def create_dicom_base(self):
if _dicom_loaded is False:
raise ModuleNotLoadedError("Dicom")
if self.header_set is False:
raise InputError("Header not loaded")
meta = Dataset()
meta.MediaStorageSOPClassUID = '1.2.840.10008.5.1.4.1.1.2' # CT Image Storage
meta.MediaStorageSOPInstanceUID = "1.2.3"
meta.ImplementationClassUID = "1.2.3.4"
meta.TransferSyntaxUID = UID.ImplicitVRLittleEndian # Implicit VR Little Endian - Default Transfer Syntax
ds = FileDataset("file", {}, file_meta=meta, preamble=b"\0" * 128)
ds.PatientsName = self.patient_name
ds.PatientID = "123456"
ds.PatientsSex = '0'
ds.PatientsBirthDate = '19010101'
ds.SpecificCharacterSet = 'ISO_IR 100'
ds.AccessionNumber = ''
ds.is_little_endian = True
ds.is_implicit_VR = True
ds.SOPClassUID = '1.2.3' # !!!!!!!!
ds.SOPInstanceUID = '1.2.3' # !!!!!!!!!!
ds.StudyInstanceUID = '1.2.3' # !!!!!!!!!!
ds.FrameofReferenceUID = '1.2.3' # !!!!!!!!!
ds.StudyDate = '19010101' # !!!!!!!
ds.StudyTime = '000000' # !!!!!!!!!!
ds.PhotometricInterpretation = 'MONOCHROME2'
ds.SamplesPerPixel = 1
ds.ImageOrientationPatient = ['1', '0', '0', '0', '1', '0']
ds.Rows = self.dimx
ds.Columns = self.dimy
ds.SliceThickness = str(self.slice_distance)
ds.PixelSpacing = [self.pixel_size, self.pixel_size]
return ds
def writeDicom(ods, mrn, studyID, outdir):
file_meta = Dataset()
file_meta.MediaStorageSOPClassUID = 'Secondary Capture Image Storage'
file_meta.MediaStorageSOPInstanceUID = '0.0'
file_meta.ImplementationClassUID = '0.0'
ds = FileDataset(studyID, {}, file_meta=file_meta, preamble="\0" * 128)
ds.Modality = ods.Modality if "Modality" in ods else ""
ds.StudyDate = ods.StudyDate if "StudyDate" in ods else ""
ds.StudyTime = ods.StudyTime if "StudyTime" in ods else ""
ds.StudyInstanceUID = '0.0'
ds.SeriesInstanceUID = '0.0'
ds.SOPInstanceUID = '0.0'
ds.SOPClassUID = 'Secondary Capture Image Storage'
ds.SecondaryCaptureDeviceManufctur = 'Python 2.7.3'
## These are the necessary imaging components of the FileDataset object.
ds.AccessionNumber = str(studyID)
ds.PatientID = str(mrn)
ds.StudyID = str(studyID)
ds.PatientName = str(studyID)
ds.PatientBirthDate = "00000000"
ds.PatientAge = calculateAge(
ods.StudyDate, ods.PatientBirthDate
) if "StudyDate" in ods and "PatientBirthDate" in ods else ""
ds.PatientSex = ods.PatientSex if "PatientSex" in ods else ""
ds.StudyDescription = ods.StudyDescription if "StudyDescription" in ods else ""
ds.SeriesDescription = ods.SeriesDescription if "SeriesDescription" in ods else ""
ds.ViewPosition = ods.ViewPosition if "ViewPosition" in ods else ""
ds.InstanceNumber = ods.InstanceNumber if "InstanceNumber" in ods else ""
ds.SeriesNumber = ods.SeriesNumber if "SeriesNumber" in ods else ""
ds.SamplesPerPixel = ods.SamplesPerPixel if "SamplesPerPixel" in ods else ""
ds.PhotometricInterpretation = ods.PhotometricInterpretation if "PhotometricInterpretation" in ods else ""
ds.PixelRepresentation = ods.PixelRepresentation if "PixelRepresentation" in ods else ""
ds.HighBit = ods.HighBit if "HighBit" in ods else ""
ds.BitsStored = ods.BitsStored if "BitsStored" in ods else ""
ds.BitsAllocated = ods.BitsAllocated if "BitsAllocated" in ods else ""
ds.Columns = ods.Columns if "Columns" in ods else ""
ds.Rows = ods.Rows if "Rows" in ods else ""
ds.PixelData = ods.PixelData if "PixelData" in ods else ""
filename = cleanString(
str(studyID) + "_" + str(ds.SeriesNumber) + "_" +
str(ds.InstanceNumber) + "_" + str(ds.Modality) + "_" +
str(ds.StudyDescription) + "_" + str(ds.SeriesDescription) + "_" +
str(ds.ViewPosition) + ".dcm")
outpath = os.path.join(outdir, filename)
ds.save_as(outpath)
return
def create_dicom(self):
""" Generates and returns Dicom RTSTRUCT object, which holds all VOIs.
:returns: a Dicom RTSTRUCT object holding any VOIs.
"""
if _dicom_loaded is False:
raise ModuleNotLoadedError("Dicom")
meta = Dataset()
meta.MediaStorageSOPClassUID = '1.2.840.10008.5.1.4.1.1.481.3' # RT Structure Set Storage SOP Class
# see https://github.com/darcymason/pydicom/blob/master/pydicom/_uid_dict.py
meta.MediaStorageSOPInstanceUID = "1.2.3"
meta.ImplementationClassUID = "1.2.3.4"
meta.TransferSyntaxUID = UID.ImplicitVRLittleEndian # Implicit VR Little Endian - Default Transfer Syntax
ds = FileDataset("file", {}, file_meta=meta, preamble=b"\0" * 128)
if self.cube is not None:
ds.PatientsName = self.cube.patient_name
else:
ds.PatientsName = ""
ds.PatientID = "123456"
ds.PatientsSex = '0'
ds.PatientsBirthDate = '19010101'
ds.SpecificCharacterSet = 'ISO_IR 100'
ds.AccessionNumber = ''
ds.is_little_endian = True
ds.is_implicit_VR = True
ds.SOPClassUID = '1.2.840.10008.5.1.4.1.1.481.3' # RT Structure Set Storage SOP Class
ds.SOPInstanceUID = '1.2.3' # !!!!!!!!!!
ds.StudyInstanceUID = '1.2.3' # !!!!!!!!!!
ds.SeriesInstanceUID = '1.2.3' # !!!!!!!!!!
ds.FrameofReferenceUID = '1.2.3' # !!!!!!!!!
ds.SeriesDate = '19010101' # !!!!!!!!
ds.ContentDate = '19010101' # !!!!!!
ds.StudyDate = '19010101' # !!!!!!!
ds.SeriesTime = '000000' # !!!!!!!!!
ds.StudyTime = '000000' # !!!!!!!!!!
ds.ContentTime = '000000' # !!!!!!!!!
ds.StructureSetLabel = 'pyTRiP plan'
ds.StructureSetDate = '19010101'
ds.StructureSetTime = '000000'
ds.StructureSetName = 'ROI'
ds.Modality = 'RTSTRUCT'
roi_label_list = []
roi_data_list = []
roi_structure_roi_list = []
# to get DICOM which can be loaded in Eclipse we need to store information about UIDs of all slices in CT
# first we check if DICOM cube is loaded
if self.cube is not None:
rt_ref_series_data = Dataset()
rt_ref_series_data.SeriesInstanceUID = '1.2.3.4.5'
rt_ref_series_data.ContourImageSequence = Sequence([])
# each CT slice corresponds to one DICOM file
for slice_dicom in self.cube.create_dicom():
slice_dataset = Dataset()
slice_dataset.ReferencedSOPClassUID = '1.2.840.10008.5.1.4.1.1.2' # CT Image Storage SOP Class
slice_dataset.ReferencedSOPInstanceUID = slice_dicom.SOPInstanceUID # most important - slice UID
rt_ref_series_data.ContourImageSequence.append(slice_dataset)
rt_ref_study_seq_data = Dataset()
rt_ref_study_seq_data.ReferencedSOPClassUID = '1.2.840.10008.3.1.2.3.2' # Study Component Management Class
rt_ref_study_seq_data.ReferencedSOPInstanceUID = '1.2.3.4.5'
rt_ref_study_seq_data.RTReferencedSeriesSequence = Sequence([rt_ref_series_data])
rt_ref_frame_study_data = Dataset()
rt_ref_frame_study_data.RTReferencedStudySequence = Sequence([rt_ref_study_seq_data])
rt_ref_frame_study_data.FrameOfReferenceUID = '1.2.3.4.5'
ds.ReferencedFrameOfReferenceSequence = Sequence([rt_ref_frame_study_data])
for i in range(self.number_of_vois()):
roi_label = self.vois[i].create_dicom_label()
roi_label.ObservationNumber = str(i + 1)
roi_label.ReferencedROINumber = str(i + 1)
roi_label.RefdROINumber = str(i + 1)
roi_contours = self.vois[i].create_dicom_contour_data(i)
roi_contours.RefdROINumber = str(i + 1)
roi_contours.ReferencedROINumber = str(i + 1)
roi_structure_roi = self.vois[i].create_dicom_structure_roi()
roi_structure_roi.ROINumber = str(i + 1)
roi_structure_roi_list.append(roi_structure_roi)
roi_label_list.append(roi_label)
roi_data_list.append(roi_contours)
ds.RTROIObservations = Sequence(roi_label_list)
ds.ROIContours = Sequence(roi_data_list)
ds.StructureSetROIs = Sequence(roi_structure_roi_list)
return ds
def create_dicom_base(self):
if _dicom_loaded is False:
raise ModuleNotLoadedError("Dicom")
if self.header_set is False:
raise InputError("Header not loaded")
# TODO tags + code datatypes are described here:
# https://www.dabsoft.ch/dicom/6/6/#(0020,0012)
# datatype codes are described here:
# ftp://dicom.nema.org/medical/DICOM/2013/output/chtml/part05/sect_6.2.html
meta = Dataset()
meta.MediaStorageSOPClassUID = '1.2.840.10008.5.1.4.1.1.2' # CT Image Storage
# Media Storage SOP Instance UID tag 0x0002,0x0003 (type UI - Unique Identifier)
meta.MediaStorageSOPInstanceUID = self._ct_sop_instance_uid
meta.ImplementationClassUID = "1.2.3.4"
meta.TransferSyntaxUID = UID.ImplicitVRLittleEndian # Implicit VR Little Endian - Default Transfer Syntax
ds = FileDataset("file", {}, file_meta=meta, preamble=b"\0" * 128)
ds.PatientsName = self.patient_name
if self.patient_id in (None, ''):
ds.PatientID = datetime.datetime.today().strftime('%Y%m%d-%H%M%S')
else:
ds.PatientID = self.patient_id # Patient ID tag 0x0010,0x0020 (type LO - Long String)
ds.PatientsSex = '' # Patient's Sex tag 0x0010,0x0040 (type CS - Code String)
# Enumerated Values: M = male F = female O = other.
ds.PatientsBirthDate = '19010101'
ds.SpecificCharacterSet = 'ISO_IR 100'
ds.AccessionNumber = ''
ds.is_little_endian = True
ds.is_implicit_VR = True
ds.SOPClassUID = '1.2.3' # !!!!!!!!
# SOP Instance UID tag 0x0008,0x0018 (type UI - Unique Identifier)
ds.SOPInstanceUID = self._ct_sop_instance_uid
# Study Instance UID tag 0x0020,0x000D (type UI - Unique Identifier)
# self._dicom_study_instance_uid may be either set in __init__ when creating new object
# or set when import a DICOM file
# Study Instance UID for structures is the same as Study Instance UID for CTs
ds.StudyInstanceUID = self._dicom_study_instance_uid
# Series Instance UID tag 0x0020,0x000E (type UI - Unique Identifier)
# self._ct_dicom_series_instance_uid may be either set in __init__ when creating new object
# or set when import a DICOM file
# Series Instance UID for structures might be different than Series Instance UID for CTs
ds.SeriesInstanceUID = self._ct_dicom_series_instance_uid
# Study Instance UID tag 0x0020,0x000D (type UI - Unique Identifier)
ds.FrameofReferenceUID = '1.2.3' # !!!!!!!!!
ds.StudyDate = datetime.datetime.today().strftime('%Y%m%d')
ds.StudyTime = datetime.datetime.today().strftime('%H%M%S')
ds.PhotometricInterpretation = 'MONOCHROME2'
ds.SamplesPerPixel = 1
ds.ImageOrientationPatient = ['1', '0', '0', '0', '1', '0']
ds.Rows = self.dimx
ds.Columns = self.dimy
ds.SliceThickness = str(self.slice_distance)
ds.PixelSpacing = [self.pixel_size, self.pixel_size]
# Add eclipse friendly IDs
ds.StudyID = '1' # Study ID tag 0x0020,0x0010 (type SH - Short String)
ds.ReferringPhysiciansName = 'py^trip' # Referring Physician's Name tag 0x0008,0x0090 (type PN - Person Name)
ds.PositionReferenceIndicator = '' # Position Reference Indicator tag 0x0020,0x1040
ds.SeriesNumber = '1' # SeriesNumber tag 0x0020,0x0011 (type IS - Integer String)
return ds
def write_dicom(pixel_array, filename, origin, origins, orientation):
file_meta = Dataset()
file_meta.MediaStorageSOPClassUID = 'Secondary Capture Image Storage'
file_meta.MediaStorageSOPInstanceUID = '1.3.6.1.4.1.9590.100.1.1.111165684411017669021768385720736873780'
file_meta.ImplementationClassUID = '1.3.6.1.4.1.9590.100.1.0.100.4.0'
ds = FileDataset(filename, {},file_meta = file_meta,preamble="\0"*128)
ds.ImageType= 'ORIGINAL\PRIMARY\AXIAL\CT'
ds.SOPClassUID = 'Secondary Capture Image Storage'
ds.SOPInstanceUID = '1.3.6.1.4.1.9590.100.1.1.111165684411017669021768385720736873780'
ds.StudyDate = str(datetime.date.today()).replace('-','')
#ds.ImageDate = str(datetime.date.today()).replace('-','')
ds.StudyTime = str(time.time())
#ds.ImageTime = str(time.time())
ds.AccessionNumber = '153745645'
ds.Modality = 'CT'
ds.Manufacturer = 'PY_BONEMAT_ABAQUS'
ds.InstitutionName = 'UNIVERISTY_OF_BATH'
ds.ReferringPhysiciansName = 'NOTAPPLICABLE'
ds.ManufacturersModelName = 'VERSION1-0-9'
ds.ReferencedImageSequence = ''
ds.PatientsName = 'SUBJECT001'
ds.PatientID = ''
ds.PatientsBirthDate = ''
ds.PatientsSex = 'F'
ds.SliceThickness = 2.7
ds.KVP = 120
ds.SpacingBetweenSlices = 1
ds.DataCollectionDiameter = 430
ds.ReconstructionDiameter = 430.00
ds.DistanceSourceToDetector = 1093
ds.DistanceSourceToPatient = 630.
ds.GantryDetectorTilt = 0.0
ds.ScanArc = 403
ds.XRayTubeCurrent = 200
ds.Exposure = 135
ds.FilterType = 'F'
ds.PatientPosition = 'HFS'
ds.StudyInstanceUID = '1.3.6.1.4.1.9590.100.1.1.124313977412360175234271287472804872093'
ds.SeriesInstanceUID = '1.3.6.1.4.1.9590.100.1.1.111165684411017669021768385720736873780.1'
#ds.ReferenceSOPClassUID = 'Secondary Capture Image Storage'
#ds.ReferencedSOPInstanceUID = '1.3.6.1.4.1.9590.100.1.1.111165684411017669021768385720736873780'
#ds.ContentDate = str(datetime.date.today()).replace('-','')
#ds.ContentTime = str(time.time())
ds.StudyID = '15346254'
ds.SeriesNumber = '8733'
ds.AcquisitionNumber = 1
ds.ImageNumber = origins.index(origin) + 1
ds.SliceLocation = origin[2]
ds.SecondaryCaptureDeviceManufctur = 'Python 2.7.3'
ds.SamplesPerPixel = 1
ds.PhotometricInterpretation = "MONOCHROME2"
ds.PixelRepresentation = 0
ds.HighBit = 15
ds.BitsStored = 16
ds.BitsAllocated = 16
ds.SmallestImagePixelValue = '\\x00\\x00'
ds.LargestImagePixelValue = '\\xff\\xff'
ds.Columns = pixel_array.shape[0]
ds.Rows = pixel_array.shape[1]
ds.PatientOrientation = ['L','P']
ds.ImagePositionPatient = origin
ds.ImageOrientationPatient = orientation
ds.PixelSpacing = [1.0, 1.0]
ds.RescaleSlope = 1.0
ds.RescaleIntercept = 0.0
if pixel_array.dtype != np.uint16:
pixel_array = pixel_array.astype(np.uint16)
ds.PixelData = pixel_array.tostring()
ds.save_as(filename)
return
