def find_study_by_patient_id_and_accession_number(self, patient_id,
accession_number):
studies = []
assoc = self._setup_c_find_assoc()
if assoc.is_established:
ds = Dataset()
ds.PatientID = patient_id
ds.StudyInstanceUID = ''
ds.StudyDate = ''
ds.StudyTime = ''
if len(accession_number):
ds.AccessionNumber = accession_number
ds.QueryRetrieveLevel = "STUDY"
response = assoc.send_c_find(ds, query_model='S')
for (status, identifier) in response:
if status.get(0x00000900).value == 65280:
studies.append(identifier)
# studies.append(identifier.get_item(0x0020000D).value)
assoc.release()
if len(studies) == 0:
logger.info("can't find studies with search conditions")
else:
latest_study_date = studies[0].get_item(0x00080020).value
latest_study_uid = studies[0].get_item(0x0020000D).value
for study in studies:
if study.get_item(0x00080020).value > latest_study_date:
latest_study_uid = study.get_item(0x0020000D).value
else:
logger.error("find_studies_by_patient_id association failed")
return latest_study_uid
def get_clean_worklist(self):
""" Generates a clean worklist """
worklist_item = Dataset()
worklist_item.StudyInstanceUID = generate_uid(prefix='1.2.840.113619.2.391.6789.', entropy_srcs=[_create_random_ascii_string(10), _create_random_ascii_string(10)])
worklist_item.Modality = 'US'
worklist_item.SpecificCharacterSet = self._specific_charset
worklist_item.AccessionNumber = '123'
worklist_item.PatientBirthDate = '19901015'
worklist_item.PatientName = 'Clean^Exam'
worklist_item.PatientID = _create_random_ascii_string(64)
worklist_item.IssuerOfPatientID = 'Issuer of patient id: Bob'
worklist_item.PatientWeight = str(100.0)
worklist_item.PatientSize = str(2.1)
worklist_item.AdmissionID = 'Admission id 3'
worklist_item.RequestedProcedureID = 'Step id 2'
worklist_item.RequestedProcedureDescription = 'Step description Clean Exam'
otherPatientIdsSq = [Dataset(), Dataset()]
for otherPatientId in otherPatientIdsSq:
otherPatientId.PatientID = 'Bob123'
otherPatientId.IssuerOfPatientID = 'Issuer of patient id: Arne'
otherPatientId.TypeOfPatientID = 'TEXT'
worklist_item.OtherPatientIDsSequence = otherPatientIdsSq
step = Dataset()
step.ScheduledPerformingPhysicianName = 'Ola Nordmann'
step.ScheduledProcedureStepStartDate = '20201224'
step.ScheduledProcedureStepStartTime = '121212'
step.ScheduledProcedureStepDescription = 'Scheduled procedure step description '
step.CommentsOnTheScheduledProcedureStep = 'Scheduled step comments '
worklist_item.ScheduledProcedureStepSequence = [step]
return worklist_item
def get_basedataset():
ds = Dataset()
ds.PatientName = ''
ds.PatientID = ''
ds.StudyInstanceUID = ''
ds.SeriesUID = ''
ds.AccessionNumber = ''
ds.QueryRetrieveLevel = ''
ds.PatientSize = ''
ds.ModalitiesInStudy = ''
ds.SOPClassesInStudy = ''
ds.StudyDescription = '*'
ds.SeriesDescription = ''
ds.FailedSOPSequence = ''
ds.DerivationCodeSequence = ''
ds.PatientSpeciesCodeSequence = ''
ds.Series = ''
ds.TransferSyntaxUID = ''
ds.SeriesInStudy = ''
ds.SeriesNumber = ''
ds.ImagesInSeries = ''
ds.SeriesInstanceUID = ''
ds.NumberOfSeriesRelatedInstances = ''
ds.StudyDate = ''
return ds
def query_study(localAE, localPort, destIP, destAE, destPort, patientID,
accessionNumber, studyInstanceUID, moodality, studyDateStart,
studyDateEnd):
# Prepare local information
ae = AE(ae_title=localAE)
ae.acse_timeout = 30
# Add a requested presentation context
ae.add_requested_context(StudyRootQueryRetrieveInformationModelFind)
# Create local Identifier dataset
ds = Dataset()
ds.PatientName = ''
ds.PatientID = patientID
ds.StudyInstanceUID = studyInstanceUID
ds.AccessionNumber = accessionNumber
ds.Modality = moodality
ds.StudyDate = studyDateStart + '-' + studyDateEnd
ds.QueryRetrieveLevel = 'STUDY'
# Associate with Peer
assoc = ae.associate(destIP, destPort, ae_title=destAE)
# Result list
studyList = []
if assoc.is_established:
# Find information from Peer
responses = assoc.send_c_find(
ds, StudyRootQueryRetrieveInformationModelFind)
# Check find result one by one
for (status, identifier) in responses:
if status:
#print('C-FIND Status:0x{0:04x}'.format(status.Status))
# Add result into list when status is pending or success
if status.Status in (0xFF00, 0xFF01):
print('Pick up Study information: %s' %
identifier.PatientID)
studyList.append(identifier)
else:
print(
'Connection timed out, was aborted or received invalid response'
)
assoc.release()
else:
print('Association rejected, aborted or never connected')
return studyList
def retrieve(
accession,
patient_id,
ae_title='GEPACSD042',
):
ae = AE('RESEARCH')
ae.add_requested_context(StudyRootQueryRetrieveInformationModelFind)
ae.add_requested_context(StudyRootQueryRetrieveInformationModelMove,
transfer_syntax=ts)
assoc = ae.associate(__getattr__('ae_titles')[ae_title][0],
__getattr__('ae_titles')[ae_title][1],
ae_title=ae_title)
logger.debug(str(assoc))
try:
# get study id
ds = Dataset()
ds.AccessionNumber = accession
ds.PatientID = patient_id
ds.QueryRetrieveLevel = 'STUDY'
ds.StudyInstanceUID = ''
StudyInstanceUID = [i.StudyInstanceUID for i in cfind(ds, assoc)][0]
identifiers = [StudyInstanceUID]
ds.StudyInstanceUID = StudyInstanceUID
cmove(ds, assoc)
# get series id
#ds.QueryRetrieveLevel = 'SERIES'
#ds.StudyInstanceUID = StudyInstanceUID
#ds.SeriesInstanceUID = ''
#ds.SeriesDescription = ''
#ds.ImageType = ''
#ds.KVP = ''
#identifiers = cfind(ds, assoc, )
#logger.debug ('Num series found: {}'.format(len(identifiers)))
#logger.debug (identifiers)
# move series
#for id in identifiers:
# ds.SeriesInstanceUID = id.SeriesInstanceUID
# cmove(ds, assoc, )
assoc.release()
except Exception as e:
assoc.release()
raise e
assert len(identifiers) > 0, "No studies found for {} from {}".format(
accession, ae_title)
return identifiers
def retrieve_study(cfg, acc_no, output_dir):
if not os.path.exists(output_dir):
try:
os.makedirs(output_dir)
except OSError as exc: # Guard against race condition
if exc.errno != errno.EEXIST:
raise
ae = AE(ae_title=cfg['pacs']['my']['aet'])
ae.requested_contexts = QueryRetrievePresentationContexts
assoc = ae.associate(cfg['pacs']['called']['ip'],
cfg['pacs']['called']['port'])
ds = Dataset()
ds.AccessionNumber = acc_no
ds.QueryRetrieveLevel = "SERIES"
ds.Modality = ""
responses = assoc.send_c_find(ds, query_model='P')
for (status, dataset) in responses:
if status.Status in (0xFF00, 0xFF01):
modality = dataset.Modality
if modality not in ('CR', 'DX'):
continue
p_id = dataset.PatientID
study_uid = dataset.StudyInstanceUID
series_uid = dataset.SeriesInstanceUID
cmd_str = r'''movescu {pacs_ip} {pacs_port} +P {port} +xa -aec {pacs_aet} -aet {aet} \
-k QueryRetrieveLevel=SERIES \
-k PatientID={p_id} \
-k StudyInstanceUID={study_uid} \
-k SeriesInstanceUID={series_uid} \
-od {output_dir} \
'''.format(pacs_ip=cfg['pacs']['called']['ip'],
pacs_port=cfg['pacs']['called']['port'],
pacs_aet=cfg['pacs']['called']['aet'],
aet=cfg['pacs']['my']['aet'],
port=cfg['pacs']['my']['port'],
p_id=p_id,
study_uid=study_uid,
series_uid=series_uid,
output_dir=output_dir)
#print(cmd_str)
os.system(cmd_str)
print("Success. acc_no={}".format(acc_no))
elif status.Status != 0x0:
print("acc_no={}, status={}".format(acc_no, hex(status.Status)))
assoc.release()
def pacs_find(hostname, port, host_ae_title, user_ae_title,
query_retrieve_level, accession_number, patient_id):
ae = AE(ae_title=user_ae_title)
ae.add_requested_context(StudyRootQueryRetrieveInformationModelFind)
ds = Dataset()
ds.AccessionNumber = accession_number
ds.PatientID = patient_id
ds.PatientBirthDate = ''
ds.StudyDescription = ''
ds.StudyInstanceUID = ''
ds.StudyDate = ''
ds.StudyTime = ''
ds.ModalitiesInStudy = ''
ds.StationName = ''
ds.NumberOfStudyRelatedInstances = ''
ds.QueryRetrieveLevel = query_retrieve_level
assoc = ae.associate(hostname, port, ae_title=host_ae_title)
a = None
matches = 0
msg = None
if assoc.is_established:
responses = assoc.send_c_find(
ds, StudyRootQueryRetrieveInformationModelFind)
for (status, identifier) in responses:
if matches == 2:
a = None
ae.shutdown()
msg = 'Multiple studies found for this query.'
break
if status:
msg = find_status_dict[status.Status][1]
if status.Status in (0xFF00, 0xFF01):
a = identifier
matches += 1
if status.Status == 0x0000 and a is None:
msg = 'No study found for this query.'
else:
msg = 'Connection timed out, was aborted or received invalid response.'
assoc.release()
else:
msg = 'Association rejected, aborted or never connected.'
matches = None
return a, matches, msg
def get_random_worklist(self):
""" Generate a random worklist """
worklist_item = Dataset()
worklist_item.StudyInstanceUID = generate_uid(prefix='1.2.840.113619.2.391.6789.', entropy_srcs=[_random_unicode_string(10, _get_random_language_string()), _random_unicode_string(10, _get_random_language_string())])
worklist_item.Modality = 'US'
worklist_item.SpecificCharacterSet = self._specific_charset
worklist_item.CurrentPatientLocation = _extend_with_random_to_length('', self._fault_provider. _get_random_string_length(64), self._fault_provider._return_None_string)
worklist_item.AccessionNumber = _random_unicode_string(16, _get_random_language_string())
worklist_item.PatientBirthDate = _random_dicom_date_after_1900()
worklist_item.PatientName = self._get_person_name()
worklist_item.PatientID = _extend_with_random_to_length('', self._fault_provider. _get_random_string_length(64), self._fault_provider._return_None_string)
self._fault_provider._sleep_random() #Possible delay
worklist_item.IssuerOfPatientID = _extend_with_random_to_length('', self._fault_provider. _get_random_string_length(64), self._fault_provider._return_None_string)
worklist_item.PatientWeight = str(random.uniform(10.0, 150.0))[:16]
worklist_item.PatientSize = str(random.uniform(1.0, 2.5))[:16]
worklist_item.AdmissionID = _extend_with_random_to_length('', self._fault_provider. _get_random_string_length(64), self._fault_provider._return_None_string)
worklist_item.RequestedProcedureID = _extend_with_random_to_length('', self._fault_provider. _get_random_string_length(16), self._fault_provider._return_None_string)
worklist_item.RequestedProcedureDescription = _extend_with_random_to_length('', self._fault_provider. _get_random_string_length(64), self._fault_provider._return_None_string)
worklist_item.ReferringPhysicianName = self._get_person_name()
otherPatientIdsSq = [Dataset(), Dataset()]
for otherPatientId in otherPatientIdsSq:
otherPatientId.PatientID = _extend_with_random_to_length('', self._fault_provider. _get_random_string_length(64), self._fault_provider._return_None_string)
otherPatientId.IssuerOfPatientID = _extend_with_random_to_length('', self._fault_provider. _get_random_string_length(64), self._fault_provider._return_None_string)
otherPatientId.TypeOfPatientID = 'TEXT'
worklist_item.OtherPatientIDsSequence = otherPatientIdsSq
step = Dataset()
step.ScheduledPerformingPhysicianName = self._get_person_name()
step.ScheduledProcedureStepStartDate = _random_dicom_date_after_1900()
step.ScheduledProcedureStepStartTime = _random_dicom_time()
step.ScheduledProcedureStepDescription = _extend_with_random_to_length('', self._fault_provider. _get_random_string_length(64), self._fault_provider._return_None_string)
step.CommentsOnTheScheduledProcedureStep = _extend_with_random_to_length('', self._fault_provider. _get_random_string_length(10240), self._fault_provider._return_None_string)
worklist_item.ScheduledProcedureStepSequence = [step]
return worklist_item
def retrieve_study(cfg, acc_no, output_dir):
if not os.path.exists(output_dir):
try:
os.makedirs(output_dir)
except OSError as exc: # Guard against race condition
if exc.errno != errno.EEXIST:
raise
ae = AE(ae_title=cfg['pacs']['my']['aet'])
ae.requested_contexts = QueryRetrievePresentationContexts
assoc_cf = ae.associate(cfg['pacs']['called']['ip'],
cfg['pacs']['called']['port'])
assoc_cm = ae.associate(cfg['pacs']['called']['ip'],
cfg['pacs']['called']['port'])
ds_q = Dataset()
ds_q.AccessionNumber = acc_no
ds_q.QueryRetrieveLevel = "SERIES"
ds_q.Modality = ""
responses_cf = assoc_cf.send_c_find(ds_q, query_model='P')
for (status_cf, dataset_cf) in responses_cf:
if status_cf.Status in (0xFF00, 0xFF01):
modality = dataset_cf.Modality
if modality not in ('CR', 'DX'):
continue
responses_cm = assoc_cm.send_c_move(dataset_cf,
cfg['pacs']['my']['aet'],
query_model='P')
for (status_cm, dataset_cm) in responses_cm:
if (status_cm.Status == 0x0):
pass
else:
print('status: {}; dataset: {}'.format(
status_cm, dataset_cm))
elif status_cf.Status != 0x0:
print("acc_no={}, status={}".format(acc_no, hex(status_cf.Status)))
assoc_cf.release()
assoc_cm.release()
ds = Dataset()
ds.file_meta = get_file_meta(dcms)
ds.is_implicit_VR = True
ds.is_little_endian = True
ds.fix_meta_info(enforce_standard=True)
dt = datetime.datetime.now()
ds.InstanceCreationDate = dt.strftime("%Y%m%d")
ds.InstanceCreationTime = dt.strftime("%H%M%S.%f")
ds.InstanceCreatorUID = "Anonymous" # TODO
ds.SOPInstanceUID = ds.file_meta.MediaStorageSOPInstanceUID
ds.SOPClassUID = ds.file_meta.MediaStorageSOPClassUID
ds.StudyDate = dcm.StudyDate
ds.StudyTime = dcm.StudyTime
ds.AccessionNumber = dcm.AccessionNumber
ds.Modality = "RTSTRUCT"
ds.Manufacturer = dcm.Manufacturer
ds.ReferringPhysicianName = dcm.ReferringPhysicianName
ds.InstitutionalDepartmentName = "Anonymous" # TODO
ds.ManufacturerModelName = dcm.ManufacturerModelName
ds.PatientName = dcm.PatientName
ds.PatientID = dcm.PatientID
ds.PatientBirthDate = dcm.PatientBirthDate
ds.PatientSex = dcm.PatientSex
ds.StudyInstanceUID = dcm.StudyInstanceUID
ds.StudyID = "Anonymous" # TODO
ds.SeriesNumber = "1" # TODO
ds.StructureSetLabel = "STRCTRLABEL"
ds.StructureSetName = "STRCTRNAME"
ds.StructureSetDate = ds.InstanceCreationDate
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
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 OnRest(output, uri, **request):
config = orthancConfig
try:
worklistdir = config["Worklists"]["Database"]
asnofile = os.sep.join([worklistdir, 'accessionid.conf'])
except KeyError:
output.AnswerBuffer('internal configuration error\n', 'text/plain')
return
try:
today = datetime.today()
try:
with open(asnofile, 'r') as f:
try:
asno = int(f.read())
except ValueError:
asno = 1
except OSError:
asno = 1
with open(asnofile, 'w') as f:
f.write(str(asno + 1))
# File meta info data elements
file_meta = FileMetaDataset()
file_meta.FileMetaInformationGroupLength = 202
file_meta.FileMetaInformationVersion = b'\x00\x01'
file_meta.MediaStorageSOPClassUID = '1.2.276.0.7230010.3.1.0.1'
file_meta.MediaStorageSOPInstanceUID = pydicom.uid.generate_uid(
prefix=None)
file_meta.TransferSyntaxUID = '1.2.840.10008.1.2.1'
file_meta.ImplementationClassUID = '1.2.276.0.7230010.3.0.1.0.0'
file_meta.ImplementationVersionName = 'ORTHANC_RESTWORKLIST_1'
# Main data elements
ds = Dataset()
ds.SpecificCharacterSet = 'ISO_IR 192'
dcm_store_path = os.sep.join([
worklistdir,
'R{:010d}-{}.{}'.format(asno, today.strftime('%Y%m%d%H%M%S'), 'wl')
])
ds.AccessionNumber = 'R{:010d}'.format(asno)
try:
ds.PatientName = '{}^{}'.format(request["get"]["lastname"],
request["get"]["firstname"])
except KeyError:
ds.PatientName = '{}^{}'.format(
request["get"]["name"], request["get"]["surname"]
) # old, buggy parameter naming -> for backwards compatibility
ds.PatientID = request["get"]["id"]
bdparts = request["get"]["birthdate"].split('.')
ds.PatientBirthDate = '{2}{1}{0}'.format(*bdparts)
ds.PatientSex = sexReplacement[request["get"][
"sex"]] # LUT for the sex identifier numbers used by Medical Office (0 = Other / Unknown, 1 = Male, 2 = Female, 3 = Other / Unknown)
ds.StudyInstanceUID = pydicom.uid.generate_uid(prefix=None)
try:
ds.RequestedProcedureDescription = request["get"]["procedure"]
except KeyError:
pass # optional argument, otherwise this tag remains empty
# Scheduled Procedure Step Sequence
scheduled_procedure_step_sequence = Sequence()
ds.ScheduledProcedureStepSequence = scheduled_procedure_step_sequence
# Scheduled Procedure Step Sequence: Scheduled Procedure Step 1
scheduled_procedure_step1 = Dataset()
try:
scheduled_procedure_step1.Modality = request["get"]["modality"]
except KeyError:
scheduled_procedure_step1.Modality = 'US' # fallback to default (backwards compatibility)
try:
scheduled_procedure_step1.ScheduledStationAETitle = request["get"][
"scheduledStation"]
except KeyError:
scheduled_procedure_step1.ScheduledStationAETitle = 'US01' # fallback to default (backwards compatibility)
scheduled_procedure_step1.ScheduledProcedureStepStartDate = today.strftime(
'%Y%m%d')
scheduled_procedure_step1.ScheduledProcedureStepStartTime = today.strftime(
'%H%M%S')
try:
scheduled_procedure_step1.ScheduledPerformingPhysicianName = request[
"get"]["physician"]
except KeyError:
pass # optional, leave empty if not specified
scheduled_procedure_step_sequence.append(scheduled_procedure_step1)
ds.file_meta = file_meta
ds.is_implicit_VR = False
ds.is_little_endian = True
ds.save_as(dcm_store_path, write_like_original=False)
output.AnswerBuffer(
gdtResponse(request["get"]["id"], today, ds.AccessionNumber,
request["get"]["procedure"]), 'text/plain')
if "UrlOnWorklistEntryAdded" in config["Worklists"]:
with urllib.request.urlopen(
config["Worklists"]["UrlOnWorklistEntryAdded"]):
orthanc.LogWarning("Called {} as configured.".format(
config["Worklists"]["UrlOnWorklistEntryAdded"]))
except KeyError as e:
output.AnswerBuffer('error: {}\n'.format(e), 'text/plain')
raise
# 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'
ds.StudyID = ''
ds.SeriesNumber = ''
def query_worklist(request):
if request.method == 'POST':
accession = request.POST['accession']
# Query Worklist by accession
scu_ae = WorkstationConfigs.objects.get(id=1).workstation_ae
# SCU
ae = AE(ae_title=scu_ae)
ae.add_requested_context(ModalityWorklistInformationFind)
ds = Dataset()
ds.PatientName = '*'
ds.AccessionNumber = accession
ds.PatientID = ''
ds.StudyInstanceUID = ''
ds.QueryRetrieveLevel = 'STUDY'
ds.ScheduledProcedureStepSequence = [Dataset()]
item = ds.ScheduledProcedureStepSequence[0]
item.modality = 'US'
# associate with SCP
scp = WorklistConfigs.objects.get(id=1)
scp_ip = scp.worklist_ip
scp_ae = scp.worklist_ae
scp_port = scp.worklist_port
assoc = ae.associate(scp_ip, scp_port, ae_title=scp_ae)
if assoc.is_established:
responses = assoc.send_c_find(ds, ModalityWorklistInformationFind)
for (status, identifier) in responses:
if status:
print('C-FIND query status: 0x{0:04x}'.format(
status.Status))
if status.Status in (0xFF00, 0xFF01) and identifier:
study_data = identifier
query_form = TechNoteForm()
context = {
'study_data':
study_data,
'patient_name':
study_data[0x10, 0x10].value,
'patient_id':
study_data[0x10, 0x20].value,
'accession':
study_data[0x08, 0x50].value,
'StudyInstanceUID':
study_data[0x20, 0x0d].value,
'modality':
study_data.ScheduledProcedureStepSequence[0][
0x08, 0x60].value,
'study_date':
study_data.ScheduledProcedureStepSequence[0][
0x40, 0x02].value,
'study_description':
study_data.ScheduledProcedureStepSequence[0][
0x40, 0x07].value,
'query_form':
query_form,
}
return render(request,
'tech_forms/query_worklist.html',
context)
else:
error = 'No match found'
else:
error = "Connection timed out, was aborted or receieved invalid response"
assoc.release()
else:
error = 'Associated rejected, aborted or never connected'
context = {
'error': error,
}
return render(request, 'tech_forms/query_worklist_error.html', context)
else:
form = QueryWorklistForm()
context = {"form": form}
return render(request, 'tech_forms/query_worklist.html', context)
def DicomRT(path, file_name, region_number):
file_path = path + 'Dicom/' + file_name
dsorg = pydicom.read_file(file_path, force=True)
dcmfiles = os.listdir(path + 'Dicom/')
IOP = dsorg.ImageOrientationPatient
plane = file_plane(IOP)
planVal = dsorg.ImagePositionPatient[plane]
planVal = float(planVal)
xp_rt = dsorg.ImagePositionPatient[0]
yp_rt = dsorg.ImagePositionPatient[1]
x_rt = dsorg.Columns
y_rt = dsorg.Rows
uid1 = generate_uid()
uid2 = generate_uid()
# File meta info data elements
file_meta = FileMetaDataset()
file_meta.FileMetaInformationGroupLength = 182
file_meta.FileMetaInformationVersion = b'\x00\x01'
file_meta.MediaStorageSOPClassUID = '1.2.840.10008.5.1.4.1.1.481.3'
file_meta.MediaStorageSOPInstanceUID = uid1 #'1.2.826.0.1.534147.578.2719282597.2020101685637449'
file_meta.TransferSyntaxUID = '1.2.840.10008.1.2.1'
file_meta.ImplementationClassUID = '1.2.40.0.13.1.1'
file_meta.ImplementationVersionName = 'dcm4che-2.0'
ds = Dataset()
# Main data elements
ds = Dataset()
ds.SOPClassUID = '1.2.840.10008.5.1.4.1.1.481.3'
ds.SOPInstanceUID = uid1 #'1.2.826.0.1.534147.578.2719282597.2020101685637449'
ds.StudyDate = dsorg.StudyDate #'20450916'
ds.StudyTime = dsorg.StudyTime # '000000'
ds.AccessionNumber = ''
ds.Modality = 'RTSTRUCT'
ds.Manufacturer = dsorg.Manufacturer # 'SIEMENS'
ds.ReferringPhysicianName = ''
ds.OperatorsName = ''
ds.ManufacturerModelName = dsorg.ManufacturerModelName # SOMATOM Definition Edge'
ds.PatientName = dsorg.PatientName # 'Covid7175'
ds.PatientID = dsorg.PatientID # 'Covid7175'
ds.PatientBirthDate = dsorg.PatientBirthDate # '19300101'
ds.PatientSex = dsorg.PatientSex # 'F'
ds.SoftwareVersions = dsorg.SoftwareVersions # 'syngo CT VA48A'
ds.StudyInstanceUID = dsorg.StudyInstanceUID #'1.2.826.0.1.3680043.9.3218.1.1.302475.1985.1592890895061.53221.0' # dsOrg.StudyInstanceUID
ds.SeriesInstanceUID = uid2 #'1.2.826.0.1.534147.578.2719282597.2020101685637450'
ds.StudyID = ''
ds.SeriesNumber = None
ds.FrameOfReferenceUID = dsorg.FrameOfReferenceUID #'1.2.826.0.1.3680043.9.3218.1.1.302475.1985.1592890895061.53224.0' # dsOrg.FrameOfReferenceUID
ds.PositionReferenceIndicator = ''
ds.StructureSetLabel = 'AIM_Multi3_' + str(
dsorg.InstanceNumber) + '_' + str(region_number) #Scaling04
ds.StructureSetDate = '20201116'
ds.StructureSetTime = '085637'
# Referenced Frame of Reference Sequence
refd_frame_of_ref_sequence = Sequence()
ds.ReferencedFrameOfReferenceSequence = refd_frame_of_ref_sequence
# Referenced Frame of Reference Sequence: Referenced Frame of Reference 1
refd_frame_of_ref1 = Dataset()
refd_frame_of_ref1.FrameOfReferenceUID = dsorg.FrameOfReferenceUID # '1.2.826.0.1.3680043.9.3218.1.1.302475.1985.1592890895061.53224.0'
# RT Referenced Study Sequence
rt_refd_study_sequence = Sequence()
refd_frame_of_ref1.RTReferencedStudySequence = rt_refd_study_sequence
# RT Referenced Study Sequence: RT Referenced Study 1
rt_refd_study1 = Dataset()
rt_refd_study1.ReferencedSOPClassUID = '1.2.840.10008.3.1.2.3.1'
rt_refd_study1.ReferencedSOPInstanceUID = dsorg.StudyInstanceUID #'1.2.826.0.1.3680043.9.3218.1.1.302475.1985.1592890895061.53221.0' #
# RT Referenced Series Sequence
rt_refd_series_sequence = Sequence()
rt_refd_study1.RTReferencedSeriesSequence = rt_refd_series_sequence
# RT Referenced Series Sequence: RT Referenced Series 1
rt_refd_series1 = Dataset()
rt_refd_series1.SeriesInstanceUID = dsorg.SeriesInstanceUID #'1.2.826.0.1.3680043.9.3218.1.1.302475.1985.1592890895061.53222.0'
# Contour Image Sequence
contour_image_sequence = Sequence()
rt_refd_series1.ContourImageSequence = contour_image_sequence
# Contour Image Sequence: Contour Image 1 ********************************
i = 0
contour_image = []
for dcmname in dcmfiles:
if '.dcm' in dcmname:
dsorg = pydicom.read_file(path + 'Dicom/' + dcmname, force=True)
contour_image.append(Dataset())
contour_image[i] = Dataset()
contour_image[
i].ReferencedSOPClassUID = '1.2.840.10008.5.1.4.1.1.2'
contour_image[
i].ReferencedSOPInstanceUID = dsorg.SOPInstanceUID #'1.2.826.0.1.3680043.9.3218.1.1.302475.1985.1592890895061.53223.0'
contour_image[i].ReferencedFrameNumber = "1"
contour_image_sequence.append(contour_image[i])
i = i + 1
# contour_image1 = Dataset()
# contour_image1.ReferencedSOPClassUID = '1.2.840.10008.5.1.4.1.1.2'
# contour_image1.ReferencedSOPInstanceUID = dsorg.SOPInstanceUID #'1.2.826.0.1.3680043.9.3218.1.1.302475.1985.1592890895061.53223.0'
# contour_image1.ReferencedFrameNumber = "1"
# contour_image_sequence.append(contour_image1)
rt_refd_series_sequence.append(rt_refd_series1)
rt_refd_study_sequence.append(rt_refd_study1)
refd_frame_of_ref_sequence.append(refd_frame_of_ref1)
# Structure Set ROI Sequence
structure_set_roi_sequence = Sequence()
ds.StructureSetROISequence = structure_set_roi_sequence
# Structure Set ROI Sequence: Structure Set ROI 1
structure_set_roi1 = Dataset()
structure_set_roi1.ROINumber = "1"
structure_set_roi1.ReferencedFrameOfReferenceUID = dsorg.FrameOfReferenceUID #'1.2.826.0.1.3680043.9.3218.1.1.302475.1985.1592890895061.53224.0' #
structure_set_roi1.ROIName = 'TestScale'
structure_set_roi1.ROIGenerationAlgorithm = ''
structure_set_roi_sequence.append(structure_set_roi1)
# ROI Contour Sequence
roi_contour_sequence = Sequence()
ds.ROIContourSequence = roi_contour_sequence
# ROI Contour Sequence: ROI Contour 1
roi_contour1 = Dataset()
# Contour Sequence
contour_sequence = Sequence()
roi_contour1.ContourSequence = contour_sequence
# Contour Sequence: Contour 1
contour = []
#dcmfiles = os.listdir(path+'Dicom/') came to beginig of the function
i = 0
for dcmname in dcmfiles:
#print(dcmname)
if '.dcm' in dcmname:
pnyfiles = os.listdir(path + 'borders/')
for pnyname in pnyfiles:
if dcmname in pnyname:
#print(pnyname)
dsorg = pydicom.read_file(path + 'Dicom/' + dcmname,
force=True)
IOP = dsorg.ImageOrientationPatient
plane = file_plane(IOP)
planVal = dsorg.ImagePositionPatient[plane]
planVal = float(planVal)
xp_rt = dsorg.ImagePositionPatient[0]
yp_rt = dsorg.ImagePositionPatient[1]
x_rt = dsorg.Columns
y_rt = dsorg.Rows
# Put Contoure pixel cordination Inside file
with open(path + 'Borders/' + pnyname, 'rb') as f:
num = np.load(f)
print(pnyname)
print(planVal)
borders = []
for t in range(len(num)):
#print(t,num[t])
if plane == 0: #"Sagittal"
x = planVal
y = newPosition(num[t][1], 0, xp_rt, yp_rt, x_rt,
y_rt)
z = newPosition(num[t][0], 1, xp_rt, yp_rt, x_rt,
y_rt)
elif plane == 1: #"Coronal"
x = newPosition(num[t][1], 0, xp_rt, yp_rt, x_rt,
y_rt)
y = planVal
z = newPosition(num[t][0], 1, xp_rt, yp_rt, x_rt,
y_rt)
elif plane == 2: # "Transverse"
x = newPosition(num[t][1], 0, xp_rt, yp_rt, x_rt,
y_rt)
y = newPosition(num[t][0], 1, xp_rt, yp_rt, x_rt,
y_rt)
z = planVal
borders.extend([x, y, z])
print(i)
contour.append(Dataset())
contour[i] = Dataset()
# Contour Image Sequence
contour_image_sequence = Sequence()
contour[i].ContourImageSequence = contour_image_sequence
# Contour Image Sequence: Contour Image 1
contour_image1 = Dataset()
contour_image1.ReferencedSOPClassUID = '1.2.840.10008.5.1.4.1.1.2'
contour_image1.ReferencedSOPInstanceUID = dsorg.SOPInstanceUID #'1.2.826.0.1.3680043.9.3218.1.1.302475.1985.1592890895061.53223.0'
contour_image1.ReferencedFrameNumber = "1"
contour_image_sequence.append(contour_image1)
contour[i].ContourGeometricType = 'CLOSED_PLANAR'
contour[i].NumberOfContourPoints = len(borders) / 3 #"4"
contour[i].ContourNumber = "1"
contour[
i].ContourData = borders # [-276.91503267973, -162.50000000000, 516.398692810457, 270.222222222222, -162.50000000000, 514.725490196078, 271.895424836601, -162.50000000000, -177.98039215686, -271.89542483660, -162.50000000000, -176.30718954248]
contour_sequence.append(contour[i])
i = i + 1
roi_contour1.ReferencedROINumber = "1"
roi_contour_sequence.append(roi_contour1)
# RT ROI Observations Sequence
rtroi_observations_sequence = Sequence()
ds.RTROIObservationsSequence = rtroi_observations_sequence
# RT ROI Observations Sequence: RT ROI Observations 1
rtroi_observations1 = Dataset()
rtroi_observations1.ObservationNumber = "1"
rtroi_observations1.ReferencedROINumber = "1"
rtroi_observations1.RTROIInterpretedType = ''
rtroi_observations1.ROIInterpreter = ''
rtroi_observations_sequence.append(rtroi_observations1)
ds.file_meta = file_meta
ds.is_implicit_VR = False
ds.is_little_endian = True
ds.save_as(path + 'RTSTRUCT/rt' + str(region_number) + '-' + file_name,
write_like_original=False)
def generate_rtplan_skeleton():
ds = Dataset()
# ----- File meta -----
file_meta = generate_rtplan_file_meta()
ds.file_meta = file_meta
# ----- Patient Module -----
ds.PatientName = 'PyMedPhys' # Required - can be empty - could fill in?
ds.PatientID = 'PMP' # Required - can be empty - could fill in?
ds.PatientSex = 'O' # Required - can be empty
ds.PatientBirthDate = '' # Required - can be empty TODO: check if RS happy
ds.StudyInstanceUID = pydicom.uid.generate_uid()
ds.StudyDate = '' # Required - can be empty
ds.StudyTime = '' # Required - can be empty'
ds.ReferringPhysicianName = '' # Required - can be empty'
ds.StudyID = '' # Required - can be empty'
ds.AccessionNumber = '' # Required - can be empty'
# ----- RT Series Module -----
ds.Modality = 'RTPLAN'
ds.SeriesInstanceUID = pydicom.uid.generate_uid()
ds.SeriesNumber = "" # Required - can be empty'
ds.OperatorsName = '' # Required - can be empty'
# ----- Frame of Reference Module -----
ds.FrameOfReferenceUID = pydicom.uid.generate_uid()
ds.PositionReferenceIndicator = '' # Required - can be empty'
# ----- General Equipment Module -----
ds.Manufacturer = '' # Required - can be empty TODO: Check if RS is happy'
# ds.ManufacturerModelName = '' # Optional TODO: Check if RS is happy'
# ----- RT General Plan Module -----
ds.RTPlanLabel = 'PyMedPhys' # Set from field definition?
ds.RTPlanName = 'PyMedPhys' # Optional, Set from field definition?
ds.RTPlanDescription = 'PyMedPhys' # Optional, Set from field definition?
# Required - can be empty TODO: Check if RS is happy
ds.RTPlanDate = datetime.now().strftime("%Y%m%d")
# Required - can be empty TODO: Check if RS is happy
ds.RTPlanTime = datetime.now().strftime("%H%M%S")
ds.PlanIntent = 'VERIFICATION'
ds.RTPlanGeometry = 'TREATMENT_DEVICE' # Structure Set will probably not exist
# ----- RT Patient Setup Sequence & Patient Setup -----
patient_setup_sequence = Sequence()
ds.PatientSetupSequence = patient_setup_sequence
patient_setup = Dataset()
patient_setup.PatientSetupNumber = '1' # or "ASYMX"
patient_setup.PatientPosition = "HFS"
patient_setup_sequence.append(patient_setup)
# ----- SOP Common Module -----
ds.SpecificCharacterSet = 'ISO_IR 192'
ds.InstanceCreationDate = '' # Optional, could fill in?
ds.InstanceCreationTime = '' # Optional, could fill in?'
ds.SOPClassUID = file_meta.MediaStorageSOPClassUID
ds.SOPInstanceUID = file_meta.MediaStorageSOPInstanceUID
ds.ApprovalStatus = 'UNAPPROVED'
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):
# make image look like an EPID with flipped data (dose->low)
flipped_image = -self.image + self.image.max() + self.image.min()
file_meta = FileMetaDataset()
# Main data elements
ds = Dataset()
ds.ImageType = ['DERIVED', 'SECONDARY', 'PORTAL']
ds.SOPClassUID = '1.2.840.10008.5.1.4.1.1.481.1'
ds.SOPInstanceUID = '1.2.840.113854.141883099300381770008774160544352783139.1.1'
ds.StudyDate = '20150212'
ds.ContentDate = '20150212'
ds.StudyTime = '124120'
ds.ContentTime = '124120'
ds.AccessionNumber = ''
ds.Modality = 'RTIMAGE'
ds.ConversionType = 'WSD'
ds.Manufacturer = 'IMPAC Medical Systems, Inc.'
ds.ReferringPhysicianName = ''
ds.StudyDescription = 'QA'
ds.SeriesDescription = 'D + Gantry_0'
ds.PhysiciansOfRecord = 'Awesome Physician'
ds.OperatorsName = ''
ds.ManufacturerModelName = 'MOSAIQ'
ds.PatientName = 'Lutz^Test Tool'
ds.PatientID = 'zzzBAC_Lutz'
ds.PatientBirthDate = ''
ds.SoftwareVersions = '2.41.01J0'
ds.StudyInstanceUID = '1.2.840.113854.141883099300381770008774160544352783139'
ds.SeriesInstanceUID = '1.2.840.113854.141883099300381770008774160544352783139.1'
ds.StudyID = '348469'
ds.SeriesNumber = "4597199"
ds.InstanceNumber = "0"
ds.PatientOrientation = ''
ds.PositionReferenceIndicator = ''
ds.SamplesPerPixel = 1
ds.PhotometricInterpretation = 'MONOCHROME2'
ds.Rows = self.image.shape[0]
ds.Columns = self.image.shape[1]
ds.BitsAllocated = 16
ds.BitsStored = 16
ds.HighBit = 15
ds.PixelRepresentation = 0
ds.RTImageLabel = 'D'
ds.RTImagePlane = 'NORMAL'
ds.XRayImageReceptorAngle = "0.0"
ds.ImagePlanePixelSpacing = [self.pixel_size, self.pixel_size]
ds.RTImagePosition = [-200.70400, 150.52800]
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.PixelData = flipped_image # XXX Array of 393216 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 write_dicom_dose_template(rtplan,beamnr,filename,phantom=False):
"""
Create a template DICOM file for storing a dose distribution corresponding to a given treatment plan.
* rtplan: a pydicom Dataset object containing a PBS ion beam plan.
* beamnr: a *string* containing the beam number to be used for referral. Should contain "PLAN" for plan dose files.
* filename: file path of the desired output DICOM file
* phantom: boolean flag to indicate whether this is for a CT (False) or phantom dose (True).
"""
unique_id = pydicom.uid.generate_uid() # create a new unique UID
plandose = beamnr.upper() == 'PLAN'
# File meta info data elements
file_meta = Dataset()
file_meta.FileMetaInformationGroupLength = 200 # maybe 210 for phantoms (can also be RS6 vs RS5)
file_meta.FileMetaInformationVersion = b'\x00\x01'
file_meta.MediaStorageSOPClassUID = '1.2.840.10008.5.1.4.1.1.481.2'
file_meta.MediaStorageSOPInstanceUID = unique_id
file_meta.TransferSyntaxUID = '1.2.840.10008.1.2'
#FIXME: we probably need to apply for an official UID here
file_meta.ImplementationClassUID = '1.2.826.0.1.3680043.1.2.100.6.40.0.76'
if sys.version_info.major == 3:
file_meta.ImplementationVersionName = 'DicomObjects.NET'
else:
file_meta.ImplementationVersionName = u'DicomObjects.NET'
# Main data elements
now = datetime.now()
ds = Dataset()
ds.AccessionNumber = ''
ds.Manufacturer = 'ACMIT Gmbh and EBG MedAustron GmbH and Medical University of Vienna' ###
ds.ManufacturerModelName = "IDEAL" ###
ds.SoftwareVersions = ideal_version.tag ###
ds.PositionReferenceIndicator = ''
ds.SpecificCharacterSet = 'ISO_IR 100'
ds.InstanceCreationDate = now.strftime("%Y%m%d") #'20171121' ###
ds.InstanceCreationTime = now.strftime("%H%M%S") # '120041' ###
ds.SOPClassUID = '1.2.840.10008.5.1.4.1.1.481.2'
ds.SOPInstanceUID = unique_id # '1.2.752.243.1.1.20180817170901595.1980.23430' ###
ds.StudyDate = str(rtplan.StudyDate) # '20171103' ###
ds.StudyTime = str(rtplan.StudyTime) # '153709' ###
ds.Modality = 'RTDOSE'
ds.ReferringPhysicianName = str(rtplan.ReferringPhysicianName) # 'Anonymized' ###
if "SeriesDescription" in rtplan:
ds.SeriesDescription = str(rtplan.SeriesDescription) ###
if "OperatorsName" in rtplan:
ds.OperatorsName = str(rtplan.OperatorsName) ###
if "PatientName" in rtplan:
ds.PatientName = str(rtplan.PatientName) ###
if "PatientID" in rtplan:
ds.PatientID = str(rtplan.PatientID) ###
if "PatientBirthDate" in rtplan:
ds.PatientBirthDate = str(rtplan.PatientBirthDate) ###
if "PatientSex" in rtplan:
ds.PatientSex = str(rtplan.PatientSex) ###
ds.SliceThickness = str("1") ### overwrite by postprocessing
ds.StudyInstanceUID = rtplan.StudyInstanceUID.strip() ###
ds.SeriesInstanceUID = rtplan.SeriesInstanceUID.strip() ###
if hasattr(rtplan,"StudyDescription"):
### absent for phantom/commissioning
ds.StudyDescription = str(rtplan.StudyDescription)
if hasattr(rtplan,"PatientIdentityRemoved"):
ds.PatientIdentityRemoved = str(rtplan.PatientIdentityRemoved) ### absent for phantom/commsissioning plans
ds.DeidentificationMethod = str(rtplan.DeidentificationMethod) ### absent for phantom/commsissioning plans
if hasattr(rtplan,"StudyID"):
ds.StudyID = rtplan.StudyID ###
if hasattr(rtplan,"SeriesNumber"):
ds.SeriesNumber = rtplan.SeriesNumber ###
if phantom:
ds.InstanceNumber = 0 # str("0") ### only for phantom/commissioning
ds.PatientOrientation = str('') ### only for phantom/commissioning
ds.ImagePositionPatient = [str(-999.999), str(-999.999), str(-999.999)] ### overwrite by postprocessing
ds.ImageOrientationPatient = [str(float(c)) for c in '100010']
ds.FrameOfReferenceUID = rtplan.FrameOfReferenceUID.strip() ###
ds.SamplesPerPixel = 1
ds.PhotometricInterpretation = 'MONOCHROME2'
ds.NumberOfFrames = str(9) ### overwrite by postprocessing
ds.FrameIncrementPointer = pydicom.tag.BaseTag(0x3004000c) # That is the tag corresponding to the "GridFrameOffsetVector". All RS dose files do it like this.
ds.Rows = 9 ### overwrite by postprocessing
ds.Columns = 9 ### overwrite by postprocessing
ds.PixelSpacing = [str('9'), str('9')] ### overwrite by postprocessing
ds.BitsAllocated = 16
ds.BitsStored = 16
ds.HighBit = 15
ds.PixelRepresentation = 0
ds.DoseUnits = 'GY'
ds.DoseType = 'PHYSICAL' ### TODO: for RBE we may want "effective"
ds.DoseSummationType = 'PLAN' if plandose else 'BEAM' ### beam/plan difference
ds.GridFrameOffsetVector = [str(c) for c in range(9) ]
ds.DoseGridScaling = 0.999999 ### overwrite by postprocessing
# Referenced RT Plan Sequence
refd_rt_plan_sequence = Sequence()
ds.ReferencedRTPlanSequence = refd_rt_plan_sequence
# Referenced RT Plan Sequence: Referenced RT Plan 1
refd_rt_plan1 = Dataset()
refd_rt_plan1.ReferencedSOPClassUID = '1.2.840.10008.5.1.4.1.1.481.8' ### different for phantoms??? check
refd_rt_plan1.ReferencedSOPInstanceUID = rtplan.SOPInstanceUID.strip()
if not plandose:
# Referenced Fraction Group Sequence ## ONLY FOR BEAMS
refd_frxn_gp_sequence = Sequence() ## ONLY FOR BEAMS
refd_rt_plan1.ReferencedFractionGroupSequence = refd_frxn_gp_sequence ## ONLY FOR BEAMS
# Referenced Fraction Group Sequence: Referenced Fraction Group 1 ## ONLY FOR BEAMS
refd_frxn_gp1 = Dataset() ## ONLY FOR BEAMS
# Referenced Beam Sequence ## ONLY FOR BEAMS
refd_beam_sequence = Sequence() ## ONLY FOR BEAMS
refd_frxn_gp1.ReferencedBeamSequence = refd_beam_sequence ## ONLY FOR BEAMS
# Referenced Beam Sequence: Referenced Beam 1 ## ONLY FOR BEAMS
refd_beam1 = Dataset() ## ONLY FOR BEAMS
refd_beam1.ReferencedBeamNumber = beamnr ### ## ONLY FOR BEAMS
refd_beam_sequence.append(refd_beam1) ## ONLY FOR BEAMS
refd_frac_grp_nr = None
for f in rtplan.FractionGroupSequence:
fnr = str(f.FractionGroupNumber)
if refd_frac_grp_nr is None:
# In case the beam number is not actually found, this is a bit of a lie.
# But we have to survive somehow when the user feeds us illegal DICOM plan files from PDM.
refd_frac_grp_nr = fnr
for refb in f.ReferencedBeamSequence:
if str(refb.ReferencedBeamNumber) == str(beamnr):
refd_frac_grp_nr = fnr
break
refd_frxn_gp1.ReferencedFractionGroupNumber = refd_frac_grp_nr ## ONLY FOR BEAMS
refd_frxn_gp_sequence.append(refd_frxn_gp1) ## ONLY FOR BEAMS
refd_rt_plan_sequence.append(refd_rt_plan1)
ds.PixelData = np.ones((9,9,9),dtype=np.uint16).tobytes() ### overwrite by postprocessing
ds.file_meta = file_meta
ds.is_implicit_VR = True
ds.is_little_endian = True
ds.save_as(filename, write_like_original=False) ###
def create_rtss_dataset(dicoms_sorted, structure_label):
rf = dicoms_sorted[0]['dataset']
SOP_class_UID = '1.2.840.10008.5.1.4.1.1.481.3'
SOP_inst_UID, ser_inst_UID = generate_uid(), generate_uid()
dt0 = datetime.min
date0, time0 = dt0.strftime("%Y%m%d"), dt0.strftime("%H%M%S")
dt = datetime.now()
date, time = dt.strftime("%Y%m%d"), dt.strftime("%H%M%S")
meta = Dataset()
meta.FileMetaInformationGroupLength = 198
meta.FileMetaInformationVersion = bytes('01', 'utf-8') # '\x00\x01'
meta.MediaStorageSOPClassUID = SOP_class_UID
meta.MediaStorageSOPInstanceUID = SOP_inst_UID
meta.TransferSyntaxUID = '1.2.840.10008.1.2'
meta.ImplementationClassUID = '1.2.40.0.13.1.1.1'
meta.ImplementationVersionName = u'1.0'
r = Dataset()
r.Manufacturer, r.StructureSetLabel, r.file_meta = u'NRG', structure_label, meta
r.OperatorsName = u'nifti2rtss'
r.is_implicit_VR, r.is_little_endian = True, True
r.SpecificCharacterSet = 'ISO_IR 100'
r.InstanceCreationDate = date
r.InstanceCreationTime = time
r.SOPClassUID = SOP_class_UID
r.SOPInstanceUID = SOP_inst_UID
r.InstanceNumber = '1'
r.SeriesNumber = None
r.StudyDate = rf.StudyDate if 'StudyDate' in rf else date0
r.StudyTime = rf.StudyTime if 'StudyTime' in rf else time0
r.AccessionNumber = rf.AccessionNumber if 'AccessionNumber' in rf else None
r.StudyDescription, r.StudyInstanceUID, r.StudyID = rf.StudyDescription, rf.StudyInstanceUID, rf.StudyID
r.PatientName, r.PatientID = rf.PatientName, rf.PatientID
r.PatientBirthDate = ''
r.PatientSex, r.ReferringPhysicianName = rf.PatientSex, rf.ReferringPhysicianName
r.Modality = 'RTSTRUCT'
r.SeriesInstanceUID = ser_inst_UID
r.SeriesDescription = u'RTSS generated by nifti2rtss'
r.SeriesDate, r.SeriesTime = date, time
r.StructureSetDate, r.StructureSetTime = date, time
#1. referenced frame of reference sequence
referenced_frame_of_ref_seq = Sequence()
r.ReferencedFrameOfReferenceSequence = referenced_frame_of_ref_seq
#2. Referenced frame of reference #1
referenced_frame_of_ref1 = Dataset()
referenced_frame_of_ref1.FrameOfReferenceUID = rf.FrameOfReferenceUID
#3. RT referenced study sequence
rt_referenced_study_seq = Sequence()
referenced_frame_of_ref1.RTReferencedStudySequence = rt_referenced_study_seq
#4. RT referenced study sequence, study #1
rt_referenced_study1 = Dataset()
rt_referenced_study1.ReferencedSOPClassUID = rf.SOPClassUID
rt_referenced_study1.ReferencedSOPInstanceUID = rf.StudyInstanceUID
#5. RT referenced series sequence
rt_referenced_series_seq = Sequence()
rt_referenced_study1.RTReferencedSeriesSequence = rt_referenced_series_seq
#6. RT referenced series 1
rt_referenced_series1 = Dataset()
rt_referenced_series1.SeriesInstanceUID = rf.SeriesInstanceUID
#7. Contour image sequence
contour_image_sequence = Sequence()
rt_referenced_series1.ContourImageSequence = contour_image_sequence
#Loop over all DICOM images
for dcms in dicoms_sorted: #range(1,numberOfDicomImages+1):
dstemp = dcms['dataset']
# Contour Image Sequence: Contour Image
contour_image = Dataset()
contour_image.ReferencedSOPClassUID = dstemp.SOPClassUID
contour_image.ReferencedSOPInstanceUID = dstemp.SOPInstanceUID
contour_image_sequence.append(contour_image)
#append all sequences
rt_referenced_series_seq.append(rt_referenced_series1)
#print('rt_referenced_series_seq', rt_referenced_series_seq)
rt_referenced_study_seq.append(rt_referenced_study1)
referenced_frame_of_ref_seq.append(referenced_frame_of_ref1)
#8. Structure set ROI sequence
structure_set_roi_sequence = Sequence()
r.StructureSetROISequence = structure_set_roi_sequence
# Structure set ROI #1
#structure_set_roi1=Dataset(); ssr1=structure_set_roi1
#ssr1.ROINumber,ROIName,ROIDescription="1","na","na"
#ssr1.ROIGenerationAlgorithm='AUTOMATIC'
#structure_set_roi_sequence.append(ssr1)
return r
logging.basicConfig(filename='pynetdicom_query.log',
filemode='w',
format='%(name)s - %(levelname)s - %(message)s')
LOGGER = logging.getLogger('pynetdicom')
LOGGER.setLevel(logging.DEBUG)
scu_ae = os.environ.get('AE_TITLE')
ae = AE(ae_title=scu_ae) # SCU
ae.add_requested_context(ModalityWorklistInformationFind)
ds = Dataset()
ds.PatientName = '*'
ds.StudyDate = ''
ds.AccessionNumber = '2198270A'
ds.PatientID = ''
ds.StudyInstanceUID = ''
ds.QueryRetrieveLevel = 'STUDY'
ds.ScheduledProcedureStepSequence = [Dataset()]
item = ds.ScheduledProcedureStepSequence[0]
item.modality = ''
# associate with SCP
scp_ip = os.environ.get('SCP_IP')
scp_ae = os.environ.get('SCP_AE')
assoc = ae.associate(scp_ip, 5010, ae_title=scp_ae)
if assoc.is_established:
responses = assoc.send_c_find(ds, ModalityWorklistInformationFind)
def handle_find(event):
print("cfind fired")
# """Handle a C-FIND request event."""
ds = event.identifier
print("Query:")
for elem in ds:
print(elem)
if 'QueryRetrieveLevel' not in ds:
print("fail!")
# Failure
yield 0xC000, None
return
#===================================================================================
#print(instances)
if ds.QueryRetrieveLevel == 'PATIENT':
if 'PatientName' in ds:
if ds.PatientName not in ['*', '', '?']:
matching = [
inst for inst in instances if inst.PatientName == ds.PatientName
]
#====================================================================================
if ds.QueryRetrieveLevel == 'STUDY':
print("context=Study")
identifier = Dataset()
identifier.PatientName ='DUMMY'
identifier.QueryRetrieveLevel = ds.QueryRetrieveLevel
yield (0xFF00, identifier)
#====================================================================================
if ds.QueryRetrieveLevel == 'WORKLIST':
print("context=worklist")
#posible keys
print("modality: ["+str(ds.Modality)+"]")
print("studyDate: ["+str(ds.StudyDate)+"]")
#print("StudyDesciption: "+str(ds.StudyDesciption))
# TODO
# Procesador del query
# generar un dataset menor cuando se procesan el query, recorriendo ese dataset y generaldo la salida
# usar los datos de entrada
for st in DB:
# Check if C-CANCEL has been received
if event.is_cancelled:
yield (0xFE00, None)
return
# ver match de modalidad
#print(st['mod'])
now = datetime.datetime.now()
#--conditionals
if st['mod'] == ds.Modality and st['fecha']==now.strftime("%Y-%m-%d"):
print("biuld...")
#print(str(st['fecha']))
identifier = Dataset()
identifier.QueryRetrieveLevel = ds.QueryRetrieveLevel
identifier.PatientName =str(st['dicomname'])
identifier.AccessionNumber =str(st['AccessionNumber'])
identifier.PatientSex=str(st['patient_sex'])
identifier.StudyDescription=str(st['procedure'])
#
identifier.StudyDate=str(st['fecha'].replace("-",''))
#identifier.PatientID =
identifier.Modality =str(st['mod'])
yield (0xFF00, identifier)
yield(0x0000,NULL)
def generate_dicom(self, file_out_name: str, gantry_angle: float = 0.0, coll_angle: float = 0.0,
table_angle: float = 0.0):
# make image look like an EPID with flipped data (dose->low)
flipped_image = -self.image + self.image.max() + self.image.min()
# File meta info data elements
file_meta = FileMetaDataset()
# Main data elements
ds = Dataset()
ds.ImageType = ['DERIVED', 'SECONDARY', 'PORTAL']
ds.SOPClassUID = '1.2.840.10008.5.1.4.1.1.481.1'
ds.SOPInstanceUID = '1.2.840.113854.323870129946883845737820671794195198978.1.1'
ds.StudyDate = '20140819'
ds.ContentDate = '20140819'
ds.StudyTime = '130944'
ds.ContentTime = '130944'
ds.AccessionNumber = ''
ds.Modality = 'RTIMAGE'
ds.ConversionType = 'WSD'
ds.Manufacturer = 'IMPAC Medical Systems, Inc.'
ds.ReferringPhysicianName = ''
ds.StudyDescription = 'QA'
ds.SeriesDescription = 'Q + Couch_270'
ds.PhysiciansOfRecord = 'I am king'
ds.OperatorsName = ''
ds.ManufacturerModelName = 'MOSAIQ'
ds.PatientName = 'Albert Einstein'
ds.PatientID = 'abc123'
ds.PatientBirthDate = ''
ds.SoftwareVersions = '2.41.01J0'
ds.StudyInstanceUID = '1.2.840.113854.323870129946883845737820671794195198978'
ds.SeriesInstanceUID = '1.2.840.113854.323870129946883845737820671794195198978.1'
ds.StudyID = '348469'
ds.SeriesNumber = "4290463"
ds.InstanceNumber = "0"
ds.PatientOrientation = ''
ds.PositionReferenceIndicator = ''
ds.SamplesPerPixel = 1
ds.PhotometricInterpretation = 'MONOCHROME2'
ds.Rows = self.shape[0]
ds.Columns = self.shape[1]
ds.BitsAllocated = 16
ds.BitsStored = 16
ds.HighBit = 15
ds.PixelRepresentation = 0
ds.RTImageLabel = 'Q'
ds.RTImagePlane = 'NORMAL'
ds.XRayImageReceptorAngle = "0.0"
ds.ImagePlanePixelSpacing = [self.pixel_size, self.pixel_size]
ds.RTImagePosition = [-200.70400, 150.523400]
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.CurveDimensions = 2
# ds.NumberOfPoints = 4
# ds.TypeOfData = 'ROI'
# ds.CurveDescription = 'VContour 30'
# ds.AxisUnits = ['PIXL', 'PIXL']
# ds.DataValueRepresentation = 3
# ds.CurveLabel = 'Field Edge (Q:MV)'
# ds.CurveData = b'\x00\x00\x00\x00 .\x81@\x00\x00\x00\x00\x10\\z@\x00\x00\x00\x00 .\x81@\x00\x00\x00\x00\x90\x93u@\x00\x00\x00\x00\xc0\x93}@\x00\x00\x00\x00\x90\x93u@\x00\x00\x00\x00\xc0\x93}@\x00\x00\x00\x00\x10\\z@'
ds.PixelData = flipped_image # XXX Array of 1572864 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)