def _set_header_from_dicom(self, dcm):
""" Creates the header metadata for this Cube class, based on a given Dicom object.
:param DICOM dcm: Dicom object which will be used for generating the header data.
"""
if not _dicom_loaded:
raise ModuleNotLoadedError("Dicom")
ds = dcm["images"][0]
self.version = "1.4"
self.created_by = "pytrip"
self.creation_info = "Created by PyTRiP98;"
self.primary_view = "transversal"
self.set_data_type(type(ds.pixel_array[0][0]))
self.patient_name = ds.PatientsName
self.slice_dimension = int(ds.Rows) # should be changed ?
self.pixel_size = float(
ds.PixelSpacing[0]) # (0028, 0030) Pixel Spacing (DS)
self.slice_thickness = ds.SliceThickness # (0018, 0050) Slice Thickness (DS)
# slice_distance != SliceThickness. One may have overlapping slices. See #342
self.slice_number = len(dcm["images"])
self.xoffset = float(ds.ImagePositionPatient[0])
self.dimx = int(ds.Rows) # (0028, 0010) Rows (US)
self.yoffset = float(ds.ImagePositionPatient[1])
self.dimy = int(ds.Columns) # (0028, 0011) Columns (US)
self.zoffset = float(ds.ImagePositionPatient[2]
) # note that zoffset should not be used.
self.dimz = len(dcm["images"])
self.z_table = True
self._set_z_table_from_dicom(dcm)
# Fix for bug #342
# TODO: slice_distance should probably be a list of distances,
# but for now we will just use the distance between the first two slices.
if len(self.slice_pos
) > 1: # _set_z_table_from_dicom() must be called before
self.slice_distance = abs(self.slice_pos[1] - self.slice_pos[0])
logger.debug("Slice distance set to {:.2f}".format(
self.slice_distance))
else:
logger.warning(
"Only a single slice found. Setting slice_distance to slice_thickness."
)
self.slice_distance = self.slice_thickness
if self.slice_thickness > self.slice_distance:
# TODO: this is probably valid dicom format, however let's print a warning for now
# as it may indicate some problem with the input dicom, as it is rather unusual.
logger.warning(
"Overlapping slices found: slice thickness is larger than the slice distance."
)
self.set_byteorder()
self.data_type = "integer"
self.num_bytes = 2
self._set_format_str()
self.header_set = True
# unique for whole structure set
self._dicom_study_instance_uid = ds.StudyInstanceUID
self._ct_dicom_series_instance_uid = ds.SeriesInstanceUID
def read_dicom_header(self, dcm):
""" Creates the header metadata for this Cube class, based on a given Dicom object.
:param Dicom dcm: Dicom object which will be used for generating the header data.
"""
if _dicom_loaded is False:
raise ModuleNotLoadedError("Dicom")
ds = dcm["images"][0]
self.version = "1.4"
self.created_by = "pytrip"
self.creation_info = "Created by PyTRiP98;"
self.primary_view = "transversal"
self.set_data_type(type(ds.pixel_array[0][0]))
self.patient_name = ds.PatientsName
self.slice_dimension = int(ds.Rows) # should be changed ?
self.pixel_size = float(ds.PixelSpacing[0])
self.slice_distance = abs(
float(dcm["images"][0].ImagePositionPatient[2]) -
float(dcm["images"][1].ImagePositionPatient[2]))
self.slice_number = len(dcm["images"])
self.xoffset = float(ds.ImagePositionPatient[0])
self.dimx = int(ds.Rows)
self.yoffset = float(ds.ImagePositionPatient[1])
self.dimy = int(ds.Columns)
self.zoffset = float(ds.ImagePositionPatient[2])
self.dimz = len(dcm["images"])
self.z_table = True
self.set_z_table(dcm)
self.set_byteorder()
self._set_format_str()
self.header_set = True
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 read_dicom_header(self, dcm):
""" Creates the header metadata for this Cube class, based on a given Dicom object.
:param Dicom dcm: Dicom object which will be used for generating the header data.
"""
if _dicom_loaded is False:
raise ModuleNotLoadedError("Dicom")
ds = dcm["images"][0]
self.version = "1.4"
self.created_by = "pytrip"
self.creation_info = "Created by PyTRiP98;"
self.primary_view = "transversal"
self.set_data_type(type(ds.pixel_array[0][0]))
self.patient_name = ds.PatientsName
self.slice_dimension = int(ds.Rows) # should be changed ?
self.pixel_size = float(ds.PixelSpacing[0]) # (0028, 0030) Pixel Spacing (DS)
self.slice_distance = ds.SliceThickness # (0018, 0050) Slice Thickness (DS)
self.slice_number = len(dcm["images"])
self.xoffset = float(ds.ImagePositionPatient[0])
self.dimx = int(ds.Rows) # (0028, 0010) Rows (US)
self.yoffset = float(ds.ImagePositionPatient[1])
self.dimy = int(ds.Columns) # (0028, 0011) Columns (US)
self.zoffset = float(ds.ImagePositionPatient[2]) # note that zoffset should not be used.
self.dimz = len(dcm["images"])
self.z_table = True
self.set_z_table(dcm)
self.set_byteorder()
self._set_format_str()
self.header_set = True
# unique for whole structure set
self._dicom_study_instance_uid = ds.StudyInstanceUID
self._ct_dicom_series_instance_uid = ds.SeriesInstanceUID
def create_dicom(self):
""" Creates a Dicom RT-Dose object from self.
This function can be used to convert a TRiP98 Dose file to Dicom format.
:returns: a Dicom RT-Dose object.
"""
if not _dicom_loaded:
raise ModuleNotLoadedError("Dicom")
if not self.header_set:
raise InputError("Header not loaded")
ds = self.create_dicom_base()
ds.Modality = 'RTDOSE'
ds.SamplesperPixel = 1
ds.BitsAllocated = self.num_bytes * 8
ds.BitsStored = self.num_bytes * 8
ds.AccessionNumber = ''
ds.SeriesDescription = 'RT Dose'
ds.DoseUnits = 'GY'
ds.DoseType = 'PHYSICAL'
ds.DoseGridScaling = self.target_dose / 10**5
ds.DoseSummationType = 'PLAN'
ds.SliceThickness = ''
ds.InstanceCreationDate = '19010101'
ds.InstanceCreationTime = '000000'
ds.NumberOfFrames = len(self.cube)
ds.PixelRepresentation = 0
ds.StudyID = '1'
ds.SeriesNumber = 14
ds.GridFrameOffsetVector = [
x * self.slice_distance for x in range(self.dimz)
]
ds.InstanceNumber = ''
ds.NumberofFrames = len(self.cube)
ds.PositionReferenceIndicator = "RF"
ds.TissueHeterogeneityCorrection = ['IMAGE', 'ROI_OVERRIDE']
ds.ImagePositionPatient = [
"%.3f" % (self.xoffset * self.pixel_size),
"%.3f" % (self.yoffset * self.pixel_size),
"%.3f" % (self.slice_pos[0])
]
ds.SOPClassUID = '1.2.840.10008.5.1.4.1.1.481.2'
ds.SOPInstanceUID = '1.2.246.352.71.7.320687012.47206.20090603085223'
ds.SeriesInstanceUID = '1.2.246.352.71.2.320687012.28240.20090603082420'
# Bind to rtplan
rt_set = Dataset()
rt_set.RefdSOPClassUID = '1.2.840.10008.5.1.4.1.1.481.5'
rt_set.RefdSOPInstanceUID = '1.2.3'
ds.ReferencedRTPlans = Sequence([rt_set])
pixel_array = np.zeros((len(self.cube), ds.Rows, ds.Columns),
dtype=self.pydata_type)
pixel_array[:][:][:] = self.cube[:][:][:]
ds.PixelData = pixel_array.tostring()
return ds
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 create_dicom(self):
""" Creates a DICOM RT-Dose object from self.
This function can be used to convert a TRiP98 Dose file to DICOM format.
:returns: a DICOM RT-Dose object.
"""
if not _dicom_loaded:
raise ModuleNotLoadedError("DICOM")
if not self.header_set:
raise InputError("Header not loaded")
ds = self.create_dicom_base()
ds.Modality = 'RTDOSE'
ds.SamplesPerPixel = 1
ds.BitsAllocated = self.num_bytes * 8
ds.BitsStored = self.num_bytes * 8
ds.AccessionNumber = ''
ds.SeriesDescription = 'RT Dose'
ds.DoseUnits = 'GY'
ds.DoseType = 'PHYSICAL'
ds.DoseGridScaling = self.target_dose / 10**5
ds.DoseSummationType = 'PLAN'
ds.SliceThickness = ''
ds.InstanceCreationDate = '19010101'
ds.InstanceCreationTime = '000000'
ds.NumberOfFrames = len(self.cube)
ds.PixelRepresentation = 0
ds.StudyID = '1'
ds.SeriesNumber = '14' # SeriesNumber tag 0x0020,0x0011 (type IS - Integer String)
ds.GridFrameOffsetVector = [
x * self.slice_distance for x in range(self.dimz)
]
ds.InstanceNumber = ''
ds.PositionReferenceIndicator = "RF"
ds.TissueHeterogeneityCorrection = ['IMAGE', 'ROI_OVERRIDE']
ds.ImagePositionPatient = [
"%.3f" % (self.xoffset * self.pixel_size),
"%.3f" % (self.yoffset * self.pixel_size),
"%.3f" % (self.slice_pos[0])
]
ds.SOPClassUID = '1.2.840.10008.5.1.4.1.1.481.2'
ds.SOPInstanceUID = '1.2.246.352.71.7.320687012.47206.20090603085223'
# 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._dose_dicom_series_instance_uid may be either set in __init__ when creating new object
# Series Instance UID might be different than Series Instance UID for CTs
ds.SeriesInstanceUID = self._dose_dicom_series_instance_uid
# Bind to rtplan
rt_set = Dataset()
rt_set.RefdSOPClassUID = '1.2.840.10008.5.1.4.1.1.481.5'
rt_set.RefdSOPInstanceUID = '1.2.3'
ds.ReferencedRTPlanSequence = Sequence([rt_set])
pixel_array = np.zeros((len(self.cube), ds.Rows, ds.Columns),
dtype=self.pydata_type)
pixel_array[:][:][:] = self.cube[:][:][:]
ds.PixelData = pixel_array.tostring()
return ds