewer() (DynamicDisplayController method) addEntry() (MCsquareCTCalibration method), [1] (MCsquareHU2Material method) (PiecewiseHU2Density method) addExoticObjective() (ObjectivesList method) addFidObjective() (ObjectivesList method) addROIContour() (ROIPanel method) addROIMask() (ROIPanel method) addScenario() (Robustness method) addToSpot() (PlanIonLayer method) addToToolbar() (DVHViewerActions method) (ImageViewerActions method) addWidget() (MainToolbar method) algo() (ConvexSolver method) allMaterialsAndElements() (MCsquareHU2Material method) analyzeDosimetricSpace() (Robustness method) analyzeErrorSpace() (Robustness method) angles (Image2D property) (Image3D property)

anonymiseDicom() (in module opentps.core.io.dicomAnonymizer) APIInterpreter (class in opentps.core) append() (ObjectivesList method) (PatientList method) appendBeam() (RTPlan method) appendContour() (RTStruct method) appendDVH() (DVHPlot method) appendGridElement() (Grid method) appendLayer() (PlanIonBeam method) (RTPlan method) appendPatientData() (Patient method) appendPatientDataList() (Patient method) appendROI() (DVHViewer method) appendSpot() (PlanIonLayer method) (RTPlan method) applyBaselineShift() (in module opentps.core.processing.imageProcessing.syntheticDeformation) applyMorphonsKernels() (in module opentps.core.processing.registration.registrationMorphons) applyTemplate() (ROITable method) applyThreshold() (in module opentps.core.processing.segmentation.segmentation3D) applyTransform3D() (in module opentps.core.processing.imageProcessing.cupyImageProcessing) (in module opentps.core.processing.imageProcessing.imageTransform3D) (in module opentps.core.processing.imageProcessing.sitkImageProcessing) applyTransform3DToImage3D() (in module opentps.core.processing.imageProcessing.cupyImageProcessing) (in module opentps.core.processing.imageProcessing.sitkImageProcessing) applyTransform3DToPoint() (in module opentps.core.processing.imageProcessing.sitkImageProcessing) applyTransform3DToVectorField3D() (in module opentps.core.processing.imageProcessing.cupyImageProcessing) (in module opentps.core.processing.imageProcessing.sitkImageProcessing) ARCPTPlanOptimizer (class in opentps.core.processing.planOptimization.planOptimization) arrayToDS() (in module opentps.core.io.dicomIO) asContextMenu() (PatientDataMenu method) asROIMaskForViewer() (ROIContourForViewer method) AUTO (DataViewer.DropModes attribute) AXIAL (Image3DViewer.ViewerTypes attribute)

B

Backtracking (class in opentps.core.processing.planOptimization.acceleration.backtracking) BaseFunc (class in opentps.core.processing.planOptimization.objectives.baseFunction) BaseProj (class in opentps.core.processing.planOptimization.objectives.projections) BDL (class in opentps.core.data.MCsquare) bdlFile (DoseCalculationConfig property) BDLWithSpotTilt (class in opentps.core.data.MCsquare) beamCumulativeMetersetWeight (RTPlan property) BeamDialog (class in opentps.gui.panels.planDesignPanel.beamDialog) BeamInitializer (class in opentps.core.processing.planOptimization.planInitializer) BeamLayer (class in opentps.gui.viewer.dataViewerComponents.imageViewerComponents.rtPlanLayer) BeamLayer_3D (class in opentps.gui.viewer.dataViewerComponents.imageViewerComponents.rtplanLayer_3D) beamletPrimaries (DoseCalculationConfig property)

beamModel (AbstractDoseCalculator property) (AbstractDoseInfluenceCalculator property) (MCsquareDoseCalculator property) beams (RTPlan property) BFGS (class in opentps.core.processing.planOptimization.solvers.bfgs) BlackEmptyPlot (class in opentps.gui.viewer.dataViewerComponents.blackEmptyPlot) BLFree (class in opentps.core.processing.planOptimization.solvers.beamletFree) BoundConstraintsOptimizer (class in opentps.core.processing.planOptimization.planOptimization) braces (PythonHighlighter attribute) BreathingSignalPanel (class in opentps.gui.panels.breathingSignalPanel) buildDataTree() (PatientDataTree method) buildPlan() (PlanDesign method)

C

cachedDynamicImage2DViewer (DataViewer property) cachedDynamicImage3DViewer (DataViewer property) cachedStaticDVHViewer (DataViewer property) cachedStaticImage2DViewer (DataViewer property) cachedStaticImage3DViewer (DataViewer property) cachedStaticImage3DViewer_3D (DataViewer property) cachedStaticProfileViewer (DataViewer property) callback (ProfileWidget property) cap() (BaseFunc method) centerOfMass (ROIMask property) checkIfUpdate() (DynamicDisplayController method) clear() (DVHCurve method) (DVHPlot method) (DVHViewer method) close() (BeamLayer method) (BeamLayer_3D method) (ContourLayer method) (CrossHairLayer method) (PolyData3DLayer_3D method) (PrimaryImage2DLayer method) (PrimaryImage3DLayer method) (PrimaryImage3DLayer_3D method) (RTPlanLayer method) (RTPlanLayer_3D method) (ScriptingFileView method) (SecondaryImage2DLayer method) (SecondaryImage3DLayer method) (TextLayer method) (vtkContour method) closeEvent() (CropWidget method) (DataViewer method) (GridFourElements method) (Image2DViewer method) (Image3DViewer method) (Image3DViewer_3D method) (MainWindow method) (ObjectivesWidget method) (PatientComboBox method) (PatientDataComboBox method) (PatientDataTree method) (ROITable method) (ViewerPanel method) closeMask() (in module opentps.core.processing.imageProcessing.cupyImageProcessing) (ROIMask method) color (ROIContour property) (ROIMask property) colorbarOn (SecondaryImage2DLayer property) (SecondaryImage3DLayer property) compareModels() (in module opentps.core.processing.dataComparison.dynamic3DModelComparison) comparisonMetric (DoseComparisonDataViewer property) (DoseComparisonImageProvider property) compute() (in module opentps.core.processing.registration.midPosition) (RegistrationDemons method) (RegistrationMorphons method) (RegistrationQuick method) (RegistrationRigid method) (RegistrationTranslation method) compute3DStructuralElement() (in module opentps.core.processing.segmentation.segmentationCT) compute_band_Dx() (DVHBand method) compute_metrics() (DVHBand method) compute_position_from_range() (in module opentps.core.processing.C_libraries.libRayTracing_wrapper) computeBeamlets() (AbstractDoseInfluenceCalculator method) (MCsquareDoseCalculator method) computeBeamletsAndLET() (MCsquareDoseCalculator method) computeCumulativeWEPL() (RSPImage method) computeDcc() (DVH method) computeDose() (AbstractDoseCalculator method) (MCsquareDoseCalculator method) (PlanOptimizer method) computeDoseAndLET() (MCsquareDoseCalculator method) computeDRRSequence() (in module opentps.core.processing.imageSimulation.DRRToolBox) computeDRRSet() (in module opentps.core.processing.imageSimulation.DRRToolBox) computeDVH() (DVH method) computeDVHBand() (PlanDeliverySimulation method) computeDVHBand4DDD() (PlanDeliverySimulation method) computeDx() (DVH method) computeELSparsity() (WeightStructure method) computeFidelityFunction() (DoseFidelity method) computeFidelityGradient() (DoseFidelity method) computeFieldNorm() (VectorField3D method) computeImageDifference() (Registration method) computeIrradiationTime() (WeightStructure method) computeMU2Protons() (BDL method) computeNOfLayers() (WeightStructure method) computePhaseRatio() (in module opentps.core.processing.deformableDataAugmentationToolBox.generateDynamicSequencesFromModel) computeRobustnessScenarios() (PlanEvaluationPanel method)

computeRobustScenario() (MCsquareDoseCalculator method) computeRobustScenarioBeamlets() (MCsquareDoseCalculator method) computeSSD() (Registration method) computeTargetMSE() (Robustness method) computeVg() (DVH method) computeVx() (DVH method) configure() (loggerConfig method) conformityIndex() (DVH method) connect() (Event method) connectComponents() (in module opentps.core.processing.imageProcessing.sitkImageProcessing) connectIfNotAlready() (Event method) connectToolBar() (DynamicDisplayController method) contour (ROIItem property) ContourLayer (class in opentps.gui.viewer.dataViewerComponents.imageViewerComponents.contourLayer) contourLayer (ProfileWidget property) contours (ContourLayer property) (RTStruct property) contoursConfig (ExportConfig property) convertHU2MassDensity() (AbstractCTCalibration method) (MCsquareCTCalibration method), [1] (PiecewiseHU2Density method) (RayStationCTCalibration method) convertHU2RSP() (AbstractCTCalibration method) (MCsquareCTCalibration method), [1] (RayStationCTCalibration method) convertHU2SP() (MCsquareHU2Material method) convertMassDensity2HU() (AbstractCTCalibration method) (MCsquareCTCalibration method), [1] (PiecewiseHU2Density method) (RayStationCTCalibration method) convertMassDensity2RSP() (AbstractCTCalibration method) (MCsquareCTCalibration method), [1] (RayStationCTCalibration method) convertMaterial2HU() (MCsquareCTCalibration method), [1] (MCsquareHU2Material method) convertRSP2HU() (AbstractCTCalibration method) (MCsquareCTCalibration method), [1] (RayStationCTCalibration method) convertRSP2MassDensity() (AbstractCTCalibration method) (MCsquareCTCalibration method), [1] (RayStationCTCalibration method) convertSP2HU() (MCsquareHU2Material method) ConvexSolver (class in opentps.core.processing.planOptimization.solvers.solver) copy() (CTImage method) (Deformation3D method) (DoseImage method) (Image3D method) (MRImage method) (PlanIonBeam method) (PlanIonLayer method) (ROIMask method) (RTPlan method) (Transform3D method) (VectorField3D method) copyIntoNewObject() (in module opentps.core.io.serializedObjectIO) CORONAL (Image3DViewer.ViewerTypes attribute) correlations() (BDL method) count() (ProfileViewer method) createBeams() (PlanDesign method) createDRRDynamic2DSequences() (in module opentps.core.processing.imageSimulation.DRRToolBox) createEmptyBeamWithSameMetaData() (PlanIonBeam method) createEmptyDoseWithSameMetaData() (DoseImage class method) createEmptyLayerWithSameMetaData() (PlanIonLayer method) createEmptyPlanWithSameMetaData() (RTPlan method) createExternalPoints() (in module opentps.core.processing.deformableDataAugmentationToolBox.weightMaps) createMaskRings() (ROIMask method) createModel() (LP method) (MIP method) createWeightMaps() (in module opentps.core.processing.deformableDataAugmentationToolBox.weightMaps) crop2DDataAroundBox() (in module opentps.core.processing.imageProcessing.crop2D) crop3DDataAroundBox() (in module opentps.core.processing.imageProcessing.resampler3D) CropWidget (class in opentps.gui.tools) crossHairEnabled (Image2DViewer property) (Image3DViewer property) (ViewController property) CrossHairLayer (class in opentps.gui.viewer.dataViewerComponents.imageViewerComponents.crossHairLayer) ct (MCsquareDoseCalculator property) ct3DLT() (in module opentps.gui.viewer.dataViewerComponents.imageViewerComponents.lookupTables) ctCalibration (AbstractDoseCalculator property) (AbstractDoseInfluenceCalculator property) (MCsquareDoseCalculator property) CTImage (class in opentps.core.data.images) currentIndexIn2DSeq (Dyn2DSeqForViewer property) currentIndexIn3DSeq (Dyn3DSeqForViewer property) currentPatient (ViewController property) currentViewer (DataViewer property)

D

D2 (DVH property) D5 (DVH property) D50 (DVH property) D95 (DVH property) D98 (DVH property) DataExplorer (class in opentps.gui.viewer.dataExplorer) DataMultiton (class in opentps.gui.viewer.dataForViewer.dataMultiton) DataType (class in opentps.core.io.dataExporter) DataViewer (class in opentps.gui.viewer.dataViewer) DataViewer.DisplayModes (class in opentps.gui.viewer.dataViewer) DataViewer.DisplayTypes (class in opentps.gui.viewer.dataViewer) DataViewer.DropModes (class in opentps.gui.viewer.dataViewer) DataViewerToolbar (class in opentps.gui.viewer.dataViewerComponents.dataViewerToolbar) decode_long() (in module opentps.core.utils.pickel2) DEFAULT (DataViewer.DisplayModes attribute) (DataViewer.DisplayTypes attribute) (DataViewer.DropModes attribute) (DoseComparisonImageProvider.Metric attribute) (Image3DViewer.ViewerTypes attribute) (Robustness.Strategies attribute) (ViewerPanel.LayoutTypes attribute) DEFAULT_OBJECTIVES_TEXT (ObjectivesWidget attribute) DEFAULT_WEIGHT (ROITable attribute) defineTargetMaskAndPrescription() (PlanDesign method) Deformation3D (class in opentps.core.data.images) deformData() (Transform3D method) deformImage() (Deformation3D method) (Transform3D method) deformImageAndMask() (in module opentps.core.processing.deformableDataAugmentationToolBox.multiProcSpawnMethods) delete_item() (PlanDesignPanel method) DICOM (ExportTypes attribute) dicomCoordinate2iecGantry() (in module opentps.core.processing.imageProcessing.imageTransform3D) dicomToIECGantry() (in module opentps.core.processing.imageProcessing.imageTransform3D) dictionarizeData() (in module opentps.core.io.serializedObjectIO) DIFFERENCE (DoseComparisonImageProvider.Metric attribute) dilateMask() (in module opentps.core.processing.imageProcessing.cupyImageProcessing) (in module opentps.core.processing.imageProcessing.sitkImageProcessing) (ROIMask method) DISABLED (Robustness.Strategies attribute) disconnect() (Event method) disconnectAll() (PatientDataItem method) DISPLAY_DVH (DataViewer.DisplayTypes attribute) DISPLAY_IMAGE2D (DataViewer.DisplayTypes attribute) DISPLAY_IMAGE3D (DataViewer.DisplayTypes attribute) DISPLAY_IMAGE3D_3D (DataViewer.DisplayTypes attribute) DISPLAY_PROFILE (DataViewer.DisplayTypes attribute) displayLayoutType (ViewController property) displayMode (DataViewer property) displayType (DataViewer property) divergences() (BDL method) dlogCols() (LogBarrier method) Dmax (DVH property) DMAX (FidObjective.Metrics attribute) DMAX_THRESH (ROITable attribute) Dmean (DVH property) DMEAN (FidObjective.Metrics attribute) DMEAN_THRESH (ROITable attribute) Dmin (DVH property)

DMIN (FidObjective.Metrics attribute) DMIN_THRESH (ROITable attribute) dose (DVH property) (DVHViewer property) dose1 (DoseComparisonImageProvider property) (ViewController property) dose2 (DoseComparisonImageProvider property) (DVHViewer property) (ViewController property) DoseCalculationConfig (class in opentps.core.processing.doseCalculation.doseCalculationConfig) DoseComparisonDataViewer (class in opentps.gui.viewer.doseComparisonDataViewer) doseComparisonDataViewer (ImageViewerActions property) doseComparisonImage (DoseComparisonImageProvider property) DoseComparisonImageProvider (class in opentps.gui.viewer.dataViewerComponents.doseComparisonImageProvider) DoseComparisonImageProvider.Metric (class in opentps.gui.viewer.dataViewerComponents.doseComparisonImageProvider) DoseComparisonMenu (class in opentps.gui.viewer.dataViewerComponents.imageViewerActions) DoseComparisonPanel (class in opentps.gui.panels.doseComparisonPanel) DoseComputationPanel (class in opentps.gui.panels.doseComputationPanel) doseConfig (ExportConfig property) DoseFidelity (class in opentps.core.processing.planOptimization.objectives.doseFidelity) doseGridSize (SparseBeamlets property) DoseImage (class in opentps.core.data.images) doseOrientation (SparseBeamlets property) doseOrigin (SparseBeamlets property) doseSpacing (SparseBeamlets property) DOSIMETRIC (Robustness.Strategies attribute) dragEnterEvent() (PatientDataTree method) drawProfile() (ProfileViewer method) dropEnabled (DataViewer property) (ViewerPanel property) dropMode (DataViewer property) (ViewController property) droppedImage (ViewController property) DroppedObject (class in opentps.gui.viewer.dataViewer) DroppedObject.DropTypes (class in opentps.gui.viewer.dataViewer) DRRsBinarizeAndCrop() (in module opentps.core.processing.imageSimulation.multiProcForkMethods) Dstd (DVH property) Dummy (class in opentps.core.processing.planOptimization.acceleration.baseAccel) (class in opentps.core.processing.planOptimization.objectives.baseFunction) dumpableCopy() (Deformation3D method) (DoseImage method) (Patient method) (PatientList method) DVH (class in opentps.core.data) DVHBand (class in opentps.gui.viewer.dataViewerComponents.dvhPlot) DVHCurve (class in opentps.gui.viewer.dataViewerComponents.dvhPlot) DVHPlot (class in opentps.gui.viewer.dataViewerComponents.dvhPlot) DVHs (DVHPlot property) DVHViewer (class in opentps.gui.viewer.dataViewerComponents.dvhPlot) DVHViewerActions (class in opentps.gui.viewer.dataViewerComponents.dvhViewerActions) Dyn2DSeqForViewer (class in opentps.gui.viewer.dataForViewer.dyn2DSeqForViewer) Dyn3DSeqForViewer (class in opentps.gui.viewer.dataForViewer.dyn3DSeqForViewer) DYNAMIC (DataViewer.DisplayModes attribute) dynamic2DSequences (Patient property) dynamic3DModels (Patient property) dynamic3DSequences (Patient property) DynamicDisplayController (class in opentps.gui.viewer.dynamicDisplayController) DynamicImage2DViewer (class in opentps.gui.viewer.dataViewerComponents.dynamicImage2DViewer) DynamicImage3DViewer (class in opentps.gui.viewer.dataViewerComponents.dynamicImage3DViewer)

E

EditableSetting (class in opentps.gui.programSettingEditor) emit() (Event method) (Patient.TypeConditionalEvent method) enabled (ProfileWidget property) enableDrop() (DataViewer method) encode_long() (in module opentps.core.utils.pickel2) EnergySeq (class in opentps.core.processing.planOptimization.objectives.energySequencing) energyToRange() (in module opentps.core.processing.rangeEnergy) energyToRangeMM() (in module opentps.core.processing.rangeEnergy) erase() (ProfileViewer method) erodeMask() (in module opentps.core.processing.imageProcessing.cupyImageProcessing) (ROIMask method) ERRORSPACE_REGULAR (Robustness.Strategies attribute) ERRORSPACE_STAT (Robustness.Strategies attribute) eval() (BaseFunc method) evaluateClinical() (in module opentps.core.processing.planOptimization.tools) Event (class in opentps.core) events() (in module opentps.core.processing.deformableDataAugmentationToolBox.BreathingSignalGeneration) exampleFolder (ProgramSettings property)

exponentiateField() (VectorField3D method) export() (ProfileViewer method) ExportConfig (class in opentps.core.io.dataExporter) exportConfig (ExportTable property) exportDicom() (DoseImage method) exportImage() (in module opentps.core.io.dataExporter) exportImageMHD() (in module opentps.core.io.mhdIO) exportPatient() (in module opentps.core.io.dataExporter) exportPatientAsDicom() (in module opentps.core.io.dataExporter) exportPlan() (in module opentps.core.io.dataExporter) ExportTable (class in opentps.gui.viewer.exportWindow) ExportTypes (class in opentps.core.io.dataExporter) ExportWindow (class in opentps.gui.viewer.exportWindow) extendAll() (in module opentps.core.processing.imageProcessing.imageTransform3D) ExtendedBeam (class in opentps.core.processing.planOptimization.planPreprocessing) ExtendedPlanIonLayer (class in opentps.core.processing.planOptimization.planPreprocessing) extendPlanLayers() (in module opentps.core.processing.planOptimization.planPreprocessing) extractROIAndRotationParams() (in module opentps.core.processing.trackingToolBox.NavigatorTracking) extremePoints() (in module opentps.core.processing.imageProcessing.sitkImageProcessing) extremePointsAfterTransform() (in module opentps.core.processing.imageProcessing.sitkImageProcessing)

F

FidObjective (class in opentps.core.data.plan) FidObjective.Metrics (class in opentps.core.data.plan) finalDosePrimaries (DoseCalculationConfig property) FISTA (class in opentps.core.processing.planOptimization.solvers.fista) FistaAccel (class in opentps.core.processing.planOptimization.acceleration.fistaAccel) FistaBacktracking (class in opentps.core.processing.planOptimization.acceleration.fistaAccel) floatToDS() (in module opentps.core.io.dicomIO) forceShiftInMask() (in module opentps.core.processing.imageProcessing.syntheticDeformation) format() (in module opentps.gui.panels.scriptingPanel.pythonHighlighter) formatBoundsForSolver() (BoundConstraintsOptimizer method) forwardProjection() (in module opentps.core.processing.imageSimulation.DRRToolBox) forwardProjectionTigre() (in module opentps.core.processing.imageSimulation.ForwardProjectorTigre) fromBeam() (ExtendedBeam class method) fromCT() (RSPImage class method) fromCTCalibration() (MCsquareCTCalibration class method), [1]

fromEvent() (Patient.TypeConditionalEvent class method) fromFile() (PiecewiseHU2Density class method) fromFiles() (MCsquareCTCalibration class method), [1] (MCsquareHU2Material class method) fromImage2D() (Image2D class method) fromImage3D() (CTImage class method) (DoseImage class method) (Image3D class method) (MRImage class method) (ROIMask class method) (RSPImage class method) fromLayer() (ExtendedPlanIonLayer class method) fromMCsquareElement() (MCsquareMolecule class method) fusionLT() (in module opentps.gui.viewer.dataViewerComponents.imageViewerComponents.lookupTables) fusionLTTo3DLT() (in module opentps.gui.viewer.dataViewerComponents.imageViewerComponents.lookupTables)

G

G4StopPow (class in opentps.core.data.CTCalibrations.MCsquareCalibration) GAMMA (DoseComparisonImageProvider.Metric attribute) gaussConv() (in module opentps.core.processing.imageProcessing.filter3D) gaussianSmoothing() (in module opentps.core.processing.imageProcessing.cupyImageProcessing) generateDefaultMetaData() (in module opentps.core.io.mhdIO) generateDeformationFromTrackers() (in module opentps.core.processing.deformableDataAugmentationToolBox.weightMaps) generateDeformationFromTrackersAndWeightMaps() (in module opentps.core.processing.deformableDataAugmentationToolBox.weightMaps) generateDeformationListFromBreathingSignalsAndModel() (in module opentps.core.processing.deformableDataAugmentationToolBox.generateDynamicSequencesFromModel) generateDynSeqFromBreathingSignalsAndModel() (in module opentps.core.processing.deformableDataAugmentationToolBox.generateDynamicSequencesFromModel) generateRandomDeformationsFromModel() (in module opentps.core.processing.deformableDataAugmentationToolBox.generateRandomSamplesFromModel) generateRandomImagesFromModel() (in module opentps.core.processing.deformableDataAugmentationToolBox.generateRandomSamplesFromModel) GenericImageForViewer (class in opentps.gui.viewer.dataForViewer.genericImageForViewer) get2DMaskCenterOfMass() (in module opentps.core.processing.imageProcessing.image2DManip) get_file_type() (in module opentps.core.io.dataLoader) get_SPR_at_position() (RSPImage method) getAverageFieldValueAroundPosition() (in module opentps.core.processing.deformableDataAugmentationToolBox.modelManipFunctions) getAverageModelValuesAroundPosition() (in module opentps.core.processing.deformableDataAugmentationToolBox.modelManipFunctions) getBeamStructure() (WeightStructure method) getBinaryContourMask() (ROIContour method) (ROIMask method) getBinaryMask() (ROIContour method) getBinaryMask_old() (ROIContour method) getBinaryMaskFromROIDRR() (in module opentps.core.processing.imageProcessing.image2DManip) getBoxAboveThreshold() (in module opentps.core.processing.segmentation.segmentation3D) getBoxAroundROI() (in module opentps.core.processing.imageProcessing.crop2D) (in module opentps.core.processing.segmentation.segmentation3D) getCenterOfMass() (ROIContour method) getConfigField() (AbstractApplicationConfig method) getContourByName() (RTStruct method) getConvergenceData() (IMPTPlanOptimizer method) (PlanOptimizer method) getDataAtPosition() (Image2D method) (Image3D method) getEnergyStructure() (WeightStructure method) getEnergyWeights() (in module opentps.core.processing.planOptimization.tools) getFieldValueAtPosition() (in module opentps.core.processing.deformableDataAugmentationToolBox.modelManipFunctions) getFolderFromMaterialNumber() (MCsquareMaterial static method) getHg() (LBFGS method) getHU2MaterialConversion() (MCsquareHU2Material method) getImageInCorrectOrientation() (in module opentps.core.processing.imageSimulation.DRRToolBox) getIndex() (PatientList method) getIndexFromPatientID() (PatientList method) getIndexFromPatientName() (PatientList method) getLayers() (ScanAlgoPlan method) getListOfActiveEnergies() (WeightStructure method) getListOfActiveLayersInBeams() (WeightStructure method) getMaterialFromName() (MCsquareHU2Material method)

getMaterialList() (MCsquareMaterial static method) getMaterialNumberFromName() (MCsquareMaterial static method) getMaterialNumbers() (MCsquareMaterial static method) getMeshGridPositions() (Image2D method) (Image3D method) getMUPerBeam() (WeightStructure method) getMUPerLayer() (WeightStructure method) getObjectiveTerms() (ObjectivesWindow method) (ROITable method) getPatientByData() (PatientList method) getPatientByPatientId() (PatientList method) getPatientDataOfType() (Patient method) getPhaseValueList() (in module opentps.core.processing.deformableDataAugmentationToolBox.generateDynamicSequencesFromModel) getPiecewiseHU2MassDensityConversion() (PiecewiseHU2Density method) getPositionFromVoxelIndex() (Image2D method) (Image3D method) getROIContour() (ROIMask method) getROIs() (ROITable method) getRotationAngles() (Transform3D method) getSaveFileName() (SaveData_dialog method) getSimulationProgress() (MCsquareDoseCalculator method) getSpotIndex() (WeightStructure method) getTemplate() (ROITable method) getTranslation() (Transform3D method) getTtransformMatrixInPixels() (in module opentps.core.processing.imageProcessing.imageTransform3D) getTypeAsString() (Patient method) (PatientData method) getVolume() (ROIMask method) getVoxelIndexFromPosition() (Image2D method) (Image3D method) (in module opentps.core.processing.imageProcessing.imageTransform3D) getWeightMapsAsImage3DList() (in module opentps.core.processing.deformableDataAugmentationToolBox.weightMaps) getWeightsStruct() (WeightStructure method) grad() (BaseFunc method) GradientDescent (class in opentps.core.processing.planOptimization.solvers.gradientDescent) grayLT() (in module opentps.gui.viewer.dataViewerComponents.imageViewerComponents.lookupTables) Grid (class in opentps.gui.viewer.grid) GRID_2BY2 (ViewerPanel.LayoutTypes attribute) gridElements (Grid property) GridFourElements (class in opentps.gui.viewer.gridFourElements) gridSize (Deformation3D property) (Image2D property) (Image3D property) (VectorField3D property) gridSizeInWorldUnit (Image2D property) (Image3D property) groupSol() (WeightStructure method) groupSpots() (WeightStructure method)

H

handleClick() (ROIItem method) hasPatientData() (Patient method) hasSameGrid() (Image2D method) (Image3D method) hide() (DVHViewerActions method) (ImageViewerActions method)

hideItem() (MainToolbar method) highlightBlock() (PythonHighlighter method) histogram (DVH property) homogeneityIndex() (DVH method)

I

iecGantryCoordinatetoDicom() (in module opentps.core.processing.imageProcessing.imageTransform3D) iecGantryToDicom() (in module opentps.core.processing.imageProcessing.imageTransform3D) IMAGE (DroppedObject.DropTypes attribute) image (PolyData3DLayer_3D property) (PrimaryImage2DLayer property) (PrimaryImage3DLayer property) (PrimaryImage3DLayer_3D property) Image2D (class in opentps.core.data.images) Image2DForViewer (class in opentps.gui.viewer.dataForViewer.image2DForViewer) image2DToSITK() (in module opentps.core.processing.imageProcessing.sitkImageProcessing) Image2DViewer (class in opentps.gui.viewer.dataViewerComponents.image2DViewer) Image3D (class in opentps.core.data.images) Image3DForViewer (class in opentps.gui.viewer.dataForViewer.image3DForViewer) image3DToSITK() (in module opentps.core.processing.imageProcessing.sitkImageProcessing) Image3DViewer (class in opentps.gui.viewer.dataViewerComponents.image3DViewer) Image3DViewer.ViewerTypes (class in opentps.gui.viewer.dataViewerComponents.image3DViewer) Image3DViewer_3D (class in opentps.gui.viewer.dataViewerComponents.image3DViewer_3D) imageArray (Image2D property) (Image3D property) imageConfig (ExportConfig property) ImageFusionPropEditor (class in opentps.gui.viewer.dataViewerComponents.imageFusionPropEditor) images (Patient property)

imageToSITK() (in module opentps.core.processing.imageProcessing.sitkImageProcessing) ImageViewerActions (class in opentps.gui.viewer.dataViewerComponents.imageViewerActions) importImageMHD() (in module opentps.core.io.mhdIO) imptMaxIter (PlanOptimizationConfig property) IMPTPlanOptimizer (class in opentps.core.processing.planOptimization.planOptimization) imptSolver (PlanOptimizationConfig property) independentScoringGrid (MCsquareDoseCalculator property) independentViewsEnabled (ViewController property) Indicator (class in opentps.core.processing.planOptimization.objectives.projections) initFromDisplacementField() (Deformation3D method) initFromImage() (Deformation3D method) (VectorField3D method) initFromTranslationAndRotationVectors() (Transform3D method) initFromVelocityField() (Deformation3D method) initializeBeam() (BeamInitializer method) initializeBeams() (PlanDesign method) initializeFidObjectiveFunction() (PlanOptimizer method) initializeWeights() (PlanOptimizer method) interpolateTrilinear() (in module opentps.core.processing.C_libraries.libInterp3_wrapper) isActivated() (WeightStructure method) isAscentOrDescentCase() (in module opentps.core.processing.deformableDataAugmentationToolBox.generateDynamicSequencesFromModel) items (MainToolbar property)

K

keywords (PythonHighlighter attribute)

kill() (MCsquareDoseCalculator method)

L

layerCumulativeMetersetWeight (RTPlan property) layers (PlanIonBeam property) (RTPlan property) layersIndices (ExtendedBeam property) layoutType (ViewerPanel property) LBFGS (class in opentps.core.processing.planOptimization.solvers.bfgs) LETImage (class in opentps.core.data.images) LineSearch (class in opentps.core.processing.planOptimization.acceleration.linesearch) List_RightClick() (PlanDesignPanel method) listAllFiles() (in module opentps.core.io.dataLoader) load() (G4StopPow method) (in module opentps.core.utils.pickel2) (MCsquareElement class method) (MCsquareMaterial class method) (MCsquareMolecule class method) (PiecewiseHU2Density method) (Robustness method) (RobustnessScenario method) (ScanAlgoPlan method)

loadBeamlets() (in module opentps.core.io.serializedObjectIO) loadData() (in module opentps.core.io.dataLoader) (in module opentps.core.io.serializedObjectIO) (PatientDataPanel method) loadDataStructure() (in module opentps.core.io.serializedObjectIO) loadMaterial() (MCsquareHU2Material method) loadRTPlan() (in module opentps.core.io.serializedObjectIO) loads() (in module opentps.core.utils.pickel2) loadSerializedObject() (in module opentps.core.io.serializedObjectIO) loadSolution() (WeightStructure method) LogBarrier (class in opentps.core.processing.planOptimization.objectives.logBarrier) logCols() (LogBarrier method) logFolder (ProgramSettings property) loggerConfig (class in opentps.core) loggingConfigFile (ProgramSettings property) lookForClosestIndex() (DynamicDisplayController method) lookupTable (GenericImageForViewer property) lookupTableName (GenericImageForViewer property) LP (class in opentps.core.processing.planOptimization.solvers.lp) LS (class in opentps.core.processing.planOptimization.solvers.localSearch)

M

mainImage (ViewController property) MainTestCase (class in opentps.gui.main) MainToolbar (class in opentps.gui.panels.mainToolbar) mainToolbar (ProgramSettingEditor property) MainToolbar.ToolbarItem (class in opentps.gui.panels.mainToolbar) MainWindow (class in opentps.gui.mainWindow) make1ContourFromSeveral() (RTStruct method) match_multiline() (PythonHighlighter method) matchProfiles() (in module opentps.core.processing.registration.registrationQuick) materialsOrderedForPrinting() (MCsquareHU2Material method) max() (Image3D method) MCSQUARE (ExportTypes attribute) mcsquareCalculationWindow (class in opentps.gui.panels.planOptimizationPanel.planOptiPanel) MCsquareConfig (class in opentps.core.data.MCsquare) MCsquareConfigEditor (class in opentps.gui.programSettingEditor) MCsquareCTCalibration (class in opentps.core.data.CTCalibrations) (class in opentps.core.data.CTCalibrations.MCsquareCalibration) MCsquareDoseCalculator (class in opentps.core.processing.doseCalculation.mcsquareDoseCalculator) MCsquareElement (class in opentps.core.data.CTCalibrations.MCsquareCalibration) mcsquareFormatted() (BDL method) (MCsquareConfig method) (MCsquareElement method) (MCsquareHU2Material method) (MCsquareMaterial method) (MCsquareMolecule method) (RangeShifter method) MCsquareHU2Material (class in opentps.core.data.CTCalibrations.MCsquareCalibration) MCsquareIOTestCase (class in opentps.core.io.mcsquareIO) MCsquareMaterial (class in opentps.core.data.CTCalibrations.MCsquareCalibration) MCsquareMolecule (class in opentps.core.data.CTCalibrations.MCsquareCalibration) meterset (PlanIonBeam property) (PlanIonLayer property) (RTPlan property) MHD (ExportTypes attribute) min() (Image3D method) MIP (class in opentps.core.processing.planOptimization.solvers.mip) module opentps opentps.core opentps.core.config opentps.core.config.logger opentps.core.data opentps.core.data.CTCalibrations opentps.core.data.CTCalibrations.MCsquareCalibration opentps.core.data.CTCalibrations.RayStationCalibration opentps.core.data.dynamicData opentps.core.data.images opentps.core.data.MCsquare opentps.core.data.plan opentps.core.io opentps.core.io.dataExporter opentps.core.io.dataLoader opentps.core.io.dicomAnonymizer opentps.core.io.dicomIO opentps.core.io.mcsquareIO opentps.core.io.mhdIO opentps.core.io.scannerReader opentps.core.io.serializedObjectIO opentps.core.processing opentps.core.processing.C_libraries opentps.core.processing.C_libraries.libInterp3_wrapper opentps.core.processing.C_libraries.libRayTracing_wrapper opentps.core.processing.dataComparison opentps.core.processing.dataComparison.dynamic3DModelComparison opentps.core.processing.dataComparison.metrics opentps.core.processing.deformableDataAugmentationToolBox opentps.core.processing.deformableDataAugmentationToolBox.BreathingSignalGeneration opentps.core.processing.deformableDataAugmentationToolBox.generateDynamicSequencesFromModel opentps.core.processing.deformableDataAugmentationToolBox.generateRandomSamplesFromModel opentps.core.processing.deformableDataAugmentationToolBox.modelManipFunctions opentps.core.processing.deformableDataAugmentationToolBox.multiProcSpawnMethods opentps.core.processing.deformableDataAugmentationToolBox.weightMaps opentps.core.processing.doseCalculation opentps.core.processing.doseCalculation.abstractDoseCalculator opentps.core.processing.doseCalculation.abstractDoseInfluenceCalculator opentps.core.processing.doseCalculation.abstractMCDoseCalculator opentps.core.processing.doseCalculation.doseCalculationConfig opentps.core.processing.doseCalculation.MCsquare opentps.core.processing.doseCalculation.MCsquare.BDL opentps.core.processing.doseCalculation.MCsquare.Materials opentps.core.processing.doseCalculation.MCsquare.Scanners opentps.core.processing.doseCalculation.mcsquareDoseCalculator opentps.core.processing.imageProcessing opentps.core.processing.imageProcessing.crop2D opentps.core.processing.imageProcessing.cupyImageProcessing opentps.core.processing.imageProcessing.filter3D opentps.core.processing.imageProcessing.image2DManip opentps.core.processing.imageProcessing.imageTransform3D opentps.core.processing.imageProcessing.resampler3D opentps.core.processing.imageProcessing.sitkImageProcessing opentps.core.processing.imageProcessing.syntheticDeformation opentps.core.processing.imageSimulation opentps.core.processing.imageSimulation.DRRToolBox opentps.core.processing.imageSimulation.ForwardProjectorTigre opentps.core.processing.imageSimulation.multiProcForkMethods opentps.core.processing.planDeliverySimulation opentps.core.processing.planDeliverySimulation.planDeliverySimulation opentps.core.processing.planEvaluation opentps.core.processing.planEvaluation.robustnessEvaluation opentps.core.processing.planOptimization opentps.core.processing.planOptimization.acceleration opentps.core.processing.planOptimization.acceleration.backtracking opentps.core.processing.planOptimization.acceleration.baseAccel opentps.core.processing.planOptimization.acceleration.fistaAccel opentps.core.processing.planOptimization.acceleration.linesearch opentps.core.processing.planOptimization.objectives opentps.core.processing.planOptimization.objectives.baseFunction opentps.core.processing.planOptimization.objectives.doseFidelity opentps.core.processing.planOptimization.objectives.energySequencing opentps.core.processing.planOptimization.objectives.logBarrier opentps.core.processing.planOptimization.objectives.norms opentps.core.processing.planOptimization.objectives.projections opentps.core.processing.planOptimization.optimizationWorkflows opentps.core.processing.planOptimization.planInitializer opentps.core.processing.planOptimization.planOptimization opentps.core.processing.planOptimization.planOptimizationConfig opentps.core.processing.planOptimization.planPreprocessing opentps.core.processing.planOptimization.solvers opentps.core.processing.planOptimization.solvers.beamletFree opentps.core.processing.planOptimization.solvers.bfgs opentps.core.processing.planOptimization.solvers.fista opentps.core.processing.planOptimization.solvers.gradientDescent opentps.core.processing.planOptimization.solvers.localSearch opentps.core.processing.planOptimization.solvers.lp opentps.core.processing.planOptimization.solvers.mip opentps.core.processing.planOptimization.solvers.solver opentps.core.processing.planOptimization.solvers.sparcling opentps.core.processing.planOptimization.tools opentps.core.processing.rangeEnergy opentps.core.processing.registration opentps.core.processing.registration.midPosition opentps.core.processing.registration.registration opentps.core.processing.registration.registrationDemons opentps.core.processing.registration.registrationMorphons opentps.core.processing.registration.registrationQuick opentps.core.processing.registration.registrationRigid opentps.core.processing.registration.registrationTranslation opentps.core.processing.segmentation opentps.core.processing.segmentation.segmentation3D opentps.core.processing.segmentation.segmentationCT opentps.core.processing.trackingToolBox opentps.core.processing.trackingToolBox.NavigatorTracking opentps.core.utils opentps.core.utils.applicationConfig opentps.core.utils.pickel2 opentps.core.utils.programSettings opentps.gui opentps.gui.main opentps.gui.mainWindow opentps.gui.panels opentps.gui.panels.breathingSignalPanel opentps.gui.panels.doseComparisonPanel opentps.gui.panels.doseComputationPanel opentps.gui.panels.mainToolbar opentps.gui.panels.patientDataPanel opentps.gui.panels.patientDataPanel.patientDataMenu opentps.gui.panels.patientDataPanel.patientDataPanel opentps.gui.panels.patientDataPanel.patientDataSelection opentps.gui.panels.patientDataWidgets opentps.gui.panels.planDesignPanel opentps.gui.panels.planDesignPanel.beamDialog opentps.gui.panels.planDesignPanel.planDesignPanel opentps.gui.panels.planDesignPanel.robustnessSettings opentps.gui.panels.planEvaluationPanel opentps.gui.panels.planOptimizationPanel opentps.gui.panels.planOptimizationPanel.objectivesWindow opentps.gui.panels.planOptimizationPanel.optimizationSettings opentps.gui.panels.planOptimizationPanel.planOptiPanel opentps.gui.panels.registrationPanel opentps.gui.panels.roiPanel opentps.gui.panels.scriptingPanel opentps.gui.panels.scriptingPanel.pythonHighlighter opentps.gui.panels.scriptingPanel.scriptingPanel opentps.gui.panels.scriptingPanel.scriptingWindow opentps.gui.programSettingEditor opentps.gui.statusBar opentps.gui.tools opentps.gui.viewController opentps.gui.viewer opentps.gui.viewer.dataExplorer opentps.gui.viewer.dataForViewer opentps.gui.viewer.dataForViewer.dataMultiton opentps.gui.viewer.dataForViewer.dyn2DSeqForViewer opentps.gui.viewer.dataForViewer.dyn3DSeqForViewer opentps.gui.viewer.dataForViewer.genericImageForViewer opentps.gui.viewer.dataForViewer.image2DForViewer opentps.gui.viewer.dataForViewer.image3DForViewer opentps.gui.viewer.dataForViewer.polyDataForViewer opentps.gui.viewer.dataForViewer.ROIContourForViewer opentps.gui.viewer.dataForViewer.ROIMaskForViewer opentps.gui.viewer.dataViewer opentps.gui.viewer.dataViewerComponents opentps.gui.viewer.dataViewerComponents.blackEmptyPlot opentps.gui.viewer.dataViewerComponents.dataViewerToolbar opentps.gui.viewer.dataViewerComponents.doseComparisonImageProvider opentps.gui.viewer.dataViewerComponents.dvhPlot opentps.gui.viewer.dataViewerComponents.dvhViewerActions opentps.gui.viewer.dataViewerComponents.dynamicImage2DViewer opentps.gui.viewer.dataViewerComponents.dynamicImage3DViewer opentps.gui.viewer.dataViewerComponents.image2DViewer opentps.gui.viewer.dataViewerComponents.image3DViewer opentps.gui.viewer.dataViewerComponents.image3DViewer_3D opentps.gui.viewer.dataViewerComponents.imageFusionPropEditor opentps.gui.viewer.dataViewerComponents.imageViewerActions opentps.gui.viewer.dataViewerComponents.imageViewerComponents opentps.gui.viewer.dataViewerComponents.imageViewerComponents.contourLayer opentps.gui.viewer.dataViewerComponents.imageViewerComponents.crossHairLayer opentps.gui.viewer.dataViewerComponents.imageViewerComponents.lookupTables opentps.gui.viewer.dataViewerComponents.imageViewerComponents.polyData3DLayer_3D opentps.gui.viewer.dataViewerComponents.imageViewerComponents.primaryImage2DLayer opentps.gui.viewer.dataViewerComponents.imageViewerComponents.primaryImage3DLayer opentps.gui.viewer.dataViewerComponents.imageViewerComponents.primaryImage3DLayer_3D opentps.gui.viewer.dataViewerComponents.imageViewerComponents.rtPlanLayer opentps.gui.viewer.dataViewerComponents.imageViewerComponents.rtplanLayer_3D opentps.gui.viewer.dataViewerComponents.imageViewerComponents.secondaryImage2DLayer opentps.gui.viewer.dataViewerComponents.imageViewerComponents.secondaryImage3DLayer opentps.gui.viewer.dataViewerComponents.imageViewerComponents.secondaryImage3DLayer_3D opentps.gui.viewer.dataViewerComponents.imageViewerComponents.textLayer opentps.gui.viewer.dataViewerComponents.patientDataPropertyEditor opentps.gui.viewer.dataViewerComponents.profileViewer opentps.gui.viewer.dataViewerComponents.profileWidget opentps.gui.viewer.doseComparisonDataViewer opentps.gui.viewer.dynamicDisplayController opentps.gui.viewer.exportWindow opentps.gui.viewer.grid opentps.gui.viewer.gridFourElements opentps.gui.viewer.viewerPanel opentps.gui.viewer.viewerToolbar

morphonsComplexConvD() (in module opentps.core.processing.registration.registrationMorphons) morphonsComplexConvS() (in module opentps.core.processing.registration.registrationMorphons) morphonsConv() (in module opentps.core.processing.registration.registrationMorphons) mouseMoveEvent() (PatientDataTree method) MRImage (class in opentps.core.data.images) multiProcDeform() (in module opentps.core.processing.deformableDataAugmentationToolBox.multiProcSpawnMethods) multiProcDRRs() (in module opentps.core.processing.imageSimulation.multiProcForkMethods)

N

name (DVH property) (Patient property) (PatientData property) nbPrimaries (AbstractMCDoseCalculator property) (MCsquareDoseCalculator property) nbProfiles (ProfileViewer property) newScriptFile() (ScriptingPanel method) newScriptingWindow() (ScriptingPanel method) newScriptingWindowSignal (ScriptingPanel attribute) nextImage() (DynamicImage2DViewer method) (DynamicImage3DViewer method)

NONE (DataViewer.DisplayTypes attribute) Norm (class in opentps.core.processing.planOptimization.objectives.norms) normGaussConv() (in module opentps.core.processing.imageProcessing.filter3D) NormL1 (class in opentps.core.processing.planOptimization.objectives.norms) NormL2 (class in opentps.core.processing.planOptimization.objectives.norms) NormL21 (class in opentps.core.processing.planOptimization.objectives.norms) numberOfFractionsPlanned (RTPlan property) numberOfSpots (PlanIonBeam property) (PlanIonLayer property) (RTPlan property) numberOfVoxels (Image3D property)

O

objective() (ConvexSolver method) objectives (ObjectivesWidget property) ObjectivesList (class in opentps.core.data.plan) ObjectivesWidget (class in opentps.gui.panels.planOptimizationPanel.planOptiPanel) ObjectivesWindow (class in opentps.gui.panels.planOptimizationPanel.objectivesWindow) onClick() (BreathingSignalPanel method) onDropEvent (ViewerPanel property) oneDimensionNavThreshold() (in module opentps.core.processing.trackingToolBox.NavigatorTracking) onLeftButtonPressed() (Image2DViewer method) (Image3DViewer method) onMouseMove() (Image2DViewer method) (Image3DViewer method) onProfileWidgetInteraction() (ProfileWidget method) onScroll() (Image2DViewer method) (Image3DViewer method) opacity (GenericImageForViewer property) openMask() (in module opentps.core.processing.imageProcessing.cupyImageProcessing) (ROIMask method) opentps module opentps.core module opentps.core.config module opentps.core.config.logger module opentps.core.data module opentps.core.data.CTCalibrations module opentps.core.data.CTCalibrations.MCsquareCalibration module opentps.core.data.CTCalibrations.RayStationCalibration module opentps.core.data.dynamicData module opentps.core.data.images module opentps.core.data.MCsquare module opentps.core.data.plan module opentps.core.io module opentps.core.io.dataExporter module opentps.core.io.dataLoader module opentps.core.io.dicomAnonymizer module opentps.core.io.dicomIO module opentps.core.io.mcsquareIO module opentps.core.io.mhdIO module opentps.core.io.scannerReader module opentps.core.io.serializedObjectIO module opentps.core.processing module opentps.core.processing.C_libraries module opentps.core.processing.C_libraries.libInterp3_wrapper module opentps.core.processing.C_libraries.libRayTracing_wrapper module opentps.core.processing.dataComparison module opentps.core.processing.dataComparison.dynamic3DModelComparison module opentps.core.processing.dataComparison.metrics module opentps.core.processing.deformableDataAugmentationToolBox module opentps.core.processing.deformableDataAugmentationToolBox.BreathingSignalGeneration module opentps.core.processing.deformableDataAugmentationToolBox.generateDynamicSequencesFromModel module opentps.core.processing.deformableDataAugmentationToolBox.generateRandomSamplesFromModel module opentps.core.processing.deformableDataAugmentationToolBox.modelManipFunctions module opentps.core.processing.deformableDataAugmentationToolBox.multiProcSpawnMethods module opentps.core.processing.deformableDataAugmentationToolBox.weightMaps module opentps.core.processing.doseCalculation module 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.MCsquare module opentps.core.processing.doseCalculation.MCsquare.BDL module opentps.core.processing.doseCalculation.MCsquare.Materials module opentps.core.processing.doseCalculation.MCsquare.Scanners module opentps.core.processing.doseCalculation.mcsquareDoseCalculator module opentps.core.processing.imageProcessing module 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 opentps.core.processing.imageProcessing.resampler3D module opentps.core.processing.imageProcessing.sitkImageProcessing module opentps.core.processing.imageProcessing.syntheticDeformation module opentps.core.processing.imageSimulation module opentps.core.processing.imageSimulation.DRRToolBox module opentps.core.processing.imageSimulation.ForwardProjectorTigre module opentps.core.processing.imageSimulation.multiProcForkMethods module opentps.core.processing.planDeliverySimulation module opentps.core.processing.planDeliverySimulation.planDeliverySimulation module opentps.core.processing.planEvaluation module opentps.core.processing.planEvaluation.robustnessEvaluation module opentps.core.processing.planOptimization module opentps.core.processing.planOptimization.acceleration module 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 opentps.core.processing.planOptimization.objectives module 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 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.solvers module 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 opentps.core.processing.planOptimization.tools module opentps.core.processing.rangeEnergy module opentps.core.processing.registration module

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 opentps.core.processing.segmentation module opentps.core.processing.segmentation.segmentation3D module opentps.core.processing.segmentation.segmentationCT module opentps.core.processing.trackingToolBox module opentps.core.processing.trackingToolBox.NavigatorTracking module opentps.core.utils module opentps.core.utils.applicationConfig module opentps.core.utils.pickel2 module opentps.core.utils.programSettings module opentps.gui module opentps.gui.main module opentps.gui.mainWindow module opentps.gui.panels module opentps.gui.panels.breathingSignalPanel module opentps.gui.panels.doseComparisonPanel module opentps.gui.panels.doseComputationPanel module opentps.gui.panels.mainToolbar module opentps.gui.panels.patientDataPanel module opentps.gui.panels.patientDataPanel.patientDataMenu module opentps.gui.panels.patientDataPanel.patientDataPanel module opentps.gui.panels.patientDataPanel.patientDataSelection module opentps.gui.panels.patientDataWidgets module opentps.gui.panels.planDesignPanel module opentps.gui.panels.planDesignPanel.beamDialog module opentps.gui.panels.planDesignPanel.planDesignPanel module opentps.gui.panels.planDesignPanel.robustnessSettings module opentps.gui.panels.planEvaluationPanel module opentps.gui.panels.planOptimizationPanel module opentps.gui.panels.planOptimizationPanel.objectivesWindow module opentps.gui.panels.planOptimizationPanel.optimizationSettings module opentps.gui.panels.planOptimizationPanel.planOptiPanel module opentps.gui.panels.registrationPanel module opentps.gui.panels.roiPanel module opentps.gui.panels.scriptingPanel module opentps.gui.panels.scriptingPanel.pythonHighlighter module opentps.gui.panels.scriptingPanel.scriptingPanel module opentps.gui.panels.scriptingPanel.scriptingWindow module opentps.gui.programSettingEditor module opentps.gui.statusBar module opentps.gui.tools module opentps.gui.viewController module opentps.gui.viewer module opentps.gui.viewer.dataExplorer module opentps.gui.viewer.dataForViewer module opentps.gui.viewer.dataForViewer.dataMultiton module opentps.gui.viewer.dataForViewer.dyn2DSeqForViewer module opentps.gui.viewer.dataForViewer.dyn3DSeqForViewer module opentps.gui.viewer.dataForViewer.genericImageForViewer module opentps.gui.viewer.dataForViewer.image2DForViewer module opentps.gui.viewer.dataForViewer.image3DForViewer module opentps.gui.viewer.dataForViewer.polyDataForViewer module opentps.gui.viewer.dataForViewer.ROIContourForViewer module opentps.gui.viewer.dataForViewer.ROIMaskForViewer module opentps.gui.viewer.dataViewer module opentps.gui.viewer.dataViewerComponents module opentps.gui.viewer.dataViewerComponents.blackEmptyPlot module opentps.gui.viewer.dataViewerComponents.dataViewerToolbar module opentps.gui.viewer.dataViewerComponents.doseComparisonImageProvider module opentps.gui.viewer.dataViewerComponents.dvhPlot module opentps.gui.viewer.dataViewerComponents.dvhViewerActions module opentps.gui.viewer.dataViewerComponents.dynamicImage2DViewer module opentps.gui.viewer.dataViewerComponents.dynamicImage3DViewer module opentps.gui.viewer.dataViewerComponents.image2DViewer module opentps.gui.viewer.dataViewerComponents.image3DViewer module opentps.gui.viewer.dataViewerComponents.image3DViewer_3D module opentps.gui.viewer.dataViewerComponents.imageFusionPropEditor module opentps.gui.viewer.dataViewerComponents.imageViewerActions module opentps.gui.viewer.dataViewerComponents.imageViewerComponents module opentps.gui.viewer.dataViewerComponents.imageViewerComponents.contourLayer module opentps.gui.viewer.dataViewerComponents.imageViewerComponents.crossHairLayer module opentps.gui.viewer.dataViewerComponents.imageViewerComponents.lookupTables module opentps.gui.viewer.dataViewerComponents.imageViewerComponents.polyData3DLayer_3D module opentps.gui.viewer.dataViewerComponents.imageViewerComponents.primaryImage2DLayer module opentps.gui.viewer.dataViewerComponents.imageViewerComponents.primaryImage3DLayer module opentps.gui.viewer.dataViewerComponents.imageViewerComponents.primaryImage3DLayer_3D module opentps.gui.viewer.dataViewerComponents.imageViewerComponents.rtPlanLayer module opentps.gui.viewer.dataViewerComponents.imageViewerComponents.rtplanLayer_3D module opentps.gui.viewer.dataViewerComponents.imageViewerComponents.secondaryImage2DLayer module opentps.gui.viewer.dataViewerComponents.imageViewerComponents.secondaryImage3DLayer module opentps.gui.viewer.dataViewerComponents.imageViewerComponents.secondaryImage3DLayer_3D module opentps.gui.viewer.dataViewerComponents.imageViewerComponents.textLayer module opentps.gui.viewer.dataViewerComponents.patientDataPropertyEditor module opentps.gui.viewer.dataViewerComponents.profileViewer module opentps.gui.viewer.dataViewerComponents.profileWidget module opentps.gui.viewer.doseComparisonDataViewer module opentps.gui.viewer.dynamicDisplayController module opentps.gui.viewer.exportWindow module opentps.gui.viewer.grid module opentps.gui.viewer.gridFourElements module opentps.gui.viewer.viewerPanel module opentps.gui.viewer.viewerToolbar module operators (PythonHighlighter attribute) optimize() (BoundConstraintsOptimizer method) (PlanOptimizer method) optimizeBeamletFree() (MCsquareDoseCalculator method) optimizeIMPT() (in module opentps.core.processing.planOptimization.optimizationWorkflows) OptiSettingsDialog (class in opentps.gui.panels.planOptimizationPanel.optimizationSettings) origin (Image2D property) (Image3D property) otherConfig (ExportConfig property)

P

parseRotCenter() (in module opentps.core.processing.imageProcessing.imageTransform3D) Patient (class in opentps.core.data) patient (ObjectivesWindow property) (PatientData property) (ROITable property) Patient.TypeConditionalEvent (class in opentps.core.data) PatientComboBox (class in opentps.gui.panels.patientDataPanel.patientDataSelection) PatientData (class in opentps.core.data) patientData (Patient property) PatientDataComboBox (class in opentps.gui.panels.patientDataWidgets) PatientDataItem (class in opentps.gui.panels.patientDataPanel.patientDataSelection) PatientDataMenu (class in opentps.gui.panels.patientDataPanel.patientDataMenu) PatientDataPanel (class in opentps.gui.panels.patientDataPanel.patientDataPanel) PatientDataPropertyEditor (class in opentps.gui.viewer.dataViewerComponents.patientDataPropertyEditor) PatientDataSelection (class in opentps.gui.panels.patientDataPanel.patientDataSelection) PatientDataTree (class in opentps.gui.panels.patientDataPanel.patientDataSelection) PatientList (class in opentps.core.data) patientList (ViewController property) patients (PatientList property) PAUSE_STATUS (ViewerToolbar attribute) PICKLE (ExportTypes attribute) PickleError PicklingError PiecewiseHU2Density (class in opentps.core.data.CTCalibrations) placeSpots() (PlanInitializer method) PLAN (DroppedObject.DropTypes attribute) plan (RTPlanLayer property) (RTPlanLayer_3D property) (ViewController property) planConfig (ExportConfig property) PlanDeliverySimulation (class in opentps.core.processing.planDeliverySimulation.planDeliverySimulation) PlanDesign (class in opentps.core.data.plan) planDesign (ObjectivesWidget property) (ObjectivesWindow property) (ROITable property) PlanDesignPanel (class in opentps.gui.panels.planDesignPanel.planDesignPanel) PlanEvaluationPanel (class in opentps.gui.panels.planEvaluationPanel) PlanInitializer (class in opentps.core.processing.planOptimization.planInitializer) PlanIonBeam (class in opentps.core.data.plan) PlanIonLayer (class in opentps.core.data.plan) PlanIonSpot (class in opentps.core.data.plan) PlanOptimizationConfig (class in opentps.core.processing.planOptimization.planOptimizationConfig) PlanOptimizer (class in opentps.core.processing.planOptimization.planOptimization)

PlanOptiPanel (class in opentps.gui.panels.planOptimizationPanel.planOptiPanel) plans (Patient property) PLAY_STATUS (ViewerToolbar attribute) playFaster() (DynamicDisplayController method) playOrPause() (DynamicDisplayController method) playSlower() (DynamicDisplayController method) PolyData3DLayer_3D (class in opentps.gui.viewer.dataViewerComponents.imageViewerComponents.polyData3DLayer_3D) PolyDataForViewer (class in opentps.gui.viewer.dataForViewer.polyDataForViewer) position (CrossHairLayer property) PositiveProj (class in opentps.core.processing.planOptimization.objectives.projections) post() (Accel method) (ConvexSolver method) postProcess() (PlanOptimizer method) pre() (Accel method) (ConvexSolver method) presets() (in module opentps.gui.viewer.dataViewerComponents.imageViewerActions) PRIMARY (DataViewer.DropModes attribute) primaryImage (DynamicImage2DViewer property) (DynamicImage3DViewer property) (Image2DViewer property) (Image3DViewer property) (Image3DViewer_3D property) PrimaryImage2DLayer (class in opentps.gui.viewer.dataViewerComponents.imageViewerComponents.primaryImage2DLayer) PrimaryImage3DLayer (class in opentps.gui.viewer.dataViewerComponents.imageViewerComponents.primaryImage3DLayer) PrimaryImage3DLayer_3D (class in opentps.gui.viewer.dataViewerComponents.imageViewerComponents.primaryImage3DLayer_3D) PrimaryImageMenu (class in opentps.gui.viewer.dataViewerComponents.imageViewerActions) primaryLayer (ProfileWidget property) primaryText (TextLayer property) print_ROINames() (RTStruct method) printInfo() (Robustness method) (RobustnessScenario method) ProfileViewer (class in opentps.gui.viewer.dataViewerComponents.profileViewer) ProfileWidget (class in opentps.gui.viewer.dataViewerComponents.profileWidget) ProfileWidget.ProfileWidgetCallback (class in opentps.gui.viewer.dataViewerComponents.profileWidget) profileWidgetEnabled (Image2DViewer property) (Image3DViewer property) (ViewController property) ProgramSettingEditor (class in opentps.gui.programSettingEditor) ProgramSettings (class in opentps.core.utils.programSettings) programSettings (ProgramSettingEditor property) programSettingsFolder (ProgramSettings property) Projection (class in opentps.core.data.images) prox() (BaseFunc method) PythonHighlighter (class in opentps.gui.panels.scriptingPanel.pythonHighlighter)

R

range (GenericImageForViewer property) RangeEditor (class in opentps.gui.viewer.dataViewerComponents.imageFusionPropEditor) rangeMMToEnergy() (in module opentps.core.processing.rangeEnergy) RangeShifter (class in opentps.core.data.plan) rangeToEnergy() (in module opentps.core.processing.rangeEnergy) RayStationCTCalibration (class in opentps.core.data.CTCalibrations) readBDL() (in module opentps.core.io.mcsquareIO) readBeamlets() (in module opentps.core.io.mcsquareIO) readBinaryMHD() (in module opentps.core.io.mhdIO) readData() (in module opentps.core.io.dataLoader) readDicomCT() (in module opentps.core.io.dicomIO) readDicomDose() (in module opentps.core.io.dicomIO) readDicomMRI() (in module opentps.core.io.dicomIO) readDicomPlan() (in module opentps.core.io.dicomIO) readDicomStruct() (in module opentps.core.io.dicomIO) readDicomVectorField() (in module opentps.core.io.dicomIO) readDose() (in module opentps.core.io.mcsquareIO) readHeaderMHD() (in module opentps.core.io.mhdIO) readMCsquareMHD() (in module opentps.core.io.mcsquareIO) readMCsquarePlan() (in module opentps.core.io.mcsquareIO) readScanner() (in module opentps.core.io.scannerReader) readSingleData() (in module opentps.core.io.dataLoader) recompute_margin() (RobustnessSettingsDialog method) recompute_robustness_analysis() (PlanEvaluationPanel method) recomputeDVH() (Robustness method) referenceImage (ContourLayer property) (ROIContourForViewer property) refreshFunct() (BreathingSignalPanel method) RefreshRateDialog (class in opentps.gui.viewer.viewerToolbar) register() (in module opentps.core.processing.imageProcessing.sitkImageProcessing) Registration (class in opentps.core.processing.registration.registration) RegistrationDemons (class in opentps.core.processing.registration.registrationDemons) RegistrationMorphons (class in opentps.core.processing.registration.registrationMorphons) RegistrationPanel (class in opentps.gui.panels.registrationPanel) RegistrationQuick (class in opentps.core.processing.registration.registrationQuick) RegistrationRigid (class in opentps.core.processing.registration.registrationRigid) RegistrationTranslation (class in opentps.core.processing.registration.registrationTranslation) regularizeField() (Registration method) rejectFunct() (BreathingSignalPanel method) reloadColor() (vtkContour method) reloadFromFS() (SparseBeamlets method) remove() (PatientList method) removeBeam() (RTPlan method) removeBeams() (SPArCling method) removeContour() (RTStruct method) removeDVH() (DVHPlot method) removeDynamicButtons() (ViewerToolbar method) removeDynamicViewer() (DynamicDisplayController method) removeGridElement() (Grid method) removeLayer() (PlanIonBeam method) removeLayers() (SPArCling method) removePatientData() (Patient method) removePatientDataList() (Patient method) removeProfile() (ProfileViewer method) removeROI() (DVHViewer method) removeROIMask() (ROIPanel method) removeRTStruct() (ROIPanel method) removeSpot() (PlanIonLayer method) removeZeroMUSpots() (PlanIonLayer method) reorderLayers() (PlanIonBeam method) reorderPlan() (RTPlan method) reorderSpots() (PlanIonLayer method) resample() (Deformation3D method) (Image3D method) (in module opentps.core.processing.imageProcessing.resampler3D) resampleCupy() (in module opentps.core.processing.imageProcessing.cupyImageProcessing) resampleFixedImage() (Registration method) resampleImage3D() (in module opentps.core.processing.imageProcessing.resampler3D) resampleImage3DOnImage3D() (in module opentps.core.processing.imageProcessing.resampler3D) resampleMovingImage() (Registration method)

resampleOn() (Image3D method) resampleOnImage3D() (in module opentps.core.processing.imageProcessing.resampler3D) resampleOpenMP() (in module opentps.core.processing.imageProcessing.resampler3D) ResampleWidget (class in opentps.gui.tools) reset() (Image2DViewer method) (Image3DViewer method) (Image3DViewer_3D method) resetDynamicParameters() (DynamicImage2DViewer method) (DynamicImage3DViewer method) resize() (in module opentps.core.processing.imageProcessing.sitkImageProcessing) resizeEvent() (GridFourElements method) (VerticalSplitter method) resliceAxes (BeamLayer property) (ContourLayer property) (PrimaryImage2DLayer property) (PrimaryImage3DLayer property) (RTPlanLayer property) (vtkContour property) resliceDataFromPhysicalPoint() (ContourLayer method) (PrimaryImage2DLayer method) (PrimaryImage3DLayer method) (vtkContour method) resultFolder (ProgramSettings property) return_parameters() (RobustnessSettingsDialog method) returnParameters() (OptiSettingsDialog method) Robustness (class in opentps.core.processing.planEvaluation.robustnessEvaluation) robustness (RobustnessSettings property) (RobustnessSettingsDialog property) Robustness.Strategies (class in opentps.core.processing.planEvaluation.robustnessEvaluation) Robustness_analysis_recomputed (PlanEvaluationPanel attribute) robustnessEnabled (ROITable property) RobustnessScenario (class in opentps.core.processing.planEvaluation.robustnessEvaluation) RobustnessSettings (class in opentps.gui.panels.planDesignPanel.robustnessSettings) RobustnessSettingsDialog (class in opentps.gui.panels.planDesignPanel.robustnessSettings) robustStrategie (RobustnessSettingsDialog property) roi (FidObjective property) Roi_name() (BreathingSignalPanel method) ROIContour (class in opentps.core.data) ROIContourForViewer (class in opentps.gui.viewer.dataForViewer.ROIContourForViewer) ROIItem (class in opentps.gui.panels.roiPanel) ROIMask (class in opentps.core.data.images) ROIMaskForViewer (class in opentps.gui.viewer.dataForViewer.ROIMaskForViewer) roiMasks (Patient property) roiName (FidObjective property) ROIPanel (class in opentps.gui.panels.roiPanel) rois (DVHViewer property) ROITable (class in opentps.gui.panels.planOptimizationPanel.objectivesWindow) rotate3DVectorFields() (in module opentps.core.processing.imageProcessing.cupyImageProcessing) rotateData() (in module opentps.core.processing.imageProcessing.cupyImageProcessing) (in module opentps.core.processing.imageProcessing.imageTransform3D) (in module opentps.core.processing.imageProcessing.sitkImageProcessing) rotateImage3D() (in module opentps.core.processing.imageProcessing.cupyImageProcessing) rotateUsingMapCoordinatesCupy() (in module opentps.core.processing.imageProcessing.cupyImageProcessing) rotateVectorsInPlace() (in module opentps.core.processing.imageProcessing.imageTransform3D) rsp (MCsquareMolecule property) RSPImage (class in opentps.core.data.images) RTPlan (class in opentps.core.data.plan) rtPlan (Image2DViewer property) (Image3DViewer property) (Image3DViewer_3D property) RTPlanLayer (class in opentps.gui.viewer.dataViewerComponents.imageViewerComponents.rtPlanLayer) RTPlanLayer_3D (class in opentps.gui.viewer.dataViewerComponents.imageViewerComponents.rtplanLayer_3D) RTPlanMenu (class in opentps.gui.viewer.dataViewerComponents.imageViewerActions) RTStruct (class in opentps.core.data) rtStructs (Patient property) run() (APIInterpreter static method) (in module opentps.gui) (in module opentps.gui.main) runWithMainWindow() (in module opentps.gui) (in module opentps.gui.main)

S

SAGITTAL (Image3DViewer.ViewerTypes attribute) save() (Robustness method) (RobustnessScenario method) (ScanAlgoPlan method) saveBeamlets() (in module opentps.core.io.serializedObjectIO) saveData() (in module opentps.core.io.serializedObjectIO) (PatientDataPanel method) SaveData_dialog (class in opentps.gui.panels.patientDataPanel.patientDataPanel) saveDataStructure() (in module opentps.core.io.serializedObjectIO) saveRTPlan() (in module opentps.core.io.serializedObjectIO) saveSerializedObjects() (in module opentps.core.io.serializedObjectIO) ScanAlgoPlan (class in opentps.core.data.plan) scannerFolder (DoseCalculationConfig property) ScipyOpt (class in opentps.core.processing.planOptimization.solvers.bfgs) scoringGridSize (MCsquareDoseCalculator property) (PlanDesign property) scoringOrigin (MCsquareDoseCalculator property) (PlanDesign property) scoringVoxelSpacing (MCsquareDoseCalculator property) (PlanDesign property) ScriptingFileView (class in opentps.gui.panels.scriptingPanel.scriptingPanel) ScriptingPanel (class in opentps.gui.panels.scriptingPanel.scriptingPanel) ScriptingWindow (class in opentps.gui.panels.scriptingPanel.scriptingWindow) SECONDARY (DataViewer.DropModes attribute) secondaryImage (DynamicImage2DViewer property) (DynamicImage3DViewer property) (Image2DViewer property) (Image3DViewer property) (Image3DViewer_3D property) (ViewController property) SecondaryImage2DLayer (class in opentps.gui.viewer.dataViewerComponents.imageViewerComponents.secondaryImage2DLayer) SecondaryImage3DLayer (class in opentps.gui.viewer.dataViewerComponents.imageViewerComponents.secondaryImage3DLayer) SecondaryImage3DLayer_3D (class in opentps.gui.viewer.dataViewerComponents.imageViewerComponents.secondaryImage3DLayer_3D) secondaryImageLayer (Image2DViewer property) (Image3DViewer property) SecondaryImageMenu (class in opentps.gui.viewer.dataViewerComponents.imageViewerActions) secondaryLayer (ProfileWidget property) secondaryText (TextLayer property) SegmentationCT (class in opentps.core.processing.segmentation.segmentationCT) segmentBody() (SegmentationCT method) segmentBones() (SegmentationCT method) segmentLungs() (SegmentationCT method) selectedCT (DoseComputationPanel property) (PlanOptiPanel property) selectedData (PatientDataComboBox property) (PatientDataMenu property) (PatientDataSelection property) selectedImage (ViewController property) selectedPlan (DoseComputationPanel property) (PlanEvaluationPanel property) selectedPlanStructure (PlanOptiPanel property) selectedPosition (GenericImageForViewer property) setBeam() (BeamLayer method) (BeamLayer_3D method) setCenter() (Transform3D method) setConfigField() (AbstractApplicationConfig method) setContourData (ProfileWidget.ProfileWidgetCallback property) setCrossHairEnabled() (Image2DViewer method) (Image3DViewer method) setCT() (mcsquareCalculationWindow method) setCurrentPatient() (DoseComparisonPanel method) (DoseComputationPanel method) (PlanDesignPanel method) (PlanEvaluationPanel method) (PlanOptiPanel method) (RegistrationPanel method) (ROIPanel method) setDisplacement() (Deformation3D method) setDisplacementArray() (Deformation3D method) setDisplacementArrayXYZ() (Deformation3D method) setDisplayTypeAndMode() (DataViewer method) setEqualSize() (GridFourElements method) (VerticalSplitter method) setFrameOfReferenceUID() (in module opentps.core.io.dicomIO) setFusion() (DoseComparisonMenu method) (SecondaryImageMenu method) setImageViewer() (ImageViewerActions method) setInitialPosition() (ProfileWidget method) setInstructionText() (StatusBar method) setLateralToolbar() (MainWindow method) setMainPanel() (MainWindow method) setMainToolbar() (ProgramSettingEditor static method) setMatrix4x4() (Transform3D method) setName() (PatientData method) (PatientDataItem method) setNewContour() (ContourLayer method) (Image3DViewer_3D method) setNominal() (Robustness method) setPatient() (ObjectivesWidget method) (PatientData method) (PatientDataComboBox method) setPiecewiseHU2MassDensityConversion() (PiecewiseHU2Density method) setPlan() (mcsquareCalculationWindow method) (RTPlanLayer method) (RTPlanLayer_3D method) setPrimaryImageData (ProfileWidget.ProfileWidgetCallback property)

setPrimaryTextLine() (TextLayer method) setProfileWidgetEnabled() (Image2DViewer method) (Image3DViewer method) setProgramSettings() (ProgramSettingEditor static method) setRangeValue() (RangeEditor method) setRefreshRate() (DynamicDisplayController method) setROI() (Registration method) setScoringParameters() (MCsquareDoseCalculator method) (PlanDesign method) setSecondaryImageData (ProfileWidget.ProfileWidgetCallback property) setSecondaryTextLine() (TextLayer method) setSpatialReferencingFromImage() (SparseBeamlets method) setSpot() (PlanIonLayer method) setTarget() (ObjectivesList method) (Robustness method) setToolBar() (DynamicDisplayController method) setUnitaryBeamlets() (SparseBeamlets method) setValue() (EditableSetting method) setVelocity() (Deformation3D method) setVelocityArray() (Deformation3D method) setVelocityArrayXYZ() (Deformation3D method) setVisible() (vtkContour method) setWorkspace() (ProgramSettingEditor method) setWWLEnabled() (Image2DViewer method) (Image3DViewer method) shape (SparseBeamlets property) show() (DVHViewerActions method) (Image3DViewer_3D method) (ImageViewerActions method) showContour() (ViewController method) showItem() (MainToolbar method) showPoints() (in module opentps.core.processing.deformableDataAugmentationToolBox.weightMaps) shrinkOrgan() (in module opentps.core.processing.imageProcessing.syntheticDeformation) signal2DGeneration() (in module opentps.core.processing.deformableDataAugmentationToolBox.BreathingSignalGeneration) signal3DGeneration() (in module opentps.core.processing.deformableDataAugmentationToolBox.BreathingSignalGeneration) signalGeneration() (BreathingSignalPanel method) (in module opentps.core.processing.deformableDataAugmentationToolBox.BreathingSignalGeneration) simplify() (PlanIonBeam method) (PlanIonLayer method) (RTPlan method) simulate4DDose() (PlanDeliverySimulation method) simulate4DDynamicDose() (PlanDeliverySimulation method) simulate4DDynamicDoseScenarios() (PlanDeliverySimulation method) simulatePlanOnContinuousSequence() (PlanDeliverySimulation method) simulationDirectory (MCsquareDoseCalculator property) simulationFolder (ProgramSettings property) simulationFolderName (MCsquareDoseCalculator property) Singleton (class in opentps.core.utils.programSettings) sitkImageToImage2D() (in module opentps.core.processing.imageProcessing.sitkImageProcessing) sitkImageToImage3D() (in module opentps.core.processing.imageProcessing.sitkImageProcessing) sliderval() (RefreshRateDialog method) slots (Event property) solve() (BLFree method) (ConvexSolver method) (LP method) (ScipyOpt method) (SPArCling method) solveForwardBackward() (FISTA method) solveGeneralizedForwardBackward() (FISTA method) spacing (Image2D property) (Image3D property) SPArCling (class in opentps.core.processing.planOptimization.solvers.sparcling) SparseBeamlets (class in opentps.core.data) splitAscentDescentSubsets() (in module opentps.core.processing.deformableDataAugmentationToolBox.generateDynamicSequencesFromModel) splitBeams() (SPArCling method) spotDefinedInXY() (PlanIonLayer method) spotIndices (ExtendedPlanIonLayer property) spotIrradiationDurations (PlanIonBeam property) (PlanIonLayer property) (RTPlan property) spotMUs (PlanIonBeam property) (PlanIonLayer property) (RTPlan property) spots (ExtendedPlanIonLayer property) (PlanIonLayer property) spotSizes() (BDL method) spotTimings (PlanIonBeam property) (PlanIonLayer property) (RTPlan property) spotWeights (PlanIonLayer property) spotX (PlanIonLayer property) spotXY (PlanIonBeam property) (PlanIonLayer property) (RTPlan property) spotY (PlanIonLayer property) startScriptFolder (ProgramSettings property) STATIC (DataViewer.DisplayModes attribute) statUncertainty (MCsquareDoseCalculator property) StatusBar (class in opentps.gui.statusBar) stop_GPU_accelration() (PlanOptimizer method) stoppingPower() (MCsquareElement method) (MCsquareMolecule method) storeOnFS() (SparseBeamlets method) subClass() (DataMultiton method) sumMuInlayer() (NormL21 method) supportedTypes() (TwoRowElement method) switchDynamicMode() (DynamicDisplayController method)

T

testRun() (MainTestCase method) testViewController() (MainTestCase method) testWrite() (MCsquareIOTestCase method) TextLayer (class in opentps.gui.viewer.dataViewerComponents.imageViewerComponents.textLayer) toList() (G4StopPow method) toMCSquareCTCalibration() (RayStationCTCalibration method) toolsMenu (DataViewerToolbar property) toSparseMatrix() (SparseBeamlets method) Transform3D (class in opentps.core.data) transform3DMatrixFromTranslationAndRotationsVectors() (in module opentps.core.processing.imageProcessing.imageTransform3D)

translateAndComputeSSD() (Registration method) translateData() (in module opentps.core.processing.imageProcessing.cupyImageProcessing) (in module opentps.core.processing.imageProcessing.imageTransform3D) (in module opentps.core.processing.imageProcessing.sitkImageProcessing) translateDataByChangingOrigin() (in module opentps.core.processing.imageProcessing.imageTransform3D) translateOrigin() (Registration method) transport_spots_inside_target() (in module opentps.core.processing.C_libraries.libRayTracing_wrapper) transport_spots_inside_target_map() (in module opentps.core.processing.C_libraries.libRayTracing_wrapper) transport_spots_to_target() (in module opentps.core.processing.C_libraries.libRayTracing_wrapper) TwoRowElement (class in opentps.gui.viewer.dataViewerComponents.patientDataPropertyEditor)

U

unDictionarize() (in module opentps.core.io.serializedObjectIO) ungroupSol() (WeightStructure method) uniqueColorLT() (in module opentps.gui.viewer.dataViewerComponents.imageViewerComponents.lookupTables) uniqueColorLTTo3DLT() (in module opentps.gui.viewer.dataViewerComponents.imageViewerComponents.lookupTables) unload() (SparseBeamlets method) unload_blGPU() (DoseFidelity method) UnpicklingError update() (BeamLayer_3D method) (Image3D method) (Image3DViewer_3D method) (PolyData3DLayer_3D method) (PrimaryImage3DLayer_3D method) (RTPlanLayer_3D method)

Update_Breath_param() (BreathingSignalPanel method) update_sol() (Accel method) update_step() (Accel method) updateOptiParams() (OptiSettingsDialog method) updateRobustStrategy() (RobustnessSettingsDialog method) updateTable() (ROITable method) updateWeightsFromPlanPencil() (in module opentps.core.io.mcsquareIO) use_GPU_acceleration() (PlanOptimizer method)

V

VectorField3D (class in opentps.core.data.images) vectorSimulation() (in module opentps.core.processing.deformableDataAugmentationToolBox.BreathingSignalGeneration) VerticalSplitter (class in opentps.gui.viewer.gridFourElements) ViewController (class in opentps.gui.viewController) viewController (MainWindow property) viewController() (in module opentps.gui) (in module opentps.gui.main) ViewerPanel (class in opentps.gui.viewer.viewerPanel) ViewerPanel.LayoutTypes (class in opentps.gui.viewer.viewerPanel) ViewerToolbar (class in opentps.gui.viewer.viewerToolbar) viewType (Image2DViewer property) (Image3DViewer property) visible (CrossHairLayer property) (MainToolbar.ToolbarItem property) (ROIContourForViewer property) (ROIMaskForViewer property) (TextLayer property)

vtkContour (class in opentps.gui.viewer.dataViewerComponents.imageViewerComponents.contourLayer) vtkOutputPort (Dyn2DSeqForViewer property) (Dyn3DSeqForViewer property) (GenericImageForViewer property) (Image2DForViewer property) (Image3DForViewer property) (PolyDataForViewer property) (ROIContourForViewer property) (ROIMaskForViewer property)

W

warp() (in module opentps.core.processing.imageProcessing.resampler3D) (VectorField3D method) waterSP() (MCsquareCTCalibration method), [1] WeightStructure (class in opentps.core.processing.planOptimization.tools) WET_raytracing() (in module opentps.core.processing.C_libraries.libRayTracing_wrapper) whichmodule() (in module opentps.core.utils.pickel2) windowLevelEnabled (ViewController property) workspace (ProgramSettings property) write() (G4StopPow method) (MCsquareCTCalibration method), [1] (MCsquareElement method) (MCsquareHU2Material method) (MCsquareMaterial method) (PiecewiseHU2Density method) writeableTable() (PiecewiseHU2Density method) writeBin() (in module opentps.core.io.mcsquareIO) writeBinaryMHD() (in module opentps.core.io.mhdIO) writeConfig() (AbstractApplicationConfig method) (in module opentps.core.io.mcsquareIO) (ProgramSettings method)

writeContours() (in module opentps.core.io.mcsquareIO) writeCT() (in module opentps.core.io.mcsquareIO) writeCTCalibrationAndBDL() (in module opentps.core.io.mcsquareIO) writeDicomCT() (in module opentps.core.io.dicomIO) writeHeader() (MCsquareHU2Material method) (PiecewiseHU2Density method) writeHeaderMHD() (in module opentps.core.io.mhdIO) writeObjectives() (in module opentps.core.io.mcsquareIO) writePlan() (in module opentps.core.io.mcsquareIO) writeRTDose() (in module opentps.core.io.dicomIO) writeRTPlan() (in module opentps.core.io.dicomIO) writeRTStruct() (in module opentps.core.io.dicomIO) wwlEnabled (Image2DViewer property) (Image3DViewer property) WWLPreset (class in opentps.gui.viewer.dataViewerComponents.imageViewerActions) wwlValue (GenericImageForViewer property)

X

xSquared (BoundConstraintsOptimizer property) (PlanOptimizer property)