Index

A

aapmtom() (in module cerr.contour.rasterseg) accumulate() (in module cerr.dvh) acquisitionDate (cerr.dataclasses.scan_info.ScanInfo attribute) acquisitionTime (cerr.dataclasses.scan_info.ScanInfo attribute) addContentTags() (in module cerr.dcm_export.iod_helper) addEquipmentTags() (in module cerr.dcm_export.iod_helper) addGeneralImageTags() (in module cerr.dcm_export.iod_helper) addImagePixelTags() (in module cerr.dcm_export.iod_helper) addImagePlaneTags() (in module cerr.dcm_export.iod_helper) addPatientTags() (in module cerr.dcm_export.iod_helper) addRefFORTags() (in module cerr.dcm_export.iod_helper) addSeriesTags() (in module cerr.dcm_export.iod_helper) addSOPCommonTags() (in module cerr.dcm_export.iod_helper)

addStructureSetTags() (in module cerr.dcm_export.iod_helper) addStudyTags() (in module cerr.dcm_export.iod_helper) aggregateRotatedResponses() (in module cerr.radiomics.texture_filters) algorithm (cerr.dataclasses.deform.Deform attribute) algorithmParams (cerr.dataclasses.deform.Deform attribute) ApprovalStatus (cerr.dataclasses.beams.Beams attribute) assocBaseScanUID (cerr.dataclasses.scan.Scan attribute) assocBeamUID (cerr.dataclasses.dose.Dose attribute) assocDeformUID (cerr.dataclasses.scan.Scan attribute) assocMovingScanUID (cerr.dataclasses.scan.Scan attribute) assocScanUID (cerr.dataclasses.dose.Dose attribute) (cerr.dataclasses.structure.Structure attribute) assocTextureUID (cerr.dataclasses.scan.Scan attribute)

B

baseScanUID (cerr.dataclasses.deform.Deform attribute) BeamDescription (cerr.dataclasses.beams.BeamSeq attribute) BeamLimitingDeviceAngle (cerr.dataclasses.beams.ControlPointSequence attribute) BeamLimitingDevicePositionSeq (cerr.dataclasses.beams.BeamSeq attribute) (class in cerr.dataclasses.beams) BeamLimitingDeviceRotationDirection (cerr.dataclasses.beams.ControlPointSequence attribute) BeamMeterset (cerr.dataclasses.beams.RefBeamSeq attribute) BeamName (cerr.dataclasses.beams.BeamSeq attribute) BeamNumber (cerr.dataclasses.beams.BeamSeq attribute)

beams (cerr.plan_container.PlanC attribute) Beams (class in cerr.dataclasses.beams) BeamSeq (class in cerr.dataclasses.beams) BeamSequence (cerr.dataclasses.beams.Beams attribute) BeamType (cerr.dataclasses.beams.BeamSeq attribute) BeamUID (cerr.dataclasses.beams.Beams attribute) bitsAllocated (cerr.dataclasses.scan_info.ScanInfo attribute) bitsStored (cerr.dataclasses.scan_info.ScanInfo attribute) bValue (cerr.dataclasses.scan_info.ScanInfo attribute)

C

calcCooccur() (in module cerr.radiomics.gray_level_cooccurence) calcIsocenter() (in module cerr.dataclasses.structure) calcJacobian() (in module cerr.registration.register) calcMaxDistBetweenPts() (in module cerr.radiomics.shape) calcNGLDM() (in module cerr.radiomics.neighbor_gray_level_dependence) calcNGTDM() (in module cerr.radiomics.neighbor_gray_tone) calcRadiomicsForImgType() (in module cerr.radiomics.ibsi1) calcRLM() (in module cerr.radiomics.run_length) calcShapeFeatures() (in module cerr.radiomics.shape) calcSZM() (in module cerr.radiomics.size_zone) calcVectorField() (in module cerr.registration.register) cerr module cerr.contour module cerr.contour.contour_processing module cerr.contour.rasterseg module cerr.dataclasses module cerr.dataclasses.beams module cerr.dataclasses.deform module cerr.dataclasses.dose module cerr.dataclasses.header module cerr.dataclasses.scan module cerr.dataclasses.scan_info module cerr.dataclasses.structure module cerr.datasets module cerr.dcm_export module cerr.dcm_export.iod_helper module cerr.dcm_export.rtstruct_iod module cerr.dvh module cerr.plan_container module cerr.radiomics module cerr.radiomics.first_order module cerr.radiomics.gray_level_cooccurence module cerr.radiomics.ibsi1 module cerr.radiomics.neighbor_gray_level_dependence module cerr.radiomics.neighbor_gray_tone module cerr.radiomics.preprocess module cerr.radiomics.run_length module

cerr.radiomics.shape module cerr.radiomics.size_zone module cerr.radiomics.texture_filters module cerr.radiomics.texture_utils module cerr.registration module cerr.registration.register module cerr.roe module cerr.utils module cerr.utils.ai_pipeline module cerr.utils.image_proc module cerr.utils.interp module cerr.utils.mask module cerr.utils.statistics module cerr.utils.uid module cerr.viewer module cerrDcmSliceDirMatch (cerr.dataclasses.dose.Dose attribute) cerrToDcmTransM (cerr.dataclasses.deform.Deform attribute) (cerr.dataclasses.scan.Scan attribute) closeMask() (in module cerr.utils.mask) compare_maps() (in module tests.test_ibsi2_filters) computeBoundingBox() (in module cerr.utils.mask) computeScalarFeatures() (in module cerr.radiomics.ibsi1) contour (cerr.dataclasses.structure.Structure attribute) Contour (class in cerr.dataclasses.structure) ControlPointIndex (cerr.dataclasses.beams.ControlPointSequence attribute) ControlPointSequence (cerr.dataclasses.beams.BeamSeq attribute) (class in cerr.dataclasses.beams) convertCerrToDcmCoords() (in module cerr.dcm_export.rtstruct_iod) convertDcmToCerrVirtualCoords() (cerr.dataclasses.deform.Deform method) (cerr.dataclasses.dose.Dose method) (cerr.dataclasses.scan.Scan method) (cerr.dataclasses.structure.Structure method) convertDcmToRealWorldUnits() (cerr.dataclasses.scan.Scan method) convertToSUV() (cerr.dataclasses.scan.Scan method) cooccurToScalarFeatures() (in module cerr.radiomics.gray_level_cooccurence) coord1OFFirstPoint (cerr.dataclasses.dose.Dose attribute) coord2OFFirstPoint (cerr.dataclasses.dose.Dose attribute) coord3OfFirstPoint (cerr.dataclasses.dose.Dose attribute) copyToScan() (in module cerr.dataclasses.structure) correctedImage (cerr.dataclasses.scan_info.ScanInfo attribute) create() (in module cerr.dcm_export.rtstruct_iod) createFieldNameFromParameters() (in module cerr.radiomics.ibsi1) createFlatFeatureDict() (in module cerr.radiomics.ibsi1) createSessionDir() (in module cerr.utils.ai_pipeline) createStructuringElement() (in module cerr.utils.mask) createUID() (in module cerr.utils.uid) CTOffset (cerr.dataclasses.scan_info.ScanInfo attribute) CumulativeMetersetWeight (cerr.dataclasses.beams.ControlPointSequence attribute)

D

dateWritten (cerr.dataclasses.dose.Dose attribute) (cerr.dataclasses.structure.Structure attribute) decayCorrection (cerr.dataclasses.scan_info.ScanInfo attribute) deform (cerr.plan_container.PlanC attribute) Deform (class in cerr.dataclasses.deform) deformOutFilePath (cerr.dataclasses.deform.Deform attribute) deformOutFileType (cerr.dataclasses.deform.Deform attribute) deformParams (cerr.dataclasses.deform.Deform attribute) deformUID (cerr.dataclasses.deform.Deform attribute) delivered (cerr.dataclasses.dose.Dose attribute) disp_diff() (in module tests.test_ibsi1_features) (in module tests.test_ibsi2_features) dose (cerr.plan_container.PlanC attribute)

Dose (class in cerr.dataclasses.dose) doseArray (cerr.dataclasses.dose.Dose attribute) doseAtNormaliznPoint (cerr.dataclasses.dose.Dose attribute) doseHist() (in module cerr.dvh) doseOffset (cerr.dataclasses.dose.Dose attribute) doseScale (cerr.dataclasses.dose.Dose attribute) doseSummationType (cerr.dataclasses.dose.Dose attribute) doseType (cerr.dataclasses.dose.Dose attribute) doseUID (cerr.dataclasses.dose.Dose attribute) doseUnits (cerr.dataclasses.dose.Dose attribute) dvfMatrix (cerr.dataclasses.deform.Deform attribute) dx (cerr.dataclasses.deform.Deform attribute) Dx() (in module cerr.dvh) dy (cerr.dataclasses.deform.Deform attribute)

E

eig() (in module cerr.radiomics.shape)

energyFilter() (in module cerr.radiomics.texture_filters)

F

fillHoles() (in module cerr.utils.mask) finterp2() (in module cerr.utils.interp) finterp3() (in module cerr.utils.interp) flipSequenceForWavelets() (in module cerr.radiomics.texture_filters) flipSliceOrderFlag() (in module cerr.dataclasses.deform) (in module cerr.dataclasses.scan)

fractionGroupID (cerr.dataclasses.dose.Dose attribute) FractionGroupSeq (class in cerr.dataclasses.beams) FractionGroupSequence (cerr.dataclasses.beams.Beams attribute) frameAcquisitionDuration (cerr.dataclasses.scan_info.ScanInfo attribute) frameOfReferenceUID (cerr.dataclasses.dose.Dose attribute) (cerr.dataclasses.scan_info.ScanInfo attribute) frameReferenceDateTime (cerr.dataclasses.scan_info.ScanInfo attribute)

G

gaborFilter() (in module cerr.radiomics.texture_filters) gaborFilter3d() (in module cerr.radiomics.texture_filters) GantryAngle (cerr.dataclasses.beams.ControlPointSequence attribute) GantryRotationDirection (cerr.dataclasses.beams.ControlPointSequence attribute) generateRastersegs() (in module cerr.contour.rasterseg) generateTextureMapFromPlanC() (in module cerr.radiomics.texture_utils) get3dLawsMask() (in module cerr.radiomics.texture_filters) get_empty_list() (in module cerr.dataclasses.deform) get_empty_np_array() (in module cerr.dataclasses.deform) get_ref_feature_vals() (in module tests.test_ibsi1_features) (in module tests.test_ibsi2_features) getAssocFilteredScanNum() (in module cerr.utils.ai_pipeline) getAssociatedBeamNum() (cerr.dataclasses.dose.Dose method) getAssocResampledScanNum() (in module cerr.utils.ai_pipeline) getAssocWarpedScanNum() (in module cerr.utils.ai_pipeline) getCERRScanArrayFromITK() (in module cerr.dataclasses.scan) getClosedMask() (in module cerr.dataclasses.structure) getColorForStructNum() (in module cerr.dataclasses.structure) getContourPolygons() (in module cerr.dataclasses.structure) getCouchLocationHough() (in module cerr.utils.mask) getDcmTagVals() (in module cerr.dcm_export.rtstruct_iod) getDeformDict() (cerr.dataclasses.deform.Deform method) getDirectionOffsets() (in module cerr.radiomics.ibsi1) getDoseAt() (cerr.dataclasses.dose.Dose method) getDoseNumFromUID() (in module cerr.dataclasses.dose) getDoseXYZVals() (cerr.dataclasses.dose.Dose method) getDown2Mask() (in module cerr.utils.mask) getDown3Mask() (in module cerr.utils.mask) getDvfVectors() (in module cerr.registration.register) getDVFXYZVals() (cerr.dataclasses.deform.Deform method) getDVH() (in module cerr.dvh) getFileMeta() (in module cerr.dcm_export.iod_helper) getIBSINameMap() (in module cerr.radiomics.ibsi1)

getITKDirection() (in module cerr.dataclasses.scan) getLabelMap() (in module cerr.dataclasses.structure) getLargestConnComps() (in module cerr.dataclasses.structure) getLawsMasks() (in module cerr.radiomics.texture_filters) getMaskList() (in module cerr.dataclasses.structure) getMatchFields() (in module cerr.radiomics.texture_filters) getMatchingIndex() (in module cerr.dataclasses.structure) getNiiAffine() (cerr.dataclasses.dose.Dose method) (cerr.dataclasses.scan.Scan method) getPatientOutline() (in module cerr.utils.mask) getRefFORSeq() (in module cerr.dcm_export.rtstruct_iod) getResampledGrid() (in module cerr.radiomics.preprocess) getROIContourSeq() (in module cerr.dcm_export.rtstruct_iod) getROIObservSeq() (in module cerr.dcm_export.rtstruct_iod) getScanArray() (cerr.dataclasses.scan.Scan method) getScanDict() (cerr.dataclasses.scan.Scan method) getScanNumFromIdentifier() (in module cerr.utils.ai_pipeline) getScanNumFromUID() (in module cerr.dataclasses.scan) getScanOrientation() (cerr.dataclasses.scan.Scan method) getScanSize() (cerr.dataclasses.scan.Scan method) getScanSpacing() (cerr.dataclasses.scan.Scan method) getScanXYZVals() (cerr.dataclasses.scan.Scan method) getSitkImage() (cerr.dataclasses.scan.Scan method) (cerr.dataclasses.structure.Structure method) getStrMask() (in module cerr.contour.rasterseg) getStructDict() (cerr.dataclasses.structure.Structure method) getStructNumFromSOPInstanceUID() (in module cerr.dataclasses.structure) getStructNumFromUID() (in module cerr.dataclasses.structure) getStructSetROISeq() (in module cerr.dcm_export.rtstruct_iod) getStructureAssociatedScan() (cerr.dataclasses.structure.Structure method) getSurfacePoints() (in module cerr.utils.mask) grid1Units (cerr.dataclasses.scan_info.ScanInfo attribute) grid2Units (cerr.dataclasses.scan_info.ScanInfo attribute)

H

halfLife (cerr.dataclasses.scan_info.ScanInfo attribute) header (cerr.plan_container.PlanC attribute)

Header (class in cerr.dataclasses.header) horizontalGridInterval (cerr.dataclasses.dose.Dose attribute)

I

Image2PhysicalTransM (cerr.dataclasses.deform.Deform attribute) (cerr.dataclasses.dose.Dose attribute) (cerr.dataclasses.scan.Scan attribute) Image2VirtualPhysicalTransM (cerr.dataclasses.deform.Deform attribute) (cerr.dataclasses.scan.Scan attribute) imageOrientationPatient (cerr.dataclasses.deform.Deform attribute) (cerr.dataclasses.dose.Dose attribute) (cerr.dataclasses.scan_info.ScanInfo attribute) imagePositionPatient (cerr.dataclasses.dose.Dose attribute) (cerr.dataclasses.scan_info.ScanInfo attribute) imagePositionPatientV (cerr.dataclasses.deform.Deform attribute) imageType (cerr.dataclasses.scan_info.ScanInfo attribute)

imageUnits (cerr.dataclasses.scan_info.ScanInfo attribute) imgResample3D() (in module cerr.radiomics.preprocess) importJson() (in module cerr.dataclasses.structure) importNii() (in module cerr.dataclasses.structure) importScanArray() (in module cerr.plan_container) importStructureMask() (in module cerr.dataclasses.structure) (in module cerr.plan_container) imquantize() (in module cerr.radiomics.preprocess) injectedDose (cerr.dataclasses.scan_info.ScanInfo attribute) injectionDate (cerr.dataclasses.scan_info.ScanInfo attribute) injectionTime (cerr.dataclasses.scan_info.ScanInfo attribute) IsocenterPosition (cerr.dataclasses.beams.ControlPointSequence attribute)

L

largestConnComps() (in module cerr.utils.mask) lawsEnergyFilter() (in module cerr.radiomics.texture_filters) lawsFilter() (in module cerr.radiomics.texture_filters) LeafJawPositions (cerr.dataclasses.beams.BeamLimitingDevicePositionSeq attribute) load_beams() (in module cerr.dataclasses.beams) load_data() (in module tests.test_ibsi1_features) (in module tests.test_ibsi2_features) (in module tests.test_ibsi2_filters) loadDcmDir() (in module cerr.plan_container)

loadDose() (in module cerr.dataclasses.dose) loadFromH5() (in module cerr.plan_container) loadNiiScan() (in module cerr.plan_container) loadNiiStructure() (in module cerr.plan_container) loadNiiVf() (in module cerr.plan_container) loadSettingsFromFile() (in module cerr.radiomics.texture_utils) loadSortedScanInfo() (in module cerr.dataclasses.scan) loadStructure() (in module cerr.dataclasses.structure) LoGFilter() (in module cerr.radiomics.texture_filters)

M

Manufacturer (cerr.dataclasses.beams.Beams attribute) manufacturer (cerr.dataclasses.scan_info.ScanInfo attribute) ManufacturerModelName (cerr.dataclasses.beams.Beams attribute) mask2scan() (in module cerr.contour.rasterseg) maxDose() (in module cerr.dvh) meanDose() (in module cerr.dvh) meanFilter() (in module cerr.radiomics.texture_filters) medianDose() (in module cerr.dvh) minDose() (in module cerr.dvh) MOCx() (in module cerr.dvh) module cerr cerr.contour cerr.contour.contour_processing cerr.contour.rasterseg cerr.dataclasses cerr.dataclasses.beams cerr.dataclasses.deform cerr.dataclasses.dose cerr.dataclasses.header cerr.dataclasses.scan cerr.dataclasses.scan_info cerr.dataclasses.structure cerr.datasets cerr.dcm_export cerr.dcm_export.iod_helper cerr.dcm_export.rtstruct_iod cerr.dvh cerr.plan_container cerr.radiomics cerr.radiomics.first_order cerr.radiomics.gray_level_cooccurence cerr.radiomics.ibsi1 cerr.radiomics.neighbor_gray_level_dependence cerr.radiomics.neighbor_gray_tone cerr.radiomics.preprocess cerr.radiomics.run_length cerr.radiomics.shape cerr.radiomics.size_zone cerr.radiomics.texture_filters cerr.radiomics.texture_utils cerr.registration cerr.registration.register cerr.roe cerr.utils cerr.utils.ai_pipeline cerr.utils.image_proc cerr.utils.interp cerr.utils.mask cerr.utils.statistics cerr.utils.uid cerr.viewer tests tests.test_ibsi1_features tests.test_ibsi2_features tests.test_ibsi2_filters tests.test_nii_export_import

MOHx() (in module cerr.dvh) morphologicalClosing() (in module cerr.utils.mask) movScanUID (cerr.dataclasses.deform.Deform attribute) mtoaapm() (in module cerr.contour.rasterseg)

N

ngldmToScalarFeatures() (in module cerr.radiomics.neighbor_gray_level_dependence) ngtdmToScalarFeatures() (in module cerr.radiomics.neighbor_gray_tone) NominalBeamEnergy (cerr.dataclasses.beams.ControlPointSequence attribute) numberMultiFrameImages (cerr.dataclasses.dose.Dose attribute) NumberOfBeams (cerr.dataclasses.beams.FractionGroupSeq attribute) NumberOfBlocks (cerr.dataclasses.beams.BeamSeq attribute) NumberOfBoli (cerr.dataclasses.beams.BeamSeq attribute)

NumberOfBrachyApplicationSetups (cerr.dataclasses.beams.FractionGroupSeq attribute) NumberOfCompensators (cerr.dataclasses.beams.BeamSeq attribute) NumberOfControlPoints (cerr.dataclasses.beams.BeamSeq attribute) numberOfDimensions (cerr.dataclasses.scan_info.ScanInfo attribute) NumberOfFractionsPlanned (cerr.dataclasses.beams.FractionGroupSeq attribute) numberOfScans (cerr.dataclasses.structure.Structure attribute) NumberOfWedges (cerr.dataclasses.beams.BeamSeq attribute)

P

padScan() (in module cerr.radiomics.preprocess) parseContours() (in module cerr.dataclasses.structure) parseDcmHeader() (in module cerr.plan_container) parseScanInfoFields() (in module cerr.dataclasses.scan) PatientBirthDate (cerr.dataclasses.beams.Beams attribute) patientBirthDate (cerr.dataclasses.scan_info.ScanInfo attribute) patientBmi (cerr.dataclasses.scan_info.ScanInfo attribute) PatientID (cerr.dataclasses.beams.Beams attribute) patientID (cerr.dataclasses.scan_info.ScanInfo attribute) patientName (cerr.dataclasses.dose.Dose attribute) (cerr.dataclasses.scan_info.ScanInfo attribute) (cerr.dataclasses.structure.Structure attribute) PatientPosition (cerr.dataclasses.beams.PatientSetupSeq attribute) PatientSetupSeq (class in cerr.dataclasses.beams) PatientSetupSequence (cerr.dataclasses.beams.Beams attribute) PatientSex (cerr.dataclasses.beams.Beams attribute) patientSex (cerr.dataclasses.scan_info.ScanInfo attribute) patientSize (cerr.dataclasses.scan_info.ScanInfo attribute) PatientSupportAngle (cerr.dataclasses.beams.ControlPointSequence attribute) patientWeight (cerr.dataclasses.scan_info.ScanInfo attribute)

petActivityConctrScaleFactor (cerr.dataclasses.scan_info.ScanInfo attribute) petCountSource (cerr.dataclasses.scan_info.ScanInfo attribute) petDecayCorrectionDateTime (cerr.dataclasses.scan_info.ScanInfo attribute) petNumSlices (cerr.dataclasses.scan_info.ScanInfo attribute) petSeriesType (cerr.dataclasses.scan_info.ScanInfo attribute) philipsImageUnits (cerr.dataclasses.scan_info.ScanInfo attribute) philipsRescaleIntercept (cerr.dataclasses.scan_info.ScanInfo attribute) philipsRescaleSlope (cerr.dataclasses.scan_info.ScanInfo attribute) PixelPaddingValue (cerr.dataclasses.beams.Beams attribute) pixelRepresentation (cerr.dataclasses.scan_info.ScanInfo attribute) PlanC (class in cerr.plan_container) points (cerr.dataclasses.structure.Segment attribute) polyFill() (in module cerr.contour.rasterseg) populateRadiopharmaFields() (in module cerr.dataclasses.scan) populateRealWorldFields() (in module cerr.dataclasses.scan) populateScanInfoFields() (in module cerr.dataclasses.scan) prctile() (in module cerr.utils.statistics) preProcessForRadiomics() (in module cerr.radiomics.preprocess) PrescriptionDescription (cerr.dataclasses.beams.Beams attribute) prescriptionDose (cerr.dataclasses.dose.Dose attribute) processImage() (in module cerr.radiomics.texture_utils)

Q

quantile() (in module cerr.utils.statistics)

R

RadiationType (cerr.dataclasses.beams.BeamSeq attribute) (cerr.dataclasses.beams.FractionGroupSeq attribute) raster_to_mask() (in module cerr.contour.rasterseg) rasterSegments (cerr.dataclasses.structure.Structure attribute) realWorldMeasurCodeMeaning (cerr.dataclasses.scan_info.ScanInfo attribute) realWorldValueIntercept (cerr.dataclasses.scan_info.ScanInfo attribute) realWorldValueSlope (cerr.dataclasses.scan_info.ScanInfo attribute) refBeamNumber (cerr.dataclasses.dose.Dose attribute) RefBeamSeq (cerr.dataclasses.beams.FractionGroupSeq attribute) (class in cerr.dataclasses.beams) ReferencedDoseSequence (cerr.dataclasses.beams.Beams attribute) referencedFrameOfReferenceUID (cerr.dataclasses.structure.Structure attribute) referencedSeriesUID (cerr.dataclasses.structure.Structure attribute) referencedSopClassUID (cerr.dataclasses.structure.Contour attribute) ReferencedSOPInstanceUID (cerr.dataclasses.beams.ReferenceSeq attribute) referencedSopInstanceUID (cerr.dataclasses.structure.Contour attribute) ReferencedStructureSetSequence (cerr.dataclasses.beams.Beams attribute) ReferenceSeq (class in cerr.dataclasses.beams) refFractionGroupNumber (cerr.dataclasses.dose.Dose attribute) refRTPlanSopInstanceUID (cerr.dataclasses.dose.Dose attribute) refStructSetSopInstanceUID (cerr.dataclasses.dose.Dose attribute) registerScans() (in module cerr.registration.register) registrationTool (cerr.dataclasses.deform.Deform attribute) rescaleIntercept (cerr.dataclasses.scan_info.ScanInfo attribute)

rescaleSlope (cerr.dataclasses.scan_info.ScanInfo attribute) rescaleType (cerr.dataclasses.scan_info.ScanInfo attribute) resizeScanAndMask() (in module cerr.utils.image_proc) ReviewDate (cerr.dataclasses.beams.Beams attribute) ReviewerName (cerr.dataclasses.beams.Beams attribute) ReviewTime (cerr.dataclasses.beams.Beams attribute) rlmToScalarFeatures() (in module cerr.radiomics.run_length) roiGenerationAlgorithm (cerr.dataclasses.structure.Structure attribute) roiGenerationDescription (cerr.dataclasses.structure.Structure attribute) ROIInterpretedType (cerr.dataclasses.structure.Structure attribute) rot3d90() (in module cerr.radiomics.texture_filters) rotate3dSequence() (in module cerr.radiomics.texture_filters) rotationInvariantFilt() (in module cerr.radiomics.texture_filters) rotationInvariantLawsEnergyFilter() (in module cerr.radiomics.texture_filters) rotationInvariantLawsFilter() (in module cerr.radiomics.texture_filters) RTPlanDate (cerr.dataclasses.beams.Beams attribute) RTPlanGeometry (cerr.dataclasses.beams.Beams attribute) RTPlanLabel (cerr.dataclasses.beams.Beams attribute) RTPlanTime (cerr.dataclasses.beams.Beams attribute) run_config() (in module tests.test_ibsi1_features) (in module tests.test_ibsi2_features) run_configs() (in module tests.test_ibsi1_features) run_ibsi_image_filters() (in module tests.test_ibsi2_filters) run_phase2() (in module tests.test_ibsi2_features) run_test() (in module tests.test_ibsi2_filters)

S

saveJson() (in module cerr.dataclasses.structure) saveNii() (cerr.dataclasses.dose.Dose method) (cerr.dataclasses.scan.Scan method) (cerr.dataclasses.structure.Structure method) saveNiiStructure() (in module cerr.plan_container) saveToH5() (in module cerr.plan_container) scaleIntercept (cerr.dataclasses.scan_info.ScanInfo attribute) scaleSlope (cerr.dataclasses.scan_info.ScanInfo attribute) scan (cerr.plan_container.PlanC attribute) Scan (class in cerr.dataclasses.scan) scanArray (cerr.dataclasses.scan.Scan attribute) scanFileName (cerr.dataclasses.scan_info.ScanInfo attribute) scanInfo (cerr.dataclasses.scan.Scan attribute) ScanInfo (class in cerr.dataclasses.scan_info) scannerType (cerr.dataclasses.scan_info.ScanInfo attribute) scanType (cerr.dataclasses.scan.Scan attribute) scanUID (cerr.dataclasses.scan.Scan attribute) Segment (class in cerr.dataclasses.structure) segments (cerr.dataclasses.structure.Contour attribute) sepsq() (in module cerr.radiomics.shape) seriesDate (cerr.dataclasses.scan_info.ScanInfo attribute) seriesDescription (cerr.dataclasses.scan_info.ScanInfo attribute) seriesInstanceUID (cerr.dataclasses.scan_info.ScanInfo attribute) seriesTime (cerr.dataclasses.scan_info.ScanInfo attribute) showMplNb() (in module cerr.viewer) showNapari() (in module cerr.viewer) sizeOfDimension1 (cerr.dataclasses.dose.Dose attribute) (cerr.dataclasses.scan_info.ScanInfo attribute)

sizeOfDimension2 (cerr.dataclasses.dose.Dose attribute) (cerr.dataclasses.scan_info.ScanInfo attribute) sizeOfDimension3 (cerr.dataclasses.dose.Dose attribute) sliceThickness (cerr.dataclasses.scan_info.ScanInfo attribute) smooth2DContour() (in module cerr.contour.contour_processing) smoothStructure() (in module cerr.contour.contour_processing) sobelFilter() (in module cerr.radiomics.texture_filters) sopClassUID (cerr.dataclasses.scan_info.ScanInfo attribute) SOPInstanceUID (cerr.dataclasses.beams.Beams attribute) sopInstanceUID (cerr.dataclasses.scan_info.ScanInfo attribute) SourceAxisDistance (cerr.dataclasses.beams.BeamSeq attribute) SourceToSurfaceDistance (cerr.dataclasses.beams.ControlPointSequence attribute) stats() (in module cerr.radiomics.first_order) structSetSopInstanceUID (cerr.dataclasses.structure.Structure attribute) structure (cerr.plan_container.PlanC attribute) Structure (class in cerr.dataclasses.structure) structureColor (cerr.dataclasses.structure.Structure attribute) structureDescription (cerr.dataclasses.structure.Structure attribute) structureFileFormat (cerr.dataclasses.structure.Structure attribute) structureName (cerr.dataclasses.structure.Structure attribute) strUID (cerr.dataclasses.structure.Structure attribute) studyDate (cerr.dataclasses.scan_info.ScanInfo attribute) studyDescription (cerr.dataclasses.scan_info.ScanInfo attribute) studyInstanceUID (cerr.dataclasses.dose.Dose attribute) (cerr.dataclasses.scan_info.ScanInfo attribute) studyTime (cerr.dataclasses.scan_info.ScanInfo attribute) suvType (cerr.dataclasses.scan_info.ScanInfo attribute) szmToScalarFeatures() (in module cerr.radiomics.size_zone)

T

TableTopEccentricAngle (cerr.dataclasses.beams.ControlPointSequence attribute) TableTopEccentricRotationDirection (cerr.dataclasses.beams.ControlPointSequence attribute) temporalPositionIndex (cerr.dataclasses.scan_info.ScanInfo attribute) test_config_a_original_feats_all_dirs() (in module tests.test_ibsi1_features) test_config_a_original_feats_merged_texture() (in module tests.test_ibsi1_features) test_config_b_bilinear_interp_feats_all_dirs() (in module tests.test_ibsi1_features) test_config_b_bilinear_interp_feats_merged_texture() (in module tests.test_ibsi1_features) test_config_c_trilinear_interp_feats_all_dirs() (in module tests.test_ibsi1_features) test_config_c_trilinear_interp_feats_merged_texture() (in module tests.test_ibsi1_features) test_gabor_filters_25d() (in module tests.test_ibsi2_filters) test_gabor_filters_2d() (in module tests.test_ibsi2_filters) test_laws_filter_2d() (in module tests.test_ibsi2_filters) test_laws_filters_3d() (in module tests.test_ibsi2_filters) test_LoG_filter_2d() (in module tests.test_ibsi2_filters) test_LoG_filters_3d() (in module tests.test_ibsi2_filters) test_mean_filt_2d() (in module tests.test_ibsi2_filters) test_mean_filters_3d() (in module tests.test_ibsi2_filters) test_rot_inv_laws_energy_filter_2d() (in module tests.test_ibsi2_filters) test_rot_inv_laws_energy_filters_3d() (in module tests.test_ibsi2_filters) test_rot_inv_laws_filter_2d() (in module tests.test_ibsi2_filters) test_rot_inv_laws_filters_3d() (in module tests.test_ibsi2_filters) test_scan_export_import() (in module tests.test_nii_export_import)

test_stats_LoG_2d() (in module tests.test_ibsi2_features) test_stats_LoG_3d() (in module tests.test_ibsi2_features) test_stats_mean_2d() (in module tests.test_ibsi2_features) test_stats_mean_3d() (in module tests.test_ibsi2_features) test_stats_original() (in module tests.test_ibsi2_features) test_stats_resampled() (in module tests.test_ibsi2_features) test_stats_rot_inv_laws_energy_2d() (in module tests.test_ibsi2_features) test_stats_rot_inv_laws_energy_3d() (in module tests.test_ibsi2_features) tests module tests.test_ibsi1_features module tests.test_ibsi2_features module tests.test_ibsi2_filters module tests.test_nii_export_import module transM (cerr.dataclasses.dose.Dose attribute) TreatmentDeliveryType (cerr.dataclasses.beams.BeamSeq attribute) TreatmentSites (cerr.dataclasses.beams.Beams attribute) trimeshSurfaceArea() (in module cerr.radiomics.shape)

U

UniformScanInfo (class in cerr.dataclasses.scan_info)

unpadScan() (in module cerr.radiomics.preprocess)

V

vectorNorm3d() (in module cerr.radiomics.shape) verticalGridInterval (cerr.dataclasses.dose.Dose attribute)

voxelThickness (cerr.dataclasses.scan_info.ScanInfo attribute) Vx() (in module cerr.dvh)

W

warpDose() (in module cerr.registration.register) warpScan() (in module cerr.registration.register) warpStructures() (in module cerr.registration.register)

windowCenter (cerr.dataclasses.scan_info.ScanInfo attribute) windowWidth (cerr.dataclasses.scan_info.ScanInfo attribute) writeFeaturesToFile() (in module cerr.radiomics.ibsi1) writer (cerr.dataclasses.dose.Dose attribute)

X

xcoordOfNormaliznPoint (cerr.dataclasses.dose.Dose attribute) xOffset (cerr.dataclasses.deform.Deform attribute) (cerr.dataclasses.scan_info.ScanInfo attribute)

xytom() (in module cerr.contour.rasterseg)

Y

ycoordOfNormaliznPoint (cerr.dataclasses.dose.Dose attribute)

yOffset (cerr.dataclasses.deform.Deform attribute) (cerr.dataclasses.scan_info.ScanInfo attribute)

Z

zcoordOfNormaliznPoint (cerr.dataclasses.dose.Dose attribute) zValue (cerr.dataclasses.scan_info.ScanInfo attribute)

zValues (cerr.dataclasses.dose.Dose attribute) zValuesV (cerr.dataclasses.deform.Deform attribute)