spydcmtk

• spydcmtk package
  • Submodules
  • spydcmtk.dcmTK module
    • BIDSConst
      • BIDSConst.anat
      • BIDSConst.code
      • BIDSConst.configf
      • BIDSConst.dwi
      • BIDSConst.fmap
      • BIDSConst.func
    • BIDS_Directory
      • BIDS_Directory.getConfigFile()
      • BIDS_Directory.getSubjList()
    • BIDS_Subject
      • BIDS_Subject.getNIIMatchingModality()
      • BIDS_Subject.getNIIMatchingModality_condition()
      • BIDS_Subject.getSessionDir()
      • BIDS_Subject.getSubjID()
      • BIDS_Subject.getTypeDir()
    • DicomSeries
      • DicomSeries.IS_BRUKER()
      • DicomSeries.IS_GE()
      • DicomSeries.IS_PHILIPS()
      • DicomSeries.IS_SIEMENS()
      • DicomSeries.anonymise()
      • DicomSeries.buildOverviewImage()
      • DicomSeries.buildVTIDict()
      • DicomSeries.buildVTSDict()
      • DicomSeries.checkIfShouldUse_SAFE_NAMING()
      • DicomSeries.doesSliceLocationNorm_Match_IOPNormal()
      • DicomSeries.filterByTag()
      • DicomSeries.getDeltaCol()
      • DicomSeries.getDeltaRow()
      • DicomSeries.getDeltaSlice()
      • DicomSeries.getDicomFullFileName()
      • DicomSeries.getImageOrientationPatient_np()
      • DicomSeries.getImagePositionPatient_np()
      • DicomSeries.getInternalPulseSequenceName()
      • DicomSeries.getManufacturer()
      • DicomSeries.getNumberOfSlicesPerVolume()
      • DicomSeries.getNumberOfTimeSteps()
      • DicomSeries.getPixelDataAsNumpy()
      • DicomSeries.getPulseSequenceName()
      • DicomSeries.getRootDir()
      • DicomSeries.getScanDuration_secs()
      • DicomSeries.getSeriesDescription()
      • DicomSeries.getSeriesInfoDict()
      • DicomSeries.getSeriesNumber()
      • DicomSeries.getSeriesOutDirName()
      • DicomSeries.getSeriesOverview()
      • DicomSeries.getSeriesTimeAsDatetime()
      • DicomSeries.getSliceNormalVector()
      • DicomSeries.getStudyOutputDir()
      • DicomSeries.getTag()
      • DicomSeries.getTagListAndNames()
      • DicomSeries.getTagObj()
      • DicomSeries.getTagValuesList()
      • DicomSeries.getTemporalResolution()
      • DicomSeries.getTemporalResolution_TR_VPS()
      • DicomSeries.getVENC()
      • DicomSeries.is3D()
      • DicomSeries.is4D()
      • DicomSeries.isCompressed()
      • DicomSeries.removeTimes()
      • DicomSeries.resetUIDs()
      • DicomSeries.setFromDirectory()
      • DicomSeries.setFromFileList()
      • DicomSeries.setTags_all()
      • DicomSeries.sliceLocations
      • DicomSeries.sortByInstanceNumber()
      • DicomSeries.sortBySlice_InstanceNumber()
      • DicomSeries.tagsToJson()
      • DicomSeries.writeToNII()
      • DicomSeries.writeToOrganisedFileStructure()
      • DicomSeries.writeToVTI()
      • DicomSeries.writeToVTS()
      • DicomSeries.yieldDataset()
    • DicomStudy
      • DicomStudy.anonymise()
      • DicomStudy.checkIfShouldUse_SAFE_NAMING()
      • DicomStudy.filterByTag()
      • DicomStudy.getNumberOfDicoms()
      • DicomStudy.getPatientOverview()
      • DicomStudy.getSeriesByID()
      • DicomStudy.getSeriesBySeriesNumber()
      • DicomStudy.getSeriesByTag()
      • DicomStudy.getSeriesByUID()
      • DicomStudy.getSeriesMatchingDescription()
      • DicomStudy.getStudyOverview()
      • DicomStudy.getStudySummary()
      • DicomStudy.getStudySummaryDict()
      • DicomStudy.getTag()
      • DicomStudy.getTagListAndNames()
      • DicomStudy.getTagValuesList()
      • DicomStudy.getTopDir()
      • DicomStudy.isCompressed()
      • DicomStudy.mergeSeriesVolumesWithTime()
      • DicomStudy.resetUIDs()
      • DicomStudy.setFromDictionary()
      • DicomStudy.setFromDirectory()
      • DicomStudy.setSafeNameMode()
      • DicomStudy.setTags_all()
      • DicomStudy.writeFDQ()
      • DicomStudy.writeToOrganisedFileStructure()
      • DicomStudy.writeToZipArchive()
    • ListOfDicomStudies
      • ListOfDicomStudies.anonymise()
      • ListOfDicomStudies.buildMSTable()
      • ListOfDicomStudies.filterByTag()
      • ListOfDicomStudies.getNumberOfDicoms()
      • ListOfDicomStudies.getStudyByDate()
      • ListOfDicomStudies.getStudyByPID()
      • ListOfDicomStudies.getStudyByTag()
      • ListOfDicomStudies.getSummaryString()
      • ListOfDicomStudies.getTableOfTagValues()
      • ListOfDicomStudies.isCompressed()
      • ListOfDicomStudies.printSummaryTable()
      • ListOfDicomStudies.resetUIDs()
      • ListOfDicomStudies.setFromDcmDict()
      • ListOfDicomStudies.setFromDirectory()
      • ListOfDicomStudies.setFromInput()
      • ListOfDicomStudies.setFromTar()
      • ListOfDicomStudies.setFromZip()
      • ListOfDicomStudies.setSafeNameMode()
      • ListOfDicomStudies.writeToOrganisedFileStructure()
      • ListOfDicomStudies.writeToZipArchive()
    • distBetweenTwoPts()
    • getJsonDict()
    • getResolution()
    • getTagFromJson()
    • organiseDicoms()
    • studySummary()
    • writeImageStackToDicom()
    • writeNumpyArrayToDicom()
    • writeVTIToDicoms()
  • spydcmtk.dcmTools module
    • DicomTags
      • DicomTags.AccessionNumber
      • DicomTags.AcquisitionMatrix
      • DicomTags.BodyPartExamined
      • DicomTags.CardiacNumberOfImages
      • DicomTags.EchoTime
      • DicomTags.FlipAngle
      • DicomTags.HeartRate
      • DicomTags.ImageOrientationPatient
      • DicomTags.ImagePositionPatient
      • DicomTags.InstanceNumber
      • DicomTags.InversionTime
      • DicomTags.MagneticFieldStrength
      • DicomTags.Manufacturer
      • DicomTags.ManufacturerModelName
      • DicomTags.Modality
      • DicomTags.NominalInterval
      • DicomTags.NumberOfAverages
      • DicomTags.PatientDateOfBirth
      • DicomTags.PatientID
      • DicomTags.PatientName
      • DicomTags.PatientOrientation
      • DicomTags.PatientPosition
      • DicomTags.PatientSex
      • DicomTags.PixelSpacing
      • DicomTags.ReceiveCoilName
      • DicomTags.RepetitionTime
      • DicomTags.SeriesDescription
      • DicomTags.SeriesInstanceUID
      • DicomTags.SeriesNumber
      • DicomTags.SliceThickness
      • DicomTags.SoftwareVersions
      • DicomTags.SpacingBetweenSlices
      • DicomTags.StudyDate
      • DicomTags.StudyDescription
      • DicomTags.StudyID
      • DicomTags.StudyInstanceUID
      • DicomTags.TriggerTime
      • DicomTags.TriggerWindow
    • NumpyEncoder
      • NumpyEncoder.default()
    • anonymiseDicomDS()
    • buildFakeDS()
    • cleanString()
    • countFilesInDir()
    • dbDateToDateTime()
    • distPts()
    • fixPath()
    • getDicomDictFromTar()
    • getDicomDictFromZip()
    • getDicomFileIdentifierStr()
    • getDicomTagsDict()
    • getPatientDirName()
    • getRootDirWithSEdirs()
    • getSaveFileNameFor_ds()
    • getSaveFileNameFor_ds_UID()
    • getSeriesDirName()
    • getStdDicomTags()
    • getStudyDirName()
    • getTagCode()
    • instanceNumberSortKey()
    • organiseDicomHeirarchyByUIDs()
    • parseJsonToDictionary()
    • readDicomFile_intoDict()
    • seriesNumbersToDicomDirList()
    • sliceLoc_InstanceNumberSortKey()
    • streamDicoms()
    • walkdir()
    • writeDictionaryToJSON()
    • writeDirectoryToNII()
    • writeOut_ds()
  • spydcmtk.dcmVTKTK module
    • NoVtkError
    • PatientMeta
      • PatientMeta.Dimensions
      • PatientMeta.ImageOrientationPatient
      • PatientMeta.ImagePositionPatient
      • PatientMeta.Origin
      • PatientMeta.PatientPosition
      • PatientMeta.PixelSpacing
      • PatientMeta.SliceLocation0
      • PatientMeta.SliceThickness
      • PatientMeta.SliceVector
      • PatientMeta.Spacing
      • PatientMeta.SpacingBetweenSlices
      • PatientMeta.Times
      • PatientMeta.buildImage2PatientCoordinateMatrix()
      • PatientMeta.getMatrix()
      • PatientMeta.getMeta()
      • PatientMeta.getMetaForDICOM()
      • PatientMeta.getMetaForVTK()
      • PatientMeta.getVTKTransform()
      • PatientMeta.getVtkMatrix()
      • PatientMeta.imageToPatientCoordinates()
      • PatientMeta.initFromDicomSeg()
      • PatientMeta.initFromDicomSeries()
      • PatientMeta.initFromDictionary()
      • PatientMeta.initFromVTI()
      • PatientMeta.patientToImageCoordinates()
      • PatientMeta.setMeta()
      • PatientMeta.transformVTKData()
      • PatientMeta.updateFromMeta()
    • addFieldDataFromDcmDataSet()
    • arrToVTI()
    • arrToVTS()
    • array_to_DcmSeg()
    • filterResampleToImage()
    • getDcmSeg_meta_depreciated()
    • mergePhaseSeries4D()
    • readImageStackToVTI()
    • scaleVTI()
    • vtkfilterFlipImageData()
    • writeArrToVTI()
    • writeVTIDict()
  • spydcmtk.spydcm module
    • INTERACTIVE
      • INTERACTIVE.buildFDQ()
      • INTERACTIVE.buildOverviewImage()
      • INTERACTIVE.buildVTS()
      • INTERACTIVE.dataSummary()
      • INTERACTIVE.displayMenu()
      • INTERACTIVE.getUserInput()
      • INTERACTIVE.quit()
      • INTERACTIVE.run()
    • MyParser
      • MyParser.error()
    • anonymiseInPlace()
    • buildTableOfDicomParamsForManuscript()
    • checkArgs()
    • convertInputsToHTML()
    • directoryToVTI()
    • directoryToVTS()
    • getAllDirsUnderRootWithDicoms()
    • getTag()
    • inspect()
    • main()
    • returnFirstDicomFound()
    • runActions()
    • vtkToHTML()
    • writeDirectoryToNII()
  • spydcmtk.spydcm_config module
  • Module contents