def dcm_initialise():
### This function based on pydicom codify output
# File meta info data elements
file_meta = Dataset()
# file_meta.FileMetaInformationGroupLength = 194 ### REQUIRES DEFINITION
file_meta.FileMetaInformationVersion = b'\x00\x01'
file_meta.MediaStorageSOPClassUID = '1.2.840.10008.5.1.4.1.1.4'
# file_meta.MediaStorageSOPInstanceUID = '1.2.40.0.13.1.75591523476291404472265359935487530723' ### REQUIRES DEFINITION
file_meta.TransferSyntaxUID = '1.2.840.10008.1.2'
file_meta.ImplementationClassUID = '1.2.276.0.7230010.3.0.3.6.1'
file_meta.ImplementationVersionName = 'PERINATAL_CUSTOM_PYDICOM'
# Main data elements
ds = Dataset()
ds.SpecificCharacterSet = 'ISO_IR 100'
# ds.ImageType = ['ORIGINAL', 'PRIMARY', 'M_FFE', 'M', 'FFE'] ### REQUIRES DEFINITION
ds.InstanceCreationDate = ''
ds.InstanceCreationTime = ''
ds.InstanceCreatorUID = '1.2.40.0.13.1.203399489339977079628124438700844270739' ### TODO: determine if required
ds.SOPClassUID = '1.2.840.10008.5.1.4.1.1.4'
# ds.SOPInstanceUID = '1.2.40.0.13.1.75591523476291404472265359935487530723' ### REQUIRES DEFINITION
ds.StudyDate = ''
ds.SeriesDate = ''
ds.AcquisitionDate = ''
ds.ContentDate = ''
ds.StudyTime = ''
ds.SeriesTime = '' # '182511.32000'
ds.AcquisitionTime = '' # '182511.32'
ds.ContentTime = '' # '182511.32'
ds.AccessionNumber = ''
ds.Modality = 'MR'
ds.Manufacturer = 'Philips Healthcare'
ds.CodeValue = ''
ds.CodingSchemeDesignator = 'DCM'
ds.CodeMeaning = ''
# Procedure Code Sequence
procedure_code_sequence = Sequence()
ds.ProcedureCodeSequence = procedure_code_sequence
# Procedure Code Sequence: Procedure Code 1
procedure_code1 = Dataset()
procedure_code1.CodeValue = '' # 'RA.MRAAOT'
procedure_code1.CodingSchemeDesignator = '' # '99ORBIS'
procedure_code1.CodeMeaning = '' # 'CE-MRA Aorta thorakal'
procedure_code1.ContextGroupExtensionFlag = 'N'
procedure_code_sequence.append(procedure_code1)
ds.OperatorsName = ''
ds.AdmittingDiagnosesDescription = ''
ds.ManufacturerModelName = 'Ingenia'
# Referenced Performed Procedure Step Sequence
refd_performed_procedure_step_sequence = Sequence()
ds.ReferencedPerformedProcedureStepSequence = refd_performed_procedure_step_sequence
# Referenced Performed Procedure Step Sequence: Referenced Performed Procedure Step 1
refd_performed_procedure_step1 = Dataset()
refd_performed_procedure_step1.InstanceCreationDate = ''
refd_performed_procedure_step1.InstanceCreationTime = ''
refd_performed_procedure_step1.InstanceCreatorUID = '1.2.40.0.13.1.203399489339977079628124438700844270739' ### TODO: determine if required
refd_performed_procedure_step1.ReferencedSOPClassUID = '1.2.840.10008.3.1.2.3.3'
refd_performed_procedure_step1.ReferencedSOPInstanceUID = '1.3.46.670589.11.17204.5.0.6524.2012082117320696006'
refd_performed_procedure_step1.InstanceNumber = "0"
refd_performed_procedure_step_sequence.append(
refd_performed_procedure_step1)
# Referenced Image Sequence
refd_image_sequence = Sequence()
ds.ReferencedImageSequence = refd_image_sequence
# Referenced Image Sequence: Referenced Image 1
refd_image1 = Dataset()
refd_image1.ReferencedSOPClassUID = '1.2.840.10008.5.1.4.1.1.4'
refd_image1.ReferencedSOPInstanceUID = '1.2.40.0.13.1.89078282904346598403696206113943676723'
refd_image_sequence.append(refd_image1)
# Referenced Image Sequence: Referenced Image 2
refd_image2 = Dataset()
refd_image2.ReferencedSOPClassUID = '1.2.840.10008.5.1.4.1.1.4'
refd_image2.ReferencedSOPInstanceUID = '1.2.40.0.13.1.295129673873169057216869911833080985343'
refd_image_sequence.append(refd_image2)
# Referenced Image Sequence: Referenced Image 3
refd_image3 = Dataset()
refd_image3.ReferencedSOPClassUID = '1.2.840.10008.5.1.4.1.1.4'
refd_image3.ReferencedSOPInstanceUID = '1.2.40.0.13.1.37560432539838529536104187971339317428'
refd_image_sequence.append(refd_image3)
ds.PatientName = 'Not Specified'
ds.PatientID = 'Not Specified'
ds.PrivateCreator = 'Philips Imaging'
ds.IssuerOfPatientID = ''
ds.PatientBirthDate = ''
ds.OtherPatientIDs = ''
ds.OtherPatientNames = ''
ds.PatientMotherBirthName = ''
# ds.PregnancyStatus = 4
ds.ScanningSequence = 'kt bFFE' # 'GR'
ds.SequenceVariant = '' # 'SP'
ds.ScanOptions = '' # 'FC'
ds.MRAcquisitionType = '3D'
ds.SequenceName = ''
ds.SliceThickness = ''
ds.RepetitionTime = "3.8"
ds.EchoTime = "1.9"
ds.NumberOfAverages = "1"
ds.ImagingFrequency = "127.768401"
ds.ImagedNucleus = '1H'
ds.EchoNumbers = "1"
ds.MagneticFieldStrength = "1.5"
ds.SpacingBetweenSlices = ""
ds.NumberOfPhaseEncodingSteps = "" # "143"
ds.EchoTrainLength = "" # "3"
ds.PercentSampling = "" # "98.4375"
ds.PercentPhaseFieldOfView = "" # "86.4864871376439"
ds.PixelBandwidth = "" # "3284"
ds.SoftwareVersions = ['5.1.7', '5.1.7.2']
ds.ProtocolName = 'Not Specified'
# ds.TriggerTime = "622" ### REQUIRES DEFINITION
# ds.LowRRValue = "632" # Not sure if needed
# ds.HighRRValue = "733" # Not sure if needed
ds.IntervalsAcquired = "" # "1132"
ds.IntervalsRejected = "" # "20"
ds.HeartRate = ""
ds.ReconstructionDiameter = "" # "379.999992370605"
ds.ReceiveCoilName = 'MULTI COIL'
ds.TransmitCoilName = 'B'
# ds.AcquisitionMatrix = [0, 148, 143, 0] # TODO: Determine if required
ds.InPlanePhaseEncodingDirection = '' # 'ROW'
ds.FlipAngle = "60"
ds.SAR = ""
ds.dBdt = ""
ds.PatientPosition = '' # 'HFS' TODO: Determine if important/required
# ds.AcquisitionDuration = 459.6679992675781 # TODO: Determine if important/required
ds.DiffusionBValue = 0.0
ds.DiffusionGradientOrientation = [0.0, 0.0, 0.0]
ds.StudyInstanceUID = '1.2.40.0.13.1.333311361771566580913219583914625766216' # TODO: determine if needs generating
ds.SeriesInstanceUID = '1.2.40.0.13.1.286595144572817015845933344548631223145' # TODO: determine if needs generating
ds.StudyID = '513842.201207030' # TODO: determine if needs generating
ds.SeriesNumber = ""
ds.AcquisitionNumber = "" # "10"
# ds.InstanceNumber = "319" ### REQUIRES DEFINITION
# ds.ImagePositionPatient = ['-56.040032677094', '-189.81796011867', '225.026188065538'] ### REQUIRES DEFINITION
# ds.ImageOrientationPatient = ['0.51319164037704', '0.85772150754928', '-0.0307911429554', '-0.0599991045892', '6.4554493292E-05', '-0.9981984496116'] ### TODO: decide if need to match Nifti affine
ds.FrameOfReferenceUID = '1.2.40.0.13.1.168070265634523572089252568290704983898' # TODO: determine if required
ds.TemporalPositionIdentifier = "" # "1"
ds.NumberOfTemporalPositions = "" # "1"
ds.PositionReferenceIndicator = ''
# ds.SliceLocation = "38.9999961150011" ### REQUIRES DEFINITION
ds.SamplesPerPixel = 1
ds.PhotometricInterpretation = 'MONOCHROME2'
# ds.Rows = 192 ### REQUIRES DEFINITION
# ds.Columns = 192 ### REQUIRES DEFINITION
# ds.PixelSpacing = ['1.97916662693023', '1.97916662693023'] ### REQUIRES DEFINITION
ds.BitsAllocated = 16
ds.BitsStored = 12
ds.HighBit = 11
ds.PixelRepresentation = 0
# ds.WindowCenter = "213.04" ### REQUIRES DEFINITION
# ds.WindowWidth = "370.49" ### REQUIRES DEFINITION
ds.LossyImageCompression = '00'
ds.RequestingPhysician = ''
ds.RequestingService = ''
ds.RequestedProcedureDescription = 'FCMR 4D FLOW MRI'
ds.PerformedStationAETitle = ''
ds.PerformedProcedureStepStartDate = '' # '20120821'
ds.PerformedProcedureStepStartTime = '' # '173207'
ds.PerformedProcedureStepEndDate = '' # '20120821'
ds.PerformedProcedureStepEndTime = '' # '173207'
ds.PerformedProcedureStepID = '' # '398712726'
ds.PerformedProcedureStepDescription = '' # 'CE-MRA Aorta thorakal'
# Performed Protocol Code Sequence
performed_protocol_code_sequence = Sequence()
ds.PerformedProtocolCodeSequence = performed_protocol_code_sequence
# Performed Protocol Code Sequence: Performed Protocol Code 1
performed_protocol_code1 = Dataset()
performed_protocol_code1.CodeValue = '' # 'RA.MRAAOT'
performed_protocol_code1.CodingSchemeDesignator = '' # '99ORBIS'
performed_protocol_code1.CodeMeaning = '' # 'CE-MRA Aorta thorakal'
performed_protocol_code1.ContextGroupExtensionFlag = 'N'
performed_protocol_code_sequence.append(performed_protocol_code1)
# Film Consumption Sequence
film_consumption_sequence = Sequence()
ds.FilmConsumptionSequence = film_consumption_sequence
ds.RequestedProcedureID = '513842.201207030'
# Real World Value Mapping Sequence
real_world_value_mapping_sequence = Sequence()
ds.RealWorldValueMappingSequence = real_world_value_mapping_sequence
# Real World Value Mapping Sequence: Real World Value Mapping 1
real_world_value_mapping1 = Dataset()
real_world_value_mapping1.RealWorldValueIntercept = 0.0
real_world_value_mapping1.RealWorldValueSlope = 0.0 # 4.280830280830281
real_world_value_mapping_sequence.append(real_world_value_mapping1)
ds.PresentationLUTShape = 'IDENTITY'
return file_meta, ds
ds.is_little_endian = True
ds.is_implicit_VR = True
# Set creation date/time
ds.SOPClassUID = 'RT Image Storage'
ds.SOPInstanceUID = "1.2.826.0.1.3680043.8.937.1.20170926.8691"
ds.ImageType = ['ORIGINAL', 'PRIMARY', 'PORTAL', '']
dt = datetime.datetime.now()
ds.StudyDate = dt.strftime('%Y%m%d')
ds.SeriesDate = dt.strftime('%Y%m%d')
ds.AcquisitionDate = dt.strftime('%Y%m%d')
ds.ContentDate = dt.strftime('%Y%m%d')
timeStr = dt.strftime('%H%M%S.%f') # long format with micro seconds
ds.StudyTime = timeStr
ds.SeriesTime = timeStr
ds.AcquisitionTime = timeStr
ds.ContentTime = timeStr
ds.AccessionNumber = ''
ds.Modality = 'RTImage'
ds.ConversionType = 'DI'
ds.Manufacturer = "GATE"
ds.ReferringPhysiciansName = ''
ds.StationName = "GATE Dose Actor"
ds.PatientName = "Phantom name"
#ds.PatientName = raw_input('Give your DICOM a name: ')
ds.PatientID = "123456"
ds.PatientBirthDate = ''
ds.PatientSex = ''
ds.DeviceSerialNumber = '9101060'
ds.StudyInstanceUID = '1.2.826.0.1.3680043.2.1125.1.35859627302800520295369011388644332'
ds.SeriesInstanceUID = '1.2.826.0.1.3680043.2.1125.1.81507923164692601234912200876243257'
