def add_required_elements_to_ds(ds: FileDataset):
dt = datetime.datetime.now()
# Append data elements required by the DICOM standarad
ds.SpecificCharacterSet = 'ISO_IR 100'
ds.InstanceCreationDate = dt.strftime('%Y%m%d')
ds.InstanceCreationTime = dt.strftime('%H%M%S.%f')
ds.StructureSetLabel = 'RTstruct'
ds.StructureSetDate = dt.strftime('%Y%m%d')
ds.StructureSetTime = dt.strftime('%H%M%S.%f')
ds.Modality = 'RTSTRUCT'
ds.Manufacturer = 'Qurit Lab'
ds.ManufacturerModelName = 'rt-utils'
ds.InstitutionName = 'BC Cancer Research Center'
# Set the transfer syntax
ds.is_little_endian = True
ds.is_implicit_VR = True
# Set values already defined in the file meta
ds.SOPClassUID = ds.file_meta.MediaStorageSOPClassUID
ds.SOPInstanceUID = ds.file_meta.MediaStorageSOPInstanceUID
ds.ApprovalStatus = 'UNAPPROVED'
def add_required_elements_to_ds(ds: FileDataset):
dt = datetime.datetime.now()
# Append data elements required by the DICOM standarad
ds.SpecificCharacterSet = "ISO_IR 100"
ds.InstanceCreationDate = dt.strftime("%Y%m%d")
ds.InstanceCreationTime = dt.strftime("%H%M%S.%f")
ds.StructureSetLabel = "RTstruct"
ds.StructureSetDate = dt.strftime("%Y%m%d")
ds.StructureSetTime = dt.strftime("%H%M%S.%f")
ds.Modality = "RTSTRUCT"
ds.Manufacturer = "Qurit"
ds.ManufacturerModelName = "rt-utils"
ds.InstitutionName = "Qurit"
# Set the transfer syntax
ds.is_little_endian = True
ds.is_implicit_VR = True
# Set values already defined in the file meta
ds.SOPClassUID = ds.file_meta.MediaStorageSOPClassUID
ds.SOPInstanceUID = ds.file_meta.MediaStorageSOPInstanceUID
ds.ApprovalStatus = "UNAPPROVED"
def convert_struct(plan, export_path):
# Check that the plan has a primary image, as we can't create a meaningful RTSTRUCT without it:
if not plan.primary_image:
plan.logger.error(
"No primary image found for plan. Unable to generate RTSTRUCT.")
return
patient_info = plan.pinnacle.patient_info
struct_sop_instuid = plan.struct_inst_uid
# Populate required values for file meta information
file_meta = Dataset()
file_meta.MediaStorageSOPClassUID = RTStructSOPClassUID
file_meta.TransferSyntaxUID = GTransferSyntaxUID
file_meta.MediaStorageSOPInstanceUID = struct_sop_instuid
file_meta.ImplementationClassUID = GImplementationClassUID
struct_filename = "RS." + struct_sop_instuid + ".dcm"
ds = FileDataset(struct_filename, {},
file_meta=file_meta,
preamble=b"\x00" * 128)
ds = FileDataset(struct_filename, {},
file_meta=file_meta,
preamble=b"\x00" * 128)
struct_series_instuid = pydicom.uid.generate_uid()
ds.ReferencedStudySequence = Sequence()
# not sure what I want here, going off of template dicom file
ds.SpecificCharacterSet = "ISO_IR 100"
ds.InstanceCreationDate = time.strftime("%Y%m%d")
ds.InstanceCreationTime = time.strftime("%H%M%S")
ds.SOPClassUID = RTStructSOPClassUID
ds.SOPInstanceUID = struct_sop_instuid
ds.Modality = RTSTRUCTModality
ds.AccessionNumber = ""
ds.Manufacturer = Manufacturer # from sample dicom file, maybe should change?
# not sure where to get information for this element can find this and
# read in from
ds.StationName = "adacp3u7"
# ds.ManufacturersModelName = 'Pinnacle3'
ReferencedStudy1 = Dataset()
ds.ReferencedStudySequence.append(ReferencedStudy1)
# Study Component Management SOP Class (chosen from template)
ds.ReferencedStudySequence[
0].ReferencedSOPClassUID = "1.2.840.10008.3.1.2.3.2"
ds.ReferencedStudySequence[
0].ReferencedSOPInstanceUID = plan.primary_image.image_info[0][
"StudyInstanceUID"]
ds.StudyInstanceUID = plan.primary_image.image_info[0]["StudyInstanceUID"]
ds.SeriesInstanceUID = struct_series_instuid
ds.PatientID = patient_info["MedicalRecordNumber"]
ds.ReferringPhysiciansName = patient_info["ReferringPhysician"]
ds.PhysiciansOfRecord = patient_info["RadiationOncologist"]
ds.StudyDescription = patient_info["Comment"]
ds.PatientSex = patient_info["Gender"][0]
ds.PatientBirthDate = patient_info["DOB"]
ds.StructureSetLabel = plan.plan_info["PlanName"]
ds.StudyID = plan.primary_image.image["StudyID"]
datetimesplit = plan.plan_info["ObjectVersion"]["WriteTimeStamp"].split()
# Read more accurate date from trial file if it is available
trial_info = plan.trial_info
if trial_info:
datetimesplit = trial_info["ObjectVersion"]["WriteTimeStamp"].split()
study_date = datetimesplit[0].replace("-", "")
study_time = datetimesplit[1].replace(":", "")
ds.StructureSetDate = study_date
ds.StructureSetTime = study_time
ds.StudyDate = study_date
ds.StudyTime = study_time
ds.ManufacturersModelName = plan.plan_info["ToolType"]
ds.SoftwareVersions = plan.plan_info["PinnacleVersionDescription"]
ds.StructureSetName = "POIandROI"
ds.SeriesNumber = "1"
ds.PatientName = patient_info["FullName"]
ds.ReferencedFrameOfReferenceSequence = Sequence()
ReferencedFrameofReference = Dataset()
ds.ReferencedFrameOfReferenceSequence.append(ReferencedFrameofReference)
ds.ReferencedFrameOfReferenceSequence[
0].FrameOfReferenceUID = plan.primary_image.image_info[0]["FrameUID"]
ds.ReferencedFrameOfReferenceSequence[
0].RTReferencedStudySequence = Sequence()
RTReferencedStudy = Dataset()
ds.ReferencedFrameOfReferenceSequence[0].RTReferencedStudySequence.append(
RTReferencedStudy)
ds.ReferencedFrameOfReferenceSequence[0].RTReferencedStudySequence[
0].ReferencedSOPClassUID = "1.2.840.10008.3.1.2.3.2"
ds.ReferencedFrameOfReferenceSequence[0].RTReferencedStudySequence[
0].ReferencedSOPInstanceUID = plan.primary_image.image_info[0][
"StudyInstanceUID"]
ds.StudyInstanceUID = plan.primary_image.image_info[0]["StudyInstanceUID"]
ds.ReferencedFrameOfReferenceSequence[0].RTReferencedStudySequence[
0].RTReferencedSeriesSequence = Sequence()
RTReferencedSeries = Dataset()
ds.ReferencedFrameOfReferenceSequence[0].RTReferencedStudySequence[
0].RTReferencedSeriesSequence.append(RTReferencedSeries)
ds.ReferencedFrameOfReferenceSequence[0].RTReferencedStudySequence[
0].RTReferencedSeriesSequence[
0].SeriesInstanceUID = plan.primary_image.image_info[0][
"SeriesUID"]
ds.ReferencedFrameOfReferenceSequence[0].RTReferencedStudySequence[
0].RTReferencedSeriesSequence[0].ContourImageSequence = Sequence()
for info in plan.primary_image.image_info:
contour_image = Dataset()
contour_image.ReferencedSOPClassUID = "1.2.840.10008.5.1.4.1.1.2"
contour_image.ReferencedSOPInstanceUID = info["InstanceUID"]
ds.ReferencedFrameOfReferenceSequence[0].RTReferencedStudySequence[
0].RTReferencedSeriesSequence[0].ContourImageSequence.append(
contour_image)
ds.ROIContourSequence = Sequence()
ds.StructureSetROISequence = Sequence()
ds.RTROIObservationsSequence = Sequence()
# Determine ISO Center
find_iso_center(plan)
ds = read_points(ds, plan)
ds = read_roi(ds, plan)
# find out where to get if its been approved or not
# find out how to insert proper 'CodeString' here
ds.ApprovalStatus = "UNAPPROVED"
# Set the transfer syntax
ds.is_little_endian = True
ds.is_implicit_VR = True
# Save the RTDose Dicom File
output_file = os.path.join(export_path, struct_filename)
plan.logger.info("Creating Struct file: %s \n" % (output_file))
ds.save_as(output_file)
def main(dir, args):
energies = [90 + i*5 for i in range(0,29)] # in MeV, they go from 90 to 230 in steps of 5 MeV
lat_sigma = [6 for energy in energies] # in mm
print(energies, lat_sigma)
parser = argparse.ArgumentParser(description='Generate an ideal CT of a water cube and a dummy RTplan with certain energy layers, defined in script. Every energy layer has a single spot at (0,0)')
parser.add_argument('--outdir', dest='outdir' , type=str, required=True )
parser.add_argument('--inDate', dest='inDate' , type=str, required=False, default='20191011')
parser.add_argument('--stDate', dest='stDate' , type=str, required=False, default='20191011')
parser.add_argument('--seDate', dest='seDate' , type=str, required=False, default='20191011')
parser.add_argument('--acDate', dest='acDate' , type=str, required=False, default='20191011')
parser.add_argument('--coDate', dest='coDate' , type=str, required=False, default='20191011')
parser.add_argument('--inTime', dest='inTime' , type=str, required=False, default='150000')
parser.add_argument('--stTime', dest='stTime' , type=str, required=False, default='150000')
parser.add_argument('--seTime', dest='seTime' , type=str, required=False, default='150000')
parser.add_argument('--acTime', dest='acTime' , type=str, required=False, default='150000')
parser.add_argument('--coTime', dest='coTime' , type=str, required=False, default='150000')
parser.add_argument('--access', dest='access' , type=str, required=False, default='0')
parser.add_argument('--manuf' , dest='manuf' , type=str, required=False, default='MGH Physics Research')
parser.add_argument('--station',dest='station' , type=str, required=False, default='Nashua')
parser.add_argument('--institution' , dest='institution', type=str, required=False, default='rbe')
parser.add_argument('--instaddr' , dest='instaddr', type=str, required=False, default='30 Fruit St, Boston MA 02114, USA')
parser.add_argument('--physician' , dest='physician', type=str, required=False, default='')
parser.add_argument('--stDesc', dest='stDesc' , type=str, required=False, default='For commissioning')
parser.add_argument('--seDesc', dest='seDesc' , type=str, required=False, default='Water cube 50x50x50cm3')
parser.add_argument('--operat', dest='operat' , type=str, required=False, default='FHG')
parser.add_argument('--manmod', dest='manmod' , type=str, required=False, default='2019')
parser.add_argument('--patname',dest='patname' , type=str, required=False, default='Cube^Water')
parser.add_argument('--patid' , dest='patid' , type=str, required=False, default='WaterCube50')
parser.add_argument('--birth' , dest='birth' , type=str, required=False, default='N/A')
parser.add_argument('--age' , dest='age' , type=str, required=False, default='N/A')
parser.add_argument('--sex' , dest='sex' , type=str, required=False, default='N/A')
parser.add_argument('--anon' , dest='anon' , type=str, required=False, default='NO')
parser.add_argument('--sw' , dest='sw' , type=str, required=False, default='pydicom1.2.2')
parser.add_argument('--lastCal',dest='lastCal' , type=str, required=False, default='')
parser.add_argument('--stuid' , dest='stuid' , type=str, required=False, default=uid.generate_uid())
parser.add_argument('--seuid' , dest='seuid' , type=str, required=False, default=uid.generate_uid())
parser.add_argument('--stid' , dest='stid' , type=str, required=False, default='1')
parser.add_argument('--sen' , dest='sen' , type=str, required=False, default='1')
parser.add_argument('--acqn' , dest='acqn' , type=str, required=False, default='1')
parser.add_argument('--forUID', dest='forUID' , type=str, required=False, default=uid.generate_uid())
parser.add_argument('--RTlabel',dest='RTlabel' , type=str, required=False, default='Test')
parser.add_argument('--RTname', dest='RTname' , type=str, required=False, default='Pristine test')
parser.add_argument('--RTdesc', dest='RTdesc' , type=str, required=False, default='Dummy energies')
parser.add_argument('--RTdate', dest='RTdate' , type=str, required=False, default='20191011')
parser.add_argument('--RTtime', dest='RTtime' , type=str, required=False, default='150000')
parser.add_argument('--RTgeom', dest='RTgeom' , type=str, required=False, default='PATIENT')
parser.add_argument('--sadX' , dest='sadX' , type=float, required=False, default=2000.0)
parser.add_argument('--sadY' , dest='sadY' , type=float, required=False, default=1800.0)
parser.add_argument('--nBlocks',dest='nBlocks' , type=int, required=False, default=0)
parser.add_argument('--isoX' , dest='isoX' , type=float, required=False, default=0.0)
parser.add_argument('--isoY' , dest='isoY' , type=float, required=False, default=0.0)
parser.add_argument('--isoZ' , dest='isoZ' , type=float, required=False, default=0.0)
parser.add_argument('--snout' , dest='snout' , type=str, required=False, default='')
parser.add_argument('--nRS' , dest='nRS' , type=int, required=False, default=0)
parser.add_argument('--rsID' , dest='rsID' , type=str, required=False, default='')
parser.add_argument('--snPos' , dest='snPos' , type=float, required=False, default=200)
parser.add_argument('--seX' , dest='seX' , type=float, required=False, default=0.0)
parser.add_argument('--seY' , dest='seY' , type=float, required=False, default=0.0)
parser.add_argument('--seZ' , dest='seZ' , type=float, required=False, default=0.0)
parser.add_argument('--ssd' , dest='ssd' , type=float, required=False, default=2000.0)
parser.add_argument('--beam' , dest='beam' , type=str , required=False, nargs='?', default='G000' )
parser.add_argument('--machine' , dest='machine' , type=str , required=False, nargs='?', default='1.1')
parser.add_argument('--dosimeter' , dest='dosimeter' , type=str , required=False, nargs='?', default='NP' )
parser.add_argument('--tuneid' , dest='tuneid' , type=str , required=False, nargs='?', default='Tune' )
parser.add_argument('--gangle' , dest='gangle' , type=int , required=False, nargs='?', default=0 )
args = parser.parse_args(args)
# Check output dir
if not os.path.exists(args.outdir):
print('Creating output folder',args.outdir)
os.mkdir(args.outdir)
os.mkdir(os.path.join(args.outdir,'ct'))
else:
print('Writing to preexisting output folder',args.outdir)
# Define geometry of water cube
rows = 512
columns = 512
slices = 512
wrows = 1 # mm
wcolumns = 1 # mm
wslices = 1 # mm
margin = 6 # pixels of air around water cube, so that water cube is 50cm * 50cm * 50cm
cube = np.full((slices, rows, columns), -1000, dtype='int16') # -1000 HU as initialization value (air)
cube[margin:-margin,margin:-margin,margin:-margin] = 0 # 0 HU cube (water)
# Generate CT image
for sl in range(slices):
# ~ break
output_file = os.path.join(args.outdir,'ct',str(sl+1)+'.dcm')
image = cube[sl]
print(output_file,image.shape)
meta = Dataset()
meta.MediaStorageSOPClassUID = '1.2.840.10008.5.1.4.1.1.2'#'CT Image Storage'
meta.MediaStorageSOPInstanceUID = uid.generate_uid()
meta.ImplementationClassUID = uid.PYDICOM_IMPLEMENTATION_UID
meta.TransferSyntaxUID = uid.ImplicitVRLittleEndian
ds = FileDataset(output_file, {}, file_meta=meta, preamble=b"\0" * 128)
ds.SpecificCharacterSet = 'ISO_IR 100'
ds.ImageType = ['DERIVED','SECONDARY','AXIAL']
ds.InstanceCreationDate = args.inDate
ds.InstanceCreationTime = args.inTime
ds.SOPClassUID = ds.file_meta.MediaStorageSOPClassUID
ds.SOPInstanceUID = ds.file_meta.MediaStorageSOPInstanceUID
ds.StudyDate = args.stDate
ds.SeriesDate = args.seDate
ds.AcquisitionDate = args.acDate
ds.ContentDate = args.coDate
ds.StudyTime = args.stTime
ds.SeriesTime = args.seTime
ds.AcquisitionTime = args.acTime
ds.ContentTime = args.coTime
ds.AccessionNumber = args.access
ds.Modality = 'CT'
ds.Manufacturer = args.manuf
ds.InstitutionName = args.institution
ds.InstitutionAddress = args.instaddr
ds.ReferringPhysicianName = args.physician
ds.StationName = args.station
ds.StudyDescription = args.stDesc
ds.SeriesDescription = args.seDesc
ds.OperatorsName = args.operat
ds.ManufacturerModelName = args.manmod
ds.PatientName = args.patname
ds.PatientID = args.patid
ds.PatientBirthDate = args.birth
ds.PatientSex = args.sex
ds.PatientAge = args.age
ds.PatientIdentityRemoved = args.anon
ds.AdditionalPatientHistory = 'Pseudo-CT'
if args.anon == "YES":
ds.DeidentificationMethod = "Manual"
ds.SliceThickness = wslices
# ~ ds.FocalSpots
# ~ ds.KVP
# ~ ds.DataCollectionDiameter
# ~ ds.ReconstructionDiameter
ds.SoftwareVersions = args.sw
# ~ ds.DistanceSourceToDetector
# ~ ds.DistanceSourceToPatient
# ~ ds.GantryDetectorTilt
# ~ ds.ExposureTime
# ~ ds.XRayTubeCurrent
# ~ ds.RotationDirection
# ~ ds.ConvolutionKerne
# ~ ds.FilterType
ds.ProtocolName = 'RESEARCH'
# ~ ds.ScanOptions = 'AXIAL MODE'
ds.DateOfLastCalibration = args.lastCal
ds.PatientPosition = 'HFS'
ds.StudyInstanceUID = args.stuid
ds.SeriesInstanceUID = args.seuid
ds.StudyID = args.stid
ds.SeriesNumber = args.sen
ds.AcquisitionNumber = args.acqn
ds.InstanceNumber = sl + 1
# Zero (origin) is at surface of water on anterior side, and centered in the other axes. Image position refers to center point of corner voxel.
ds.ImagePositionPatient = [(-columns/2+0.5)*wcolumns,(-margin+0.5)*wrows, (slices/2-0.5-sl)*wslices]
ds.ImageOrientationPatient = ['1', '0', '0', '0', '1', '0']
ds.FrameOfReferenceUID = args.forUID
ds.PositionReferenceIndicator = ''#'OM'
ds.SliceLocation = ds.ImagePositionPatient[2]
ds.SamplesPerPixel = 1
ds.PhotometricInterpretation= 'MONOCHROME2'
ds.Rows = rows
ds.Columns = columns
ds.PixelSpacing = [wcolumns, wrows]
ds.BitsAllocated = 16
ds.BitsStored = 16
ds.HighBit = 15
ds.PixelRepresentation = 1
ds.SmallestImagePixelValue = np.amin(image).tobytes()
ds.LargestImagePixelValue = np.amax(image).tobytes()
ds.WindowCenter = 0
ds.WindowWidth = 1000
ds.RescaleIntercept = 0
ds.RescaleSlope = 1
ds.RescaleType = "HU"
ds.PixelData = image.tobytes()
# ~ ds.PixelPaddingValue = -2000
ds.save_as(output_file, False)
# Generate RTplan with certain energies
meta = Dataset()
meta.MediaStorageSOPClassUID = '1.2.840.10008.5.1.4.1.1.481.8' #RT Ion Plan Storage
meta.MediaStorageSOPInstanceUID = uid.generate_uid()
meta.ImplementationClassUID = uid.PYDICOM_IMPLEMENTATION_UID
meta.TransferSyntaxUID = uid.ImplicitVRLittleEndian
output_file = os.path.join(args.outdir,'rtplan.dcm')
ds = FileDataset(output_file, {}, file_meta=meta, preamble=b"\0" * 128)
ds.SpecificCharacterSet = 'ISO_IR 100'
ds.InstanceCreationDate = args.inDate
ds.InstanceCreationTime = args.inTime
ds.SOPClassUID = ds.file_meta.MediaStorageSOPClassUID
ds.SOPInstanceUID = ds.file_meta.MediaStorageSOPInstanceUID
ds.StudyDate = args.stDate
ds.SeriesDate = args.seDate
ds.StudyTime = args.stTime
ds.SeriesTime = args.seTime
ds.AccessionNumber = ''
ds.Modality = 'RTPLAN'
ds.Manufacturer = args.manuf
ds.InstitutionName = args.institution
ds.ReferringPhysicianName = args.physician
ds.StudyDescription = args.stDesc
ds.SeriesDescription = args.seDesc
ds.OperatorsName = args.operat
ds.ManufacturerModelName = args.manmod
ds.PatientName = args.patname
ds.PatientID = args.patid
ds.PatientBirthDate = args.birth
ds.PatientSex = args.sex
ds.PatientAge = args.age
ds.PatientIdentityRemoved = args.anon
if args.anon=="YES":
ds.DeidentificationMethod = "Manual"
ds.SoftwareVersions = args.sw
ds.DateOfLastCalibration = args.lastCal
ds.StudyInstanceUID = args.stuid
ds.SeriesInstanceUID = args.seuid
ds.StudyID = args.stid
ds.SeriesNumber = args.sen
ds.InstanceNumber = args.acqn
ds.FrameOfReferenceUID = args.forUID
ds.PositionReferenceIndicator = ''
ds.RTPlanLabel = args.RTlabel
ds.RTPlanName = args.RTname
ds.RTPlanDescription = args.RTdesc
ds.RTPlanDate = args.RTdate
ds.RTPlanTime = args.RTtime
ds.RTPlanGeometry = args.RTgeom
ds.FractionGroupSequence = Sequence()
dsfx = Dataset()
dsfx.FractionGroupNumber = 1
dsfx.FractionGroupDescription = ''
dsfx.NumberOfFractionsPlanned = 1
dsfx.NumberOfBeams = 1
dsfx.NumberOfBrachyApplicationSetups = 0
dsfx.ReferencedBeamSequence = Sequence()
dsfx_b = Dataset()
dsfx_b.BeamDoseSpecificationPoint = [args.isoX,args.isoY,args.isoZ]
dsfx_b.BeamDose = 1 #dummy
dsfx_b.BeamMeterset = float(len(energies)*1e9)#1e9 protons per spot
dsfx_b.ReferencedBeamNumber = 1
dsfx.ReferencedBeamSequence.append(dsfx_b)
ds.FractionGroupSequence.append(dsfx)
ds.PatientSetupSequence = Sequence()
pss = Dataset()
pss.PatientPosition = 'HFS'
pss.PatientSetupNumber = 1
pss.PatientSetupLabel = 'Standard'
ds.PatientSetupSequence.append(pss)
ds.IonBeamSequence = Sequence()
be = Dataset()
ds.IonBeamSequence.append(be)
be.BeamName = args.beam
be.IonControlPointSequence = Sequence()
be.TreatmentMachineName = args.machine
be.InstitutionName = args.institution
be.PrimaryDosimeterUnit = args.dosimeter
be.Manufacturer = args.manuf
be.InstitutionName = args.institution
be.ManufacturerModelName = args.machine
be.InstitutionAddress = args.instaddr
be.TreatmentMachineName = args.machine
be.PrimaryDosimeterUnit = args.dosimeter
be.BeamNumber = '1'
be.BeamName = args.beam
be.BeamDescription = 'Gantry from top'
be.BeamType = 'STATIC'
be.RadiationType = 'PROTON'
be.TreatmentDeliveryType = 'TREATMENT'
be.NumberOfWedges = 0
be.NumberOfCompensators = 0
be.NumberOfBoli = 0
be.NumberOfBlocks = args.nBlocks
be.FinalCumulativeMetersetWeight = int(1e9*len(energies)) # 1e9 protons per spot (energy)
be.NumberOfControlPoints = 2*len(energies)
be.ScanMode = 'MODULATED'
be.VirtualSourceAxisDistances = [args.sadX, args.sadY]
if not args.snout == '':
be.SnoutSequence = Sequence()
sds = Dataset()
sds.AccessoryCode = args.snout
sds.SnoutID = args.snout
be.SnoutSequence.append(sds)
be.NumberOfRangeShifters = args.nRS
if args.nRS == 1:
be.RangeShifterSequence = Sequence()
rsds = Dataset()
rsds.AccessoryCode = 'Undefined Accessory Code'
rsds.RangeShifterNumber = 1
rsds.RangeShifterID = args.rsID
rsds.RangeShifterType = 'BINARY'
be.RangeShifterSequence.append(rsds)
be.NumberOfLateralSpreadingDevices = 0
be.NumberOfRangeModulators = 0
be.PatientSupportType = 'TABLE'
cweight = 0
for i,energy in enumerate(energies[::-1]):
for j in range(2):
icpoi = Dataset()
icpoi.NominalBeamEnergyUnit = 'MEV'
icpoi.ControlPointIndex = i*2 + j
icpoi.NominalBeamEnergy = str(energy)
if j == 0:
icpoi.GantryAngle = args.gangle
icpoi.GantryRotationDirection = 'NONE'
icpoi.BeamLimitingDeviceAngle = 0
icpoi.BeamLimitingDeviceRotationDirection = 'NONE'
icpoi.PatientSupportAngle = 0
icpoi.PatientSupportRotationDirection = 'NONE'
icpoi.TableTopVerticalPosition = 0
icpoi.TableTopLongitudinalPosition = 0
icpoi.TableTopLateralPosition = 0
icpoi.IsocenterPosition = [args.isoX,args.isoY,args.isoZ]
icpoi.SurfaceEntryPoint = [args.seX,args.seY,args.seZ]
icpoi.SourceToSurfaceDistance = args.ssd
icpoi.CumulativeMetersetWeight = cweight
if j == 0:
icpoi.TableTopPitchAngle = 0
icpoi.TableTopPitchRotationDirection = 'NONE'
icpoi.TableTopRollAngle = 0
icpoi.TableTopRollRotationDirection = 'NONE'
icpoi.GantryPitchAngle = 0.0
icpoi.GantryPitchRotationDirection = 'NONE'
icpoi.SnoutPosition = args.snPos
icpoi.ScanSpotTuneID = args.tuneid
icpoi.NumberOfScanSpotPositions = 1
icpoi.ScanSpotPositionMap = [0.0, 0.0]
icpoi.ScanSpotMetersetWeights = 1e9 if j == 0 else 0
cweight += icpoi.ScanSpotMetersetWeights
icpoi.ScanningSpotSize = [lat_sigma[len(energies)-i-1],lat_sigma[len(energies)-i-1]]
icpoi.NumberOfPaintings = 1
be.IonControlPointSequence.append(icpoi)
be.ReferencedPatientSetupNumber = 1
be.ReferencedToleranceTableNumber = 0
ds.ApprovalStatus = 'UNAPPROVED'
# ~ ds.ReviewDate = args.inDate
# ~ ds.ReviewTime = args.inTime
# ~ ds.ReviewerName = 'You'
ds.save_as(output_file, False)
print('Done, saved to',output_file)
def convert_plan(plan, export_path):
# Check that the plan has a primary image, as we can't create a meaningful RTPLAN without it:
if not plan.primary_image:
plan.logger.error(
"No primary image found for plan. Unable to generate RTPLAN.")
return
# TODO Fix the RTPLAN export functionality and remove this warning
plan.logger.warning(
"RTPLAN export functionality is currently not validated and not stable. Use with caution."
)
patient_info = plan.pinnacle.patient_info
plan_info = plan.plan_info
trial_info = plan.trial_info
image_info = plan.primary_image.image_info[0]
machine_info = plan.machine_info
patient_position = plan.patient_position
# Get the UID for the Plan
planInstanceUID = plan.plan_inst_uid
# Populate required values for file meta information
file_meta = Dataset()
file_meta.MediaStorageSOPClassUID = RTPlanSOPClassUID
file_meta.TransferSyntaxUID = GTransferSyntaxUID
file_meta.MediaStorageSOPInstanceUID = planInstanceUID
file_meta.ImplementationClassUID = GImplementationClassUID
# Create the FileDataset instance (initially no data elements, but
# file_meta supplied)
RPfilename = "RP." + file_meta.MediaStorageSOPInstanceUID + ".dcm"
ds = FileDataset(RPfilename, {},
file_meta=file_meta,
preamble=b"\x00" * 128)
ds.SpecificCharacterSet = "ISO_IR 100"
ds.InstanceCreationDate = time.strftime("%Y%m%d")
ds.InstanceCreationTime = time.strftime("%H%M%S")
ds.SOPClassUID = RTPlanSOPClassUID # RT Plan Storage
ds.SOPInstanceUID = planInstanceUID
datetimesplit = plan_info["ObjectVersion"]["WriteTimeStamp"].split()
datetimesplit = plan_info["ObjectVersion"]["WriteTimeStamp"].split()
# Read more accurate date from trial file if it is available
trial_info = plan.trial_info
if trial_info:
datetimesplit = trial_info["ObjectVersion"]["WriteTimeStamp"].split()
ds.StudyDate = datetimesplit[0].replace("-", "")
ds.StudyTime = datetimesplit[1].replace(":", "")
ds.AccessionNumber = ""
ds.Modality = RTPLANModality
ds.Manufacturer = Manufacturer
ds.OperatorsName = ""
ds.ManufacturersModelName = plan_info["ToolType"]
ds.SoftwareVersions = [plan_info["PinnacleVersionDescription"]]
ds.PhysiciansOfRecord = patient_info["RadiationOncologist"]
ds.PatientName = patient_info["FullName"]
ds.PatientBirthDate = patient_info["DOB"]
ds.PatientID = patient_info["MedicalRecordNumber"]
ds.PatientSex = patient_info["Gender"][0]
ds.StudyInstanceUID = image_info["StudyInstanceUID"]
ds.SeriesInstanceUID = planInstanceUID
ds.StudyID = plan.primary_image.image["StudyID"]
ds.FrameOfReferenceUID = image_info["FrameUID"]
ds.PositionReferenceIndicator = ""
ds.RTPlanLabel = plan.plan_info["PlanName"] + ".0"
ds.RTPlanName = plan.plan_info["PlanName"]
ds.RTPlanDescription = plan.pinnacle.patient_info["Comment"]
ds.RTPlanDate = ds.StudyDate
ds.RTPlanTime = ds.StudyTime
# ds.PlanIntent = "" #Not sure where to get this informationd, will likely
# be 'CURATIVE' or 'PALIATIVE'
ds.RTPlanGeometry = "PATIENT"
# ds.DoseReferenceSequence = Sequence() #figure out what goes in DoseReferenceSequence... Should be like a target volume and reference point I think...
# ds.ToleranceTableSequence = Sequence() #figure out where to get this
# information
ds.FractionGroupSequence = Sequence()
ds.BeamSequence = Sequence()
ds.PatientSetupSequence = Sequence() # need one per beam
ds.ReferencedStructureSetSequence = Sequence()
ReferencedStructureSet1 = Dataset()
ds.ReferencedStructureSetSequence.append(ReferencedStructureSet1)
ds.ReferencedStructureSetSequence[
0].ReferencedSOPClassUID = RTStructSOPClassUID
ds.ReferencedStructureSetSequence[
0].ReferencedSOPInstanceUID = plan.struct_inst_uid
ds.ApprovalStatus = "UNAPPROVED" # find out where to get this information
ds.FractionGroupSequence.append(Dataset())
ds.FractionGroupSequence[0].ReferencedBeamSequence = Sequence()
metersetweight = ["0"]
num_fractions = 0
beam_count = 0
beam_list = trial_info["BeamList"] if trial_info["BeamList"] else []
if len(beam_list) == 0:
plan.logger.warning(
"No Beams found in Trial. Unable to generate RTPLAN.")
return None
for beam in beam_list:
beam_count = beam_count + 1
plan.logger.info("Exporting Plan for beam: " + beam["Name"])
ds.PatientSetupSequence.append(Dataset())
ds.PatientSetupSequence[beam_count -
1].PatientPosition = patient_position
ds.PatientSetupSequence[beam_count - 1].PatientSetupNumber = beam_count
ds.FractionGroupSequence[0].ReferencedBeamSequence.append(Dataset())
ds.FractionGroupSequence[0].ReferencedBeamSequence[
beam_count - 1].ReferencedBeamNumber = beam_count
ds.BeamSequence.append(Dataset())
# figure out what to put here
ds.BeamSequence[beam_count - 1].Manufacturer = Manufacturer
ds.BeamSequence[beam_count - 1].BeamNumber = beam_count
ds.BeamSequence[beam_count - 1].TreatmentDeliveryType = "TREATMENT"
ds.BeamSequence[beam_count -
1].ReferencedPatientSetupNumber = beam_count
ds.BeamSequence[beam_count - 1].SourceAxisDistance = "1000"
ds.BeamSequence[beam_count - 1].FinalCumulativeMetersetWeight = "1"
ds.BeamSequence[beam_count - 1].PrimaryDosimeterUnit = "MU"
ds.BeamSequence[beam_count - 1].PrimaryFluenceModeSequence = Sequence()
ds.BeamSequence[beam_count - 1].PrimaryFluenceModeSequence.append(
Dataset())
ds.BeamSequence[
beam_count -
1].PrimaryFluenceModeSequence[0].FluenceMode = "STANDARD"
ds.BeamSequence[beam_count - 1].BeamName = beam["FieldID"]
ds.BeamSequence[beam_count - 1].BeamDescription = beam["Name"]
if "Photons" in beam["Modality"]:
ds.BeamSequence[beam_count - 1].RadiationType = "PHOTON"
elif "Electrons" in beam["Modality"]:
ds.BeamSequence[beam_count - 1].RadiationType = "ELECTRON"
else:
ds.BeamSequence[beam_count - 1].RadiationType = ""
if "STATIC" in beam["SetBeamType"].upper():
ds.BeamSequence[beam_count -
1].BeamType = beam["SetBeamType"].upper()
else:
ds.BeamSequence[beam_count - 1].BeamType = "DYNAMIC"
ds.BeamSequence[beam_count - 1].TreatmentMachineName = beam[
"MachineNameAndVersion"].partition(":")[0]
doserefpt = None
for point in plan.points:
if point["Name"] == beam["PrescriptionPointName"]:
doserefpt = plan.convert_point(point)
plan.logger.debug("Dose reference point found: " +
point["Name"])
if not doserefpt:
plan.logger.debug("No dose reference point, setting to isocenter")
doserefpt = plan.iso_center
plan.logger.debug("Dose reference point: " + str(doserefpt))
ds.FractionGroupSequence[0].ReferencedBeamSequence[
beam_count - 1].BeamDoseSpecificationPoint = doserefpt
ds.BeamSequence[beam_count - 1].ControlPointSequence = Sequence()
cp_manager = {}
if "CPManagerObject" in beam["CPManager"]:
cp_manager = beam["CPManager"]["CPManagerObject"]
else:
cp_manager = beam["CPManager"]
numctrlpts = cp_manager["NumberOfControlPoints"]
currentmeterset = 0.0
plan.logger.debug("Number of control points: " + str(numctrlpts))
x1 = ""
x2 = ""
y1 = ""
y2 = ""
leafpositions = []
for cp in cp_manager["ControlPointList"]:
metersetweight.append(cp["Weight"])
if x1 == "":
x1 = -cp["LeftJawPosition"] * 10
if x2 == "":
x2 = cp["RightJawPosition"] * 10
if y2 == "":
y2 = cp["TopJawPosition"] * 10
if y1 == "":
y1 = -cp["BottomJawPosition"] * 10
points = cp["MLCLeafPositions"]["RawData"]["Points[]"].split(",")
p_count = 0
leafpositions1 = []
leafpositions2 = []
for p in points:
leafpoint = float(p.strip())
# logger.debug("leafpoints: ", leafpoints)
if p_count % 2 == 0:
leafpositions1.append(-leafpoint * 10)
else:
leafpositions2.append(leafpoint * 10)
p_count += 1
if p_count == len(points):
leafpositions1 = list(reversed(leafpositions1))
leafpositions2 = list(reversed(leafpositions2))
leafpositions = leafpositions1 + leafpositions2
gantryangle = cp["Gantry"]
colangle = cp["Collimator"]
psupportangle = cp["Couch"]
numwedges = 0
if (cp["WedgeContext"]["WedgeName"] == "No Wedge"
or cp["WedgeContext"]["WedgeName"] == ""):
wedgeflag = False
plan.logger.debug("Wedge is no name")
numwedges = 0
elif ("edw" in cp["WedgeContext"]["WedgeName"]
or "EDW" in cp["WedgeContext"]["WedgeName"]):
plan.logger.debug("Wedge present")
wedgetype = "DYNAMIC"
wedgeflag = True
numwedges = 1
wedgeangle = cp["WedgeContext"]["Angle"]
wedgeinorout = ""
wedgeinorout = cp["WedgeContext"]["Orientation"]
if "WedgeBottomToTop" == wedgeinorout:
wedgename = (cp["WedgeContext"]["WedgeName"].upper() +
wedgeangle + "IN")
wedgeorientation = (
"0") # temporary until I find out what to put here
elif "WedgeTopToBottom" == wedgeinorout:
wedgename = (cp["WedgeContext"]["WedgeName"].upper() +
wedgeangle + "OUT")
wedgeorientation = "180"
plan.logger.debug("Wedge name = ", wedgename)
elif "UP" in cp["WedgeContext"]["WedgeName"]:
plan.logger.debug("Wedge present")
wedgetype = "STANDARD"
wedgeflag = True
numwedges = 1
wedgeangle = cp["WedgeContext"]["Angle"]
wedgeinorout = ""
wedgeinorout = cp["WedgeContext"]["Orientation"]
if int(wedgeangle) == 15:
numberinname = "30"
elif int(wedgeangle) == 45:
numberinname = "20"
elif int(wedgeangle) == 30:
numberinname = "30"
elif int(wedgeangle) == 60:
numberinname = "15"
if "WedgeRightToLeft" == wedgeinorout:
wedgename = "W" + str(
int(wedgeangle)) + "R" + numberinname # + "U"
wedgeorientation = (
"90") # temporary until I find out what to put here
elif "WedgeLeftToRight" == wedgeinorout:
wedgename = "W" + str(
int(wedgeangle)) + "L" + numberinname # + "U"
wedgeorientation = "270"
elif "WedgeTopToBottom" == wedgeinorout:
wedgename = ("W" + str(int(wedgeangle)) + "OUT" +
numberinname) # + "U"
wedgeorientation = (
"180") # temporary until I find out what to put here
elif "WedgeBottomToTop" == wedgeinorout:
wedgename = ("W" + str(int(wedgeangle)) + "IN" +
numberinname) # + "U"
wedgeorientation = (
"0") # temporary until I find out what to put here
plan.logger.debug("Wedge name = ", wedgename)
# Get the prescription for this beam
prescription = [
p for p in trial_info["PrescriptionList"]
if p["Name"] == beam["PrescriptionName"]
][0]
# Get the machine name and version and energy name for this beam
machinenameandversion = beam["MachineNameAndVersion"].split(": ")
machinename = machinenameandversion[0]
machineversion = machinenameandversion[1]
machineenergyname = beam["MachineEnergyName"]
beam_energy = re.findall(r"[-+]?\d*\.\d+|\d+",
beam["MachineEnergyName"])[0]
# Find the DosePerMuAtCalibration parameter from the machine data
dose_per_mu_at_cal = -1
if (machine_info["Name"] == machinename
and machine_info["VersionTimestamp"] == machineversion):
for energy in machine_info["PhotonEnergyList"]:
if energy["Name"] == machineenergyname:
dose_per_mu_at_cal = energy["PhysicsData"]["OutputFactor"][
"DosePerMuAtCalibration"]
plan.logger.debug("Using DosePerMuAtCalibration of: " +
str(dose_per_mu_at_cal))
prescripdose = beam["MonitorUnitInfo"]["PrescriptionDose"]
normdose = beam["MonitorUnitInfo"]["NormalizedDose"]
if normdose == 0:
ds.FractionGroupSequence[0].ReferencedBeamSequence[
beam_count - 1].BeamMeterset = 0
else:
ds.FractionGroupSequence[0].ReferencedBeamSequence[
beam_count - 1].BeamDose = (prescripdose / 100)
ds.FractionGroupSequence[0].ReferencedBeamSequence[
beam_count -
1].BeamMeterset = prescripdose / (normdose *
dose_per_mu_at_cal)
gantryrotdir = "NONE"
if (
"GantryIsCCW" in cp_manager
): # This may be a problem here!!!! Not sure how to Pinnacle does this, could be 1 if CW, must be somewhere that states if gantry is rotating or not
if cp_manager["GantryIsCCW"] == 1:
gantryrotdir = "CC"
if "GantryIsCW" in cp_manager:
if cp_manager["GantryIsCW"] == 1:
gantryrotdir = "CW"
plan.logger.debug("Beam MU: " +
str(ds.FractionGroupSequence[0].
ReferencedBeamSequence[beam_count -
1].BeamMeterset))
doserate = 0
if "DoseRate" in beam: # TODO What to do if DoseRate isn't available in Beam?
doserate = beam["DoseRate"]
if ("STEP" in beam["SetBeamType"].upper()
and "SHOOT" in beam["SetBeamType"].upper()):
plan.logger.debug("Using Step & Shoot")
ds.BeamSequence[beam_count -
1].NumberOfControlPoints = numctrlpts * 2
ds.BeamSequence[beam_count -
1].SourceToSurfaceDistance = beam["SSD"] * 10
if numwedges > 0:
ds.BeamSequence[beam_count - 1].WedgeSequence = Sequence()
ds.BeamSequence[beam_count - 1].WedgeSequence.append(
Dataset()
) # I am assuming only one wedge per beam (which makes sense because you can't change it during beam)
ds.BeamSequence[beam_count - 1].WedgeSequence[
0].WedgeNumber = 1 # might need to change this
ds.BeamSequence[beam_count -
1].WedgeSequence[0].WedgeType = wedgetype
ds.BeamSequence[beam_count -
1].WedgeSequence[0].WedgeAngle = wedgeangle
ds.BeamSequence[beam_count -
1].WedgeSequence[0].WedgeID = wedgename
ds.BeamSequence[
beam_count -
1].WedgeSequence[0].WedgeOrientation = wedgeorientation
ds.BeamSequence[beam_count -
1].WedgeSequence[0].WedgeFactor = ""
metercount = 1
for j in range(0, numctrlpts * 2):
ds.BeamSequence[beam_count - 1].ControlPointSequence.append(
Dataset())
ds.BeamSequence[
beam_count -
1].ControlPointSequence[j].ControlPointIndex = j
ds.BeamSequence[beam_count - 1].ControlPointSequence[
j].BeamLimitingDevicePositionSequence = Sequence()
ds.BeamSequence[beam_count - 1].ControlPointSequence[
j].ReferencedDoseReferenceSequence = Sequence()
ds.BeamSequence[beam_count - 1].ControlPointSequence[
j].ReferencedDoseReferenceSequence.append(Dataset())
if j % 2 == 1: # odd number control point
currentmeterset = currentmeterset + float(
metersetweight[metercount])
metercount = metercount + 1
ds.BeamSequence[beam_count - 1].ControlPointSequence[
j].CumulativeMetersetWeight = currentmeterset
ds.BeamSequence[
beam_count -
1].ControlPointSequence[j].ReferencedDoseReferenceSequence[
0].CumulativeDoseReferenceCoefficient = currentmeterset
ds.BeamSequence[
beam_count -
1].ControlPointSequence[j].ReferencedDoseReferenceSequence[
0].ReferencedDoseReferenceNumber = "1"
if j == 0: # first control point beam meterset always zero
ds.BeamSequence[beam_count - 1].ControlPointSequence[
j].NominalBeamEnergy = beam_energy
ds.BeamSequence[
beam_count -
1].ControlPointSequence[j].DoseRateSet = doserate
ds.BeamSequence[beam_count - 1].ControlPointSequence[
j].GantryRotationDirection = "NONE"
# logger.debug("Gantry angle list length: ", len(gantryangles))
# logger.debug("current controlpoint: ", j)
ds.BeamSequence[
beam_count -
1].ControlPointSequence[j].GantryAngle = gantryangle
ds.BeamSequence[beam_count - 1].ControlPointSequence[
j].BeamLimitingDeviceAngle = colangle
ds.BeamSequence[beam_count - 1].ControlPointSequence[
j].BeamLimitingDeviceRotationDirection = "NONE"
ds.BeamSequence[
beam_count -
1].ControlPointSequence[j].SourceToSurfaceDistance = (
beam["SSD"] * 10)
if numwedges > 0:
ds.BeamSequence[beam_count - 1].ControlPointSequence[
j].WedgePositionSequence = Sequence()
ds.BeamSequence[beam_count - 1].ControlPointSequence[
j].WedgePositionSequence.append(Dataset())
ds.BeamSequence[beam_count - 1].ControlPointSequence[
j].WedgePositionSequence[0].WedgePosition = "IN"
ds.BeamSequence[
beam_count -
1].ControlPointSequence[j].WedgePositionSequence[
0].ReferencedWedgeNumber = "1"
ds.BeamSequence[beam_count - 1].ControlPointSequence[
j].BeamLimitingDevicePositionSequence.append(
Dataset()) # This will be the x jaws
ds.BeamSequence[beam_count - 1].ControlPointSequence[
j].BeamLimitingDevicePositionSequence.append(
Dataset()) # this will be the y jaws
ds.BeamSequence[beam_count - 1].ControlPointSequence[
j].BeamLimitingDevicePositionSequence[
0].RTBeamLimitingDeviceType = "ASYMX"
ds.BeamSequence[beam_count - 1].ControlPointSequence[
j].BeamLimitingDevicePositionSequence[
0].LeafJawPositions = [x1, x2]
ds.BeamSequence[beam_count - 1].ControlPointSequence[
j].BeamLimitingDevicePositionSequence[
1].RTBeamLimitingDeviceType = "ASYMY"
ds.BeamSequence[beam_count - 1].ControlPointSequence[
j].BeamLimitingDevicePositionSequence[
1].LeafJawPositions = [y1, y2]
ds.BeamSequence[beam_count - 1].ControlPointSequence[
j].BeamLimitingDevicePositionSequence.append(
Dataset()) # this will be the MLC
ds.BeamSequence[beam_count - 1].ControlPointSequence[
j].BeamLimitingDevicePositionSequence[
2].RTBeamLimitingDeviceType = "MLCX"
ds.BeamSequence[beam_count - 1].ControlPointSequence[
j].BeamLimitingDevicePositionSequence[
2].LeafJawPositions = leafpositions
ds.BeamSequence[
beam_count -
1].ControlPointSequence[j].SourceToSurfaceDistance = (
beam["SSD"] * 10)
ds.BeamSequence[beam_count - 1].ControlPointSequence[
j].BeamLimitingDeviceRotationDirection = "NONE"
ds.BeamSequence[beam_count - 1].ControlPointSequence[
j].PatientSupportAngle = psupportangle
ds.BeamSequence[beam_count - 1].ControlPointSequence[
j].PatientSupportRotationDirection = "NONE"
ds.BeamSequence[beam_count - 1].ControlPointSequence[
j].IsocenterPosition = plan.iso_center
ds.BeamSequence[beam_count - 1].ControlPointSequence[
j].GantryRotationDirection = gantryrotdir
else:
ds.BeamSequence[beam_count - 1].ControlPointSequence[
j].BeamLimitingDevicePositionSequence.append(
Dataset()
) # This will be the mlcs for control points other than the first
ds.BeamSequence[beam_count - 1].ControlPointSequence[
j].BeamLimitingDevicePositionSequence[
0].RTBeamLimitingDeviceType = "MLCX"
ds.BeamSequence[beam_count - 1].ControlPointSequence[
j].BeamLimitingDevicePositionSequence[
0].LeafJawPositions = leafpositions
ds.BeamSequence[beam_count - 1].NumberOfWedges = (
numwedges
) # this is temporary value, will read in from file later
ds.BeamSequence[beam_count -
1].NumberOfCompensators = "0" # Also temporary
ds.BeamSequence[beam_count - 1].NumberOfBoli = "0"
ds.BeamSequence[beam_count - 1].NumberOfBlocks = "0" # Temp
ds.BeamSequence[beam_count -
1].BeamLimitingDeviceSequence = Sequence()
ds.BeamSequence[beam_count -
1].BeamLimitingDeviceSequence.append(Dataset())
ds.BeamSequence[beam_count -
1].BeamLimitingDeviceSequence.append(Dataset())
ds.BeamSequence[beam_count -
1].BeamLimitingDeviceSequence.append(Dataset())
ds.BeamSequence[beam_count - 1].BeamLimitingDeviceSequence[
0].RTBeamLimitingDeviceType = "ASYMX"
ds.BeamSequence[beam_count - 1].BeamLimitingDeviceSequence[
1].RTBeamLimitingDeviceType = "ASYMY"
ds.BeamSequence[beam_count - 1].BeamLimitingDeviceSequence[
2].RTBeamLimitingDeviceType = "MLCX"
ds.BeamSequence[
beam_count -
1].BeamLimitingDeviceSequence[0].NumberOfLeafJawPairs = "1"
ds.BeamSequence[
beam_count -
1].BeamLimitingDeviceSequence[1].NumberOfLeafJawPairs = "1"
ds.BeamSequence[
beam_count -
1].BeamLimitingDeviceSequence[2].NumberOfLeafJawPairs = (
p_count / 2)
bounds = [
"-200",
"-190",
"-180",
"-170",
"-160",
"-150",
"-140",
"-130",
"-120",
"-110",
"-100",
"-95",
"-90",
"-85",
"-80",
"-75",
"-70",
"-65",
"-60",
"-55",
"-50",
"-45",
"-40",
"-35",
"-30",
"-25",
"-20",
"-15",
"-10",
"-5",
"0",
"5",
"10",
"15",
"20",
"25",
"30",
"35",
"40",
"45",
"50",
"55",
"60",
"65",
"70",
"75",
"80",
"85",
"90",
"95",
"100",
"110",
"120",
"130",
"140",
"150",
"160",
"170",
"180",
"190",
"200",
]
ds.BeamSequence[beam_count - 1].BeamLimitingDeviceSequence[
2].LeafPositionBoundaries = bounds
else:
plan.logger.debug("Not using Step & Shoot")
ds.BeamSequence[beam_count -
1].NumberOfControlPoints = numctrlpts + 1
ds.BeamSequence[beam_count -
1].SourceToSurfaceDistance = beam["SSD"] * 10
if numwedges > 0:
ds.BeamSequence[beam_count - 1].WedgeSequence = Sequence()
ds.BeamSequence[beam_count - 1].WedgeSequence.append(Dataset())
# I am assuming only one wedge per beam (which makes sense
# because you can't change it during beam)
ds.BeamSequence[beam_count -
1].WedgeSequence[0].WedgeNumber = 1
# might need to change this
ds.BeamSequence[beam_count -
1].WedgeSequence[0].WedgeType = wedgetype
ds.BeamSequence[beam_count -
1].WedgeSequence[0].WedgeAngle = wedgeangle
ds.BeamSequence[beam_count -
1].WedgeSequence[0].WedgeID = wedgename
ds.BeamSequence[
beam_count -
1].WedgeSequence[0].WedgeOrientation = wedgeorientation
ds.BeamSequence[beam_count -
1].WedgeSequence[0].WedgeFactor = ""
for j in range(0, numctrlpts + 1):
ds.BeamSequence[beam_count - 1].ControlPointSequence.append(
Dataset())
ds.BeamSequence[
beam_count -
1].ControlPointSequence[j].ControlPointIndex = j
ds.BeamSequence[beam_count - 1].ControlPointSequence[
j].BeamLimitingDevicePositionSequence = Sequence()
ds.BeamSequence[beam_count - 1].ControlPointSequence[
j].ReferencedDoseReferenceSequence = Sequence()
ds.BeamSequence[beam_count - 1].ControlPointSequence[
j].ReferencedDoseReferenceSequence.append(Dataset())
ds.BeamSequence[beam_count - 1].ControlPointSequence[
j].CumulativeMetersetWeight = metersetweight[j]
if j == 0: # first control point beam meterset always zero
ds.BeamSequence[beam_count - 1].ControlPointSequence[
j].NominalBeamEnergy = beam_energy
ds.BeamSequence[
beam_count -
1].ControlPointSequence[j].DoseRateSet = doserate
ds.BeamSequence[beam_count - 1].ControlPointSequence[
j].GantryRotationDirection = "NONE"
# logger.debug("Gantry angle list length: ", len(gantryangles))
# logger.debug("current controlpoint: ", j)
ds.BeamSequence[
beam_count -
1].ControlPointSequence[j].GantryAngle = gantryangle
ds.BeamSequence[beam_count - 1].ControlPointSequence[
j].BeamLimitingDeviceAngle = colangle
ds.BeamSequence[
beam_count -
1].ControlPointSequence[j].SourceToSurfaceDistance = (
beam["SSD"] * 10)
ds.BeamSequence[beam_count - 1].ControlPointSequence[
j].ReferencedDoseReferenceSequence[
0].CumulativeDoseReferenceCoefficient = "0"
ds.BeamSequence[beam_count - 1].ControlPointSequence[
j].ReferencedDoseReferenceSequence[
0].ReferencedDoseReferenceNumber = "1"
if numwedges > 0:
WedgePosition1 = Dataset()
ds.BeamSequence[beam_count - 1].ControlPointSequence[
j].WedgePositionSequence = Sequence()
ds.BeamSequence[beam_count - 1].ControlPointSequence[
j].WedgePositionSequence.append(WedgePosition1)
ds.BeamSequence[beam_count - 1].ControlPointSequence[
j].WedgePositionSequence[0].WedgePosition = "IN"
ds.BeamSequence[
beam_count -
1].ControlPointSequence[j].WedgePositionSequence[
0].ReferencedWedgeNumber = "1"
ds.BeamSequence[beam_count - 1].ControlPointSequence[
j].BeamLimitingDevicePositionSequence.append(
Dataset()) # This will be the x jaws
ds.BeamSequence[beam_count - 1].ControlPointSequence[
j].BeamLimitingDevicePositionSequence.append(
Dataset()) # this will be the y jaws
ds.BeamSequence[beam_count - 1].ControlPointSequence[
j].BeamLimitingDevicePositionSequence[
0].RTBeamLimitingDeviceType = "ASYMX"
ds.BeamSequence[beam_count - 1].ControlPointSequence[
j].BeamLimitingDevicePositionSequence[
0].LeafJawPositions = [x1, x2]
ds.BeamSequence[beam_count - 1].ControlPointSequence[
j].BeamLimitingDevicePositionSequence[
1].RTBeamLimitingDeviceType = "ASYMY"
ds.BeamSequence[beam_count - 1].ControlPointSequence[
j].BeamLimitingDevicePositionSequence[
1].LeafJawPositions = [y1, y2]
ds.BeamSequence[beam_count - 1].ControlPointSequence[
j].BeamLimitingDevicePositionSequence.append(
Dataset()) # this will be the MLC
ds.BeamSequence[beam_count - 1].ControlPointSequence[
j].BeamLimitingDevicePositionSequence[
2].RTBeamLimitingDeviceType = "MLCX"
ds.BeamSequence[beam_count - 1].ControlPointSequence[
j].BeamLimitingDevicePositionSequence[
2].LeafJawPositions = leafpositions
ds.BeamSequence[
beam_count -
1].ControlPointSequence[j].SourceToSurfaceDistance = (
beam["SSD"] * 10)
ds.BeamSequence[beam_count - 1].ControlPointSequence[
j].BeamLimitingDeviceRotationDirection = "NONE"
ds.BeamSequence[beam_count - 1].ControlPointSequence[
j].PatientSupportAngle = psupportangle
ds.BeamSequence[beam_count - 1].ControlPointSequence[
j].PatientSupportRotationDirection = "NONE"
ds.BeamSequence[beam_count - 1].ControlPointSequence[
j].IsocenterPosition = plan.iso_center
ds.BeamSequence[beam_count - 1].ControlPointSequence[
j].GantryRotationDirection = gantryrotdir
ds.BeamSequence[beam_count - 1].NumberOfWedges = numwedges
ds.BeamSequence[beam_count - 1].NumberOfCompensators = (
"0"
) # this is temporary value, will read in from file later
ds.BeamSequence[beam_count -
1].NumberOfBoli = "0" # Also temporary
ds.BeamSequence[beam_count -
1].NumberOfBlocks = "0" # Temp
else:
# This will be the mlcs for control points other than the first
ds.BeamSequence[beam_count - 1].ControlPointSequence[
j].BeamLimitingDevicePositionSequence.append(Dataset())
ds.BeamSequence[beam_count - 1].ControlPointSequence[
j].BeamLimitingDevicePositionSequence[
0].RTBeamLimitingDeviceType = "MLCX"
ds.BeamSequence[beam_count - 1].ControlPointSequence[
j].BeamLimitingDevicePositionSequence[
0].LeafJawPositions = leafpositions
ds.BeamSequence[beam_count - 1].ControlPointSequence[
j].ReferencedDoseReferenceSequence[
0].CumulativeDoseReferenceCoefficient = "1"
ds.BeamSequence[beam_count - 1].ControlPointSequence[
j].ReferencedDoseReferenceSequence[
0].ReferencedDoseReferenceNumber = "1"
ds.BeamSequence[beam_count -
1].BeamLimitingDeviceSequence = Sequence()
ds.BeamSequence[beam_count -
1].BeamLimitingDeviceSequence.append(Dataset())
ds.BeamSequence[beam_count -
1].BeamLimitingDeviceSequence.append(Dataset())
ds.BeamSequence[beam_count -
1].BeamLimitingDeviceSequence.append(Dataset())
ds.BeamSequence[beam_count - 1].BeamLimitingDeviceSequence[
0].RTBeamLimitingDeviceType = "ASYMX"
ds.BeamSequence[beam_count - 1].BeamLimitingDeviceSequence[
1].RTBeamLimitingDeviceType = "ASYMY"
ds.BeamSequence[beam_count - 1].BeamLimitingDeviceSequence[
2].RTBeamLimitingDeviceType = "MLCX"
ds.BeamSequence[
beam_count -
1].BeamLimitingDeviceSequence[0].NumberOfLeafJawPairs = "1"
ds.BeamSequence[
beam_count -
1].BeamLimitingDeviceSequence[1].NumberOfLeafJawPairs = "1"
ds.BeamSequence[
beam_count -
1].BeamLimitingDeviceSequence[2].NumberOfLeafJawPairs = (
p_count / 2)
bounds = [
"-200",
"-190",
"-180",
"-170",
"-160",
"-150",
"-140",
"-130",
"-120",
"-110",
"-100",
"-95",
"-90",
"-85",
"-80",
"-75",
"-70",
"-65",
"-60",
"-55",
"-50",
"-45",
"-40",
"-35",
"-30",
"-25",
"-20",
"-15",
"-10",
"-5",
"0",
"5",
"10",
"15",
"20",
"25",
"30",
"35",
"40",
"45",
"50",
"55",
"60",
"65",
"70",
"75",
"80",
"85",
"90",
"95",
"100",
"110",
"120",
"130",
"140",
"150",
"160",
"170",
"180",
"190",
"200",
]
ds.BeamSequence[beam_count - 1].BeamLimitingDeviceSequence[
2].LeafPositionBoundaries = bounds
ctrlptlist = False
wedgeflag = False
numwedges = 0
beginbeam = False
# Get the prescription for this beam
prescription = [
p for p in trial_info["PrescriptionList"]
if p["Name"] == beam["PrescriptionName"]
][0]
num_fractions = prescription["NumberOfFractions"]
ds.FractionGroupSequence[0].FractionGroupNumber = 1
ds.FractionGroupSequence[0].NumberOfFractionsPlanned = num_fractions
ds.FractionGroupSequence[0].NumberOfBeams = beam_count
ds.FractionGroupSequence[0].NumberOfBrachyApplicationSetups = "0"
# Save the RTPlan Dicom File
output_file = os.path.join(export_path, RPfilename)
plan.logger.info("Creating Plan file: %s \n" % (output_file))
ds.save_as(output_file)
