Index

A

archiveDataFromListPath() (in module mspt.zip.zipFiles) arraySpots (mspt.dicomReader.scanningPath.ScanningPathSingleBeam attribute) arrayX (mspt.dicomReader.scanningPath.ScanningPathSingleBeam attribute)

arrayY (mspt.dicomReader.scanningPath.ScanningPathSingleBeam attribute) authorizedKeys (mspt.simulator.globalVariables.GlobalVariables attribute)

B

beamletSimul() (in module mspt.scanning.deliverySimulation_Static_Dynamic) buildCumulHisto() (in module mspt.dataViewer.dvh) buildDataSpotToReturn() (mspt.dicomReader.scanningPath.ScanningPathSingleBeam method) buildDVHForVOIs() (mspt.dataViewer.dvh.DVH method) buildFuncBPvsEner() (mspt.physics.ddCurvesManager.DDCurves method) buildFuncDoseAtBPVsEnergy() (mspt.physics.ddCurvesManager.DDCurves method) buildFuncEnervsBP() (mspt.physics.ddCurvesManager.DDCurves method)

buildHistogram() (in module mspt.dataViewer.dvh) buildMediumToTable() (mspt.physics.stoppingPower.StoppingPower method) buildNormDistrFunction() (in module mspt.motion.motionMonitor) (in module mspt.motion.motionNoisyCos) buildPatient() (mspt.patient.patient.Patient method) buildScanningPath() (mspt.dicomReader.scanningPath.ScanningPathSingleBeam method) buildSettingsForScanningDelivery() (mspt.simulator.globalVariables.GlobalVariables method) buildSliceScanningOrder() (mspt.dicomReader.scanningPath.ScanningPathSingleBeam method)

C

calcRadiolDepth() (in module mspt.patient.tools) calcRadiolDepthFewRays() (in module mspt.patient.tools) calculateSSD0() (mspt.patient.patient.Patient method) checkConfigData() (mspt.simulator.globalVariables.GlobalVariables method) checkFrameOfReferenceUID() (mspt.dicomReader.dicomManager.DicomManager method) checkFullRTPlan() (mspt.dicomReader.dicomManager.DicomManager method) checkSameStudyInstanceUID() (mspt.dicomReader.dicomManager.DicomManager method) clearSubplot() (in module mspt.dataViewer.plotDataGraphs) closeDVH() (mspt.dataViewer.dvh.DVH method) closePlot() (in module mspt.dataViewer.array2DViewer) (in module mspt.dataViewer.plotDataGraphs) compensationFindStartSpotEnerLayer() (mspt.scanning.deliverySimulation_Static_Dynamic.simulatorDelivery method) computeBeamletStatic() (mspt.scanning.deliverySimulation_Static_Dynamic.simulatorDelivery method) computeDisplacementVectors() (mspt.scanning.deliverySimulation_Static_Dynamic.simulatorDelivery method) computeDvData() (mspt.dataViewer.dvh.DVH method)

computeEnergyLoss() (in module mspt.physics.ddCurvesManager) computeEnergyReceivedByStructures() (mspt.patient.patient.Patient method) computeEnergyRemaining() (in module mspt.physics.ddCurvesManager) computeLocalizedRadiologicalDepth() (mspt.patient.patient.Patient method) computeNbProtonsMCSimul() (in module mspt.physics.ddCurvesManager) computeRadiologicalDepth() (mspt.patient.patient.Patient method) computeStoppingPowerArray() (mspt.patient.patient.Patient method) computeVdData() (mspt.dataViewer.dvh.DVH method) coordinatesToIndex() (in module mspt.dicomReader.scanningPath) coordinatesToIndexFromImagePosition() (in module mspt.dicomReader.tools) createZipArchiveForFiles() (in module mspt.zip.zipFiles) crossProduct() (in module mspt.dicomReader.tools) cumulDose() (in module mspt.physics.ddCurvesManager)

D

dataForAttribute() (mspt.dicomReader.dicomCTReader.DicomCTReader method) (mspt.dicomReader.dicomGeneralReader.DicomGeneralReader method) (mspt.dicomReader.dicomRDReader.DicomRDReader method) (mspt.dicomReader.dicomRPReader.DicomRPReader method) (mspt.dicomReader.dicomRSReader.DicomRSReader method) (mspt.dicomReader.dicomReader.DicomReader method) dataForEnergy() (mspt.physics.ddCurvesManager.DDCurves method) dcmType (mspt.dicomReader.dicomCTReader.DicomCTReader attribute) (mspt.dicomReader.dicomGeneralReader.DicomGeneralReader attribute) (mspt.dicomReader.dicomRDReader.DicomRDReader attribute) (mspt.dicomReader.dicomRPReader.DicomRPReader attribute) (mspt.dicomReader.dicomRSReader.DicomRSReader attribute) (mspt.dicomReader.dicomReader.DicomReader attribute) DDCurves (class in mspt.physics.ddCurvesManager) decrementRepaint() (mspt.dicomReader.scanningPath.ScanningPathSingleBeam method) DicomCTReader (class in mspt.dicomReader.dicomCTReader) dicomData (mspt.dicomReader.dicomRDReader.DicomRDReader attribute) DicomGeneralReader (class in mspt.dicomReader.dicomGeneralReader) DicomManager (class in mspt.dicomReader.dicomManager) DicomRDReader (class in mspt.dicomReader.dicomRDReader) DicomReader (class in mspt.dicomReader.dicomReader) DicomRPReader (class in mspt.dicomReader.dicomRPReader) DicomRSReader (class in mspt.dicomReader.dicomRSReader)

displayImageFromArray() (in module mspt.dataViewer.array2DViewer) displayPlot() (in module mspt.dataViewer.array2DViewer) (in module mspt.dataViewer.plotDataGraphs) displaySliceOrderingInfo() (mspt.patient.patient.Patient method) distEuclideanP1P2() (in module mspt.mathTools.tools) doseCorrectionFactor() (mspt.physics.ddCurvesManager.DDCurves method) DoseUnits (mspt.dicomReader.dicomRDReader.DicomRDReader attribute) drawData() (in module mspt.dataViewer.plotDataGraphs) drawDvData() (mspt.dataViewer.dvh.DVH method) drawDVHs() (mspt.dataViewer.dvh.DVH method) drawPlot() (in module mspt.dataViewer.plotDataGraphs) drawVdData() (mspt.dataViewer.dvh.DVH method) DVH (class in mspt.dataViewer.dvh)

E

Email (class in mspt.email.Email) euclideanDistance() (in module mspt.dicomReader.scanningPath) evaluateDifference() (mspt.simulator.tools.Tools method) exportAllDVHToCSV() (in module mspt.dataViewer.dvh) exportDvDataToCSVFile() (in module mspt.dataViewer.dvh) exportDVHToCSVFile() (in module mspt.dataViewer.dvh)

exportListDataToCSV() (in module mspt.simulator.simulatorMSPT) exportSliceOrderingInfo() (mspt.patient.patient.Patient method) exportVdDataToCSVFile() (in module mspt.dataViewer.dvh) extendBoundingBox() (mspt.dicomReader.scanningPath.ScanningPathSingleBeam method) extendMap() (mspt.dicomReader.scanningPath.ScanningPathSingleBeam method)

F

fillArraysScanningPath() (mspt.dicomReader.scanningPath.ScanningPathSingleBeam method) fillIndicesVOIPatient() (mspt.patient.patient.Patient method) fillListEnergies() (mspt.dicomReader.scanningPath.ScanningPathSingleBeam method) fillPatientCT() (in module mspt.patient.tools) fillPatientDensity() (in module mspt.patient.tools) fillPatientDose() (in module mspt.patient.tools) fillPatientStopPwr() (in module mspt.patient.tools) fillRepaintingArray() (mspt.dicomReader.scanningPath.ScanningPathSingleBeam method) fillSpotSizeList() (mspt.dicomReader.scanningPath.ScanningPathSingleBeam method) fillSpotTypeArray() (mspt.dicomReader.scanningPath.ScanningPathSingleBeam method) findBoundingBoxScanningPath() (mspt.dicomReader.scanningPath.ScanningPathSingleBeam method) findBraggPeak() (in module mspt.physics.ddCurvesManager) (mspt.scanning.deliverySimulation_Static_Dynamic.simulatorDelivery method)

findCorrespondingEnergy() (mspt.dicomReader.scanningPath.ScanningPathSingleBeam method) findDoseAtBPForEner() (mspt.physics.ddCurvesManager.DDCurves method) findEnergyForBraggPeak() (mspt.physics.ddCurvesManager.DDCurves method) findminMax() (in module mspt.dataViewer.plotDataGraphs) findShape3DArray() (mspt.dicomReader.scanningPath.ScanningPathSingleBeam method) findSpacing() (mspt.dicomReader.scanningPath.ScanningPathSingleBeam method) findStartingPointForMotion() (mspt.dicomReader.scanningPath.ScanningPathSingleBeam method) fractionGroupSequence (mspt.dicomReader.dicomRPReader.DicomRPReader attribute) fromCTToIECFixedCoord() (in module mspt.mathTools.tools) fromIECFixedToCTCoord() (in module mspt.mathTools.tools) fullPlan() (mspt.dicomReader.dicomManager.DicomManager method)

G

generateApproxDDCurveForEnergy() (mspt.physics.ddCurvesManager.DDCurves method) generateTableMissingEnergy() (mspt.physics.ddCurvesManager.DDCurves method) get3DPixelArray() (mspt.dicomReader.dicomCTReader.DicomCTReader method) getAttributeForSlice() (mspt.dicomReader.dicomCTReader.DicomCTReader method) getAttributeInSeries() (mspt.dicomReader.dicomCTReader.DicomCTReader method) getConversionTableCTToMassDens() (in module mspt.dicomReader.ctToDensityConv) getConversionTableStpPwrForEnergy() (mspt.physics.stoppingPower.StoppingPower method) getCumulDelivDuration() (mspt.scanning.deliverySimulation_Static_Dynamic.simulatorDelivery method) getCurrentFigure() (in module mspt.dataViewer.plotDataGraphs) getCurrentTime() (mspt.scanning.deliverySimulation_Static_Dynamic.simulatorDelivery method) getDicomReaderForScanningPath() (mspt.dicomReader.dicomManager.DicomManager method) getDicomReaders() (mspt.dicomReader.dicomManager.DicomManager method) getDicomReadersForPatient() (mspt.dicomReader.dicomManager.DicomManager method) getDispIndices() (mspt.patient.patient.Patient method) getDisplacementVectorAtTime() (mspt.motion.motionBreathCough.MotionBreathCough method) (mspt.motion.motionBreathHiccup.MotionBreathHiccup method) (mspt.motion.motionCos.MotionCos method) (mspt.motion.motionManager.Motion method) (mspt.motion.motionNoisyCos.MotionNoisyCos method) getDoseForVolume() (in module mspt.dataViewer.dvh) getDvDataForVOI() (mspt.dataViewer.dvh.DVH method) getDVHForVOI() (mspt.dataViewer.dvh.DVH method) getEnergySliceWeights() (mspt.dicomReader.scanningPath.ScanningPathSingleBeam method) getFileListForDirectory() (in module mspt.zip.zipFiles) getFrameOfReferenceUID() (mspt.dicomReader.dicomCTReader.DicomCTReader method) (mspt.dicomReader.dicomGeneralReader.DicomGeneralReader method) (mspt.dicomReader.dicomRSReader.DicomRSReader method) getHistory() (mspt.motion.motionManager.Motion method) (mspt.motion.motionMonitor.MotionMonitor method) getIsocenterInd() (mspt.patient.patient.Patient method) getListEnergies() (mspt.dicomReader.scanningPath.ScanningPathSingleBeam method) getMapWithEnhancedSpot() (mspt.dicomReader.scanningPath.ScanningPathSingleBeam method) getMapWithMargin() (mspt.dicomReader.scanningPath.ScanningPathSingleBeam method) getMaskForContour() (in module mspt.dicomReader.tools) getMasksForAssociatedDicomImage() (mspt.dicomReader.dicomRSReader.DicomRSReader method)

getMatrixHotAndColdSpot() (mspt.simulator.tools.Tools method) getMotionMeasurement() (mspt.motion.motionMonitor.MotionMonitor method) getNumberOfRepaintingsPerSlice() (mspt.dicomReader.scanningPath.ScanningPathSingleBeam method) getNumberOfROIs() (mspt.dicomReader.dicomRSReader.DicomRSReader method) getPath() (mspt.dicomReader.dicomRDReader.DicomRDReader method) getPatientArrayForAttr() (mspt.patient.patient.Patient method) getPatientDataForDisplVector() (mspt.patient.patient.Patient method) getPatientExtentInDynamicModel() (mspt.patient.patient.Patient method) getPatientExtentInStaticModel() (mspt.patient.patient.Patient method) getPatientMask() (mspt.patient.patient.Patient method) getPlannedWeightForSpotInd() (mspt.dicomReader.scanningPath.ScanningPathSingleBeam method) getRepaintingFactor() (mspt.dicomReader.scanningPath.ScanningPathSingleBeam method) getRescalingPixelInfoSeries() (mspt.dicomReader.dicomCTReader.DicomCTReader method) getROINameForRefROINumber() (mspt.dicomReader.dicomRSReader.DicomRSReader method) getROIObservationForRefROINumber() (mspt.dicomReader.dicomRSReader.DicomRSReader method) getScanningPath() (mspt.dicomReader.dicomRPReader.DicomRPReader method) getSliceOrderFromPlan() (mspt.dicomReader.scanningPath.ScanningPathSingleBeam method) getSpacingInfo() (mspt.patient.patient.Patient method) getSpacingSeries() (mspt.dicomReader.dicomCTReader.DicomCTReader method) getStopPwrCorrecFactor() (mspt.physics.stoppingPower.StoppingPower method) getSubDoseDataForMask() (in module mspt.dataViewer.dvh) getUnpaddedPatientDataForAttr() (mspt.patient.patient.Patient method) getVdDataForVOI() (mspt.dataViewer.dvh.DVH method) getVectorInDiffCoordSystm() (mspt.scanning.deliverySimulation_Static_Dynamic.simulatorDelivery method) getVolumeForDose() (in module mspt.dataViewer.dvh) getWeightForSpotInd() (mspt.dicomReader.scanningPath.ScanningPathSingleBeam method) GlobalVariables (class in mspt.simulator.globalVariables)

H

hotAndColdSpotsPerStrcuture() (mspt.patient.patient.Patient method)

htmlTextBoldRed() (in module mspt.email.Email)

I

importCorrecStopPwrData() (mspt.physics.stoppingPower.StoppingPower method) importNewStopPwrData() (mspt.physics.stoppingPower.StoppingPower method) indexToCoordinates() (in module mspt.dicomReader.scanningPath) indexToCoordinatesFromImagePosition() (in module mspt.dicomReader.tools) initPatientWithDicomData() (mspt.patient.patient.Patient method)

interp() (in module mspt.mathTools.tools) isEnergyLayerEmpty() (in module mspt.dicomReader.scanningPath) isPatientInTheVolume() (mspt.scanning.deliverySimulation_Static_Dynamic.simulatorDelivery method) isPointNearOtherSpot() (mspt.dicomReader.scanningPath.ScanningPathSingleBeam method)

L

listEnergies (mspt.dicomReader.scanningPath.ScanningPathSingleBeam attribute) loadData() (in module mspt.dataViewer.array2DViewer) loadDicomSeriesFromDirectory() (mspt.dicomReader.dicomCTReader.DicomCTReader method) loadDoseCorrectionFactor() (mspt.physics.ddCurvesManager.DDCurves method) loadMassStoppingPowerFromNewData() (mspt.physics.stoppingPower.StoppingPower method)

loadMassStoppingPowerFromPSTARData() (mspt.physics.stoppingPower.StoppingPower method) loadRTDosePlanFile() (mspt.dicomReader.dicomRDReader.DicomRDReader method) loadRTPlanFile() (mspt.dicomReader.dicomRPReader.DicomRPReader method) loadRTStrucSetFile() (mspt.dicomReader.dicomRSReader.DicomRSReader method) locateSpots() (mspt.dicomReader.scanningPath.ScanningPathSingleBeam method)

M

mail() (mspt.email.Email.Email method) makePlotLegend() (in module mspt.dataViewer.plotDataGraphs) monitorPatientMotionAtTime() (mspt.motion.motionMonitor.MotionMonitor method) Motion (class in mspt.motion.motionManager) MotionBreathCough (class in mspt.motion.motionBreathCough) MotionBreathHiccup (class in mspt.motion.motionBreathHiccup) MotionCos (class in mspt.motion.motionCos) MotionMonitor (class in mspt.motion.motionMonitor) MotionNoisyCos (class in mspt.motion.motionNoisyCos) MSPT (class in mspt.simulator.simulatorMSPT) mspt (module) mspt.dataViewer (module) mspt.dataViewer.array2DViewer (module) mspt.dataViewer.dvh (module) mspt.dataViewer.plotDataGraphs (module) mspt.dicomReader (module) mspt.dicomReader.ctToDensityConv (module) mspt.dicomReader.dicomCTReader (module) mspt.dicomReader.dicomGeneralReader (module) mspt.dicomReader.dicomManager (module) mspt.dicomReader.dicomRDReader (module) mspt.dicomReader.dicomReader (module) mspt.dicomReader.dicomRPReader (module) mspt.dicomReader.dicomRSReader (module) mspt.dicomReader.scanningPath (module) mspt.dicomReader.tools (module) mspt.email (module)

mspt.email.Email (module) mspt.extensionsC (module) mspt.extensionsC.PythonExtensionAllPlatforms (module) mspt.mathTools (module) mspt.mathTools.tools (module) mspt.motion (module) mspt.motion.motionBreathCough (module) mspt.motion.motionBreathHiccup (module) mspt.motion.motionCos (module) mspt.motion.motionManager (module) mspt.motion.motionMonitor (module) mspt.motion.motionNoisyCos (module) mspt.patient (module) mspt.patient.patient (module) mspt.patient.tools (module) mspt.physics (module) mspt.physics.ddCurvesManager (module) mspt.physics.stoppingPower (module) mspt.scanning (module) mspt.scanning.deliverySimulation_Static_Dynamic (module) mspt.simulator (module) mspt.simulator.globalVariables (module) mspt.simulator.simulatorMSPT (module) mspt.simulator.tools (module) mspt.zip (module) mspt.zip.zipFiles (module)

N

newSubplot() (in module mspt.dataViewer.plotDataGraphs) nextSpotIndex() (mspt.dicomReader.scanningPath.ScanningPathSingleBeam method) normalizeDVH() (mspt.dataViewer.dvh.DVH method) numberOfCols (mspt.dicomReader.dicomCTReader.DicomCTReader attribute)

numberOfFrames (mspt.dicomReader.dicomCTReader.DicomCTReader attribute) numberOfRows (mspt.dicomReader.dicomCTReader.DicomCTReader attribute) numberOfUnitTimeToDeliverWeight() (mspt.scanning.deliverySimulation_Static_Dynamic.simulatorDelivery method)

O

openPNGImageToArray() (in module mspt.dataViewer.array2DViewer)

P

Patient (class in mspt.patient.patient) PixelArray (mspt.dicomReader.dicomRDReader.DicomRDReader attribute) plotHorizontalLine() (in module mspt.dataViewer.plotDataGraphs) plotVerticalLine() (in module mspt.dataViewer.plotDataGraphs) precomputeMassStopPowerRatios() (mspt.physics.stoppingPower.StoppingPower method)

printAttributeInSeries() (mspt.dicomReader.dicomCTReader.DicomCTReader method) processConfigMotionSimul() (mspt.simulator.globalVariables.GlobalVariables method) processConfigStaticSimul() (mspt.simulator.globalVariables.GlobalVariables method) processDVHForDoseDistribution() (in module mspt.dataViewer.dvh) processDynamicDoseDistrib() (mspt.scanning.deliverySimulation_Static_Dynamic.simulatorDelivery method)

R

readCSVFilesInFolder() (mspt.physics.ddCurvesManager.DDCurves method) readFile() (mspt.physics.ddCurvesManager.DDCurves method) repaintingMethodSlice (mspt.dicomReader.scanningPath.ScanningPathSingleBeam attribute) repaintingMethodVolume (mspt.dicomReader.scanningPath.ScanningPathSingleBeam attribute) repaintingNonVolOrder() (mspt.dicomReader.scanningPath.ScanningPathSingleBeam method)

repaintingVolOrder() (mspt.dicomReader.scanningPath.ScanningPathSingleBeam method) rot3D() (in module mspt.mathTools.tools) rotateCoordinates() (in module mspt.mathTools.tools) rotationMatrixForAngle() (in module mspt.mathTools.tools) rtPlanPath (mspt.dicomReader.dicomRPReader.DicomRPReader attribute)

S

save2DListToCSV() (in module mspt.dataViewer.dvh) (mspt.simulator.simulatorMSPT.MSPT method) save2DSliceToCSV() (mspt.simulator.simulatorMSPT.MSPT method) saveCompensatedRTPlan() (mspt.simulator.tools.Tools method) saveDataToImagePNG() (in module mspt.dataViewer.array2DViewer) saveDoseDistrAsRDDcmFile() (mspt.patient.patient.Patient method) saveDvAsCSV() (mspt.dataViewer.dvh.DVH method) saveDVHAsCSV() (mspt.dataViewer.dvh.DVH method) saveDVHAsImage() (mspt.dataViewer.dvh.DVH method) saveEntireDVHAsCSV() (mspt.dataViewer.dvh.DVH method) saveFigure() (in module mspt.dataViewer.array2DViewer) savePlotImage() (in module mspt.dataViewer.plotDataGraphs) saveVdAsCSV() (mspt.dataViewer.dvh.DVH method) ScanningPathMultipleBeams (class in mspt.dicomReader.scanningPath) ScanningPathSingleBeam (class in mspt.dicomReader.scanningPath)

setIsocenter() (mspt.patient.patient.Patient method) setNextSpotIndex() (mspt.dicomReader.scanningPath.ScanningPathSingleBeam method) setReceivedDose() (mspt.patient.patient.Patient method) shape() (mspt.patient.patient.Patient method) showHotColdSpots() (mspt.simulator.tools.Tools method) simulateDelivery() (mspt.scanning.deliverySimulation_Static_Dynamic.simulatorDelivery method) simulatorDelivery (class in mspt.scanning.deliverySimulation_Static_Dynamic) singleRay() (in module mspt.patient.tools) sortDcmSlicesInSeries() (mspt.dicomReader.dicomCTReader.DicomCTReader method) SpacingInfo (mspt.dicomReader.dicomRDReader.DicomRDReader attribute) StoppingPower (class in mspt.physics.stoppingPower) storeData() (in module mspt.dataViewer.array2DViewer) storeDictStatisticsRepaint() (mspt.scanning.deliverySimulation_Static_Dynamic.simulatorDelivery method) storeMatrixAsImage() (in module mspt.dataViewer.array2DViewer)

T

timeDeliverSpotWeight() (mspt.scanning.deliverySimulation_Static_Dynamic.simulatorDelivery method) Tools (class in mspt.simulator.tools)

tripletwise() (in module mspt.dicomReader.tools) truncateVal() (in module mspt.dicomReader.tools)

U

updateNbRepaintingsForMargins() (mspt.dicomReader.scanningPath.ScanningPathSingleBeam method) updateSpot() (mspt.dicomReader.scanningPath.ScanningPathSingleBeam method) updateTime() (mspt.scanning.deliverySimulation_Static_Dynamic.simulatorDelivery method)

updateVecDispl() (in module mspt.motion.motionBreathCough) (in module mspt.motion.motionBreathHiccup) updateXYArrayForMargin() (mspt.dicomReader.scanningPath.ScanningPathSingleBeam method)

W

weightDeliveredByUnitTime() (mspt.scanning.deliverySimulation_Static_Dynamic.simulatorDelivery method)

X

XServer_is_running() (in module mspt.dataViewer.array2DViewer)