def DICOM_MR_backbone(self, SeriesInstanceUID):
# Main data elements
ds = Dataset()
ds.SpecificCharacterSet = 'ISO_IR 101' # latin-2
ds.ImageType = ['ORIGINAL', 'PRIMARY', 'OTHER']
ds.SOPClassUID = '1.2.840.10008.5.1.4.1.1.4' # MR
ds.SOPInstanceUID = f'2.5.{uuid.uuid4().int:d}'
ds.StudyDate = '' # YYYYMMDD
ds.StudyTime = '' # HHMMSS
ds.AccessionNumber = ''
ds.Modality = 'MR'
ds.Manufacturer = 'Jakub Dzik'
ds.ReferringPhysicianName = ''
ds.PatientName = 'Anonymized'
ds.PatientID = '1234'
ds.PatientBirthDate = ''
ds.PatientSex = ''
ds.ContrastBolusAgent = ''
ds.ScanningSequence = 'EP'
ds.SequenceVariant = 'NONE'
ds.ScanOptions = ''
ds.MRAcquisitionType = '3D'
ds.EchoTime = ''
ds.EchoTrainLength = ''
ds.PatientPosition = ''
ds.StudyInstanceUID = self.StudyInstanceUID
ds.SeriesInstanceUID = SeriesInstanceUID
ds.StudyID = ''
ds.AcquisitionNumber = ''
ds.FrameOfReferenceUID = self.FrameOfReferenceUID
ds.Laterality = ''
ds.PositionReferenceIndicator = ''
ds.SamplesPerPixel = 1
ds.PhotometricInterpretation = 'MONOCHROME2'
ds.CommentsOnThePerformedProcedureStep = ''
ds.RequestedProcedureID = 'MOZGOWIE'
ds.ReasonForTheRequestedProcedure = ''
ds.RequestedProcedurePriority = ''
ds.PatientTransportArrangements = ''
ds.RequestedProcedureLocation = ''
ds.RequestedProcedureComments = ''
ds.ReasonForTheImagingServiceRequest = ''
ds.IssueDateOfImagingServiceRequest = '20210222'
ds.IssueTimeOfImagingServiceRequest = '084604.947'
ds.OrderEntererLocation = ''
ds.OrderCallbackPhoneNumber = ''
ds.ImagingServiceRequestComments = ''
ds.PresentationLUTShape = 'IDENTITY'
ds.is_implicit_VR = False
ds.is_little_endian = True
return ds
def generate_dicom(self, file_out_name: str, gantry_angle: float = 0.0, coll_angle: float = 0.0,
table_angle: float = 0.0):
file_meta = FileMetaDataset()
file_meta.FileMetaInformationGroupLength = 196
file_meta.FileMetaInformationVersion = b'\x00\x01'
file_meta.MediaStorageSOPClassUID = '1.2.840.10008.5.1.4.1.1.481.1'
file_meta.MediaStorageSOPInstanceUID = '1.2.246.352.64.1.5468686515961995030.4457606667843517571'
file_meta.TransferSyntaxUID = '1.2.840.10008.1.2'
file_meta.ImplementationClassUID = '1.2.246.352.70.2.1.120.1'
file_meta.ImplementationVersionName = 'MergeCOM3_410'
# Main data elements
ds = Dataset()
ds.SpecificCharacterSet = 'ISO_IR 100'
ds.ImageType = ['ORIGINAL', 'PRIMARY', 'PORTAL']
ds.InstanceCreationDate = '20161230'
ds.InstanceCreationTime = '215510'
ds.SOPClassUID = '1.2.840.10008.5.1.4.1.1.481.1'
ds.SOPInstanceUID = '1.2.246.352.64.1.5468686515961995030.4457606667843517571'
ds.StudyDate = '20161230'
ds.ContentDate = '20161230'
ds.StudyTime = '215441.936'
ds.ContentTime = '215441.936'
ds.AccessionNumber = ''
ds.Modality = 'RTIMAGE'
ds.ConversionType = ''
ds.Manufacturer = 'Varian Medical Systems'
ds.ReferringPhysicianName = ''
ds.StationName = 'NDS-WKS-SN9999'
ds.OperatorsName = 'King Kong'
ds.ManufacturerModelName = 'VMS.XI.Service'
ds.PatientName = 'Grace Hopper'
ds.PatientID = 'VMS.XI.Service'
ds.PatientBirthDate = '19000101'
ds.PatientBirthTime = '000000'
ds.PatientSex = ''
ds.SoftwareVersions = '2.5.13.2'
ds.StudyInstanceUID = '1.2.246.352.64.4.5644626269434644263.1905029945372990626'
ds.SeriesInstanceUID = '1.2.246.352.64.2.5508761605912087323.11665958260371685307'
ds.StudyID = 'fdd794f2-8520-4c4a-aecc-e4446c1730ff'
ds.SeriesNumber = None
ds.AcquisitionNumber = "739774555"
ds.InstanceNumber = "1"
ds.PatientOrientation = ''
ds.FrameOfReferenceUID = '1.2.246.352.64.3.4714322356925391886.9391210174715030407'
ds.PositionReferenceIndicator = ''
ds.SamplesPerPixel = 1
ds.PhotometricInterpretation = 'MONOCHROME1'
ds.PlanarConfiguration = 0
ds.Rows = self.shape[0]
ds.Columns = self.shape[1]
ds.BitsAllocated = 16
ds.BitsStored = 16
ds.HighBit = 15
ds.PixelRepresentation = 0
ds.WindowCenter = "32767.0"
ds.WindowWidth = "65535.0"
ds.RescaleIntercept = "0.0"
ds.RescaleSlope = "1.0"
ds.RescaleType = 'US'
ds.RTImageLabel = 'MV_180'
ds.RTImageDescription = ""
ds.ReportedValuesOrigin = 'ACTUAL'
ds.RTImagePlane = 'NORMAL'
ds.XRayImageReceptorTranslation = [0.00, 0.00, 1000 - self.sid]
ds.XRayImageReceptorAngle = "0.0"
ds.RTImageOrientation = [1, 0, 0, 0, -1, 0]
ds.ImagePlanePixelSpacing = [self.pixel_size, self.pixel_size]
ds.RTImagePosition = [-214.872, 214.872]
ds.RadiationMachineName = 'TrueBeam from Hell'
ds.RadiationMachineSAD = "1000.0"
ds.RTImageSID = self.sid
ds.PrimaryDosimeterUnit = 'MU'
ds.GantryAngle = str(gantry_angle)
ds.BeamLimitingDeviceAngle = str(coll_angle)
ds.PatientSupportAngle = str(table_angle)
ds.TableTopVerticalPosition = "-24.59382842824"
ds.TableTopLongitudinalPosition = "200.813502948597"
ds.TableTopLateralPosition = "3.00246706215532"
ds.PixelData = self.image # XXX Array of 3276800 bytes excluded
ds.file_meta = file_meta
ds.is_implicit_VR = True
ds.is_little_endian = True
ds.save_as(file_out_name, write_like_original=False)
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
