def empty_dicom():
file_meta = FileMetaDataset()
file_meta.FileMetaInformationGroupLength = 206
file_meta.FileMetaInformationVersion = b'\x00\x01'
file_meta.MediaStorageSOPClassUID = '1.2.840.10008.5.1.4.1.1.2'
file_meta.MediaStorageSOPInstanceUID = '1.2.826.0.1.3680043.8.498.51645380419494159785729751472725175471'
file_meta.TransferSyntaxUID = '1.2.840.10008.1.2.1'
file_meta.ImplementationClassUID = '1.2.826.0.1.3680043.8.498.1'
file_meta.ImplementationVersionName = 'PYDICOM 2.0.0'
ds = Dataset()
ds.ImageType = ['ORIGINAL', 'PRIMARY', 'AXIAL']
ds.SOPClassUID = '1.2.840.10008.5.1.4.1.1.2'
ds.SOPInstanceUID = '1.2.826.0.1.3680043.8.498.51645380419494159785729751472725175471'
ds.Modality = 'CT'
ds.StudyInstanceUID = '1.2.826.0.1.3680043.8.498.75112040858074996916346159754932379994'
ds.SeriesInstanceUID = '1.2.826.0.1.3680043.8.498.64119849432490865623274415908957426618'
ds.InstanceNumber = "1"
ds.FrameOfReferenceUID = '1.2.826.0.1.3680043.8.498.10194591012322579188814682575529857631'
ds.ImagesInAcquisition = "1"
ds.SamplesPerPixel = 1
ds.PhotometricInterpretation = 'MONOCHROME2'
ds.BitsAllocated = 8
ds.BitsStored = 8
ds.HighBit = 7
ds.PixelRepresentation = 0
return ds, file_meta
def get_file_meta(dcm, root_uid):
file_meta = FileMetaDataset()
# From pydicom
file_meta.MediaStorageSOPClassUID = (
pydicom._storage_sopclass_uids.RTStructureSetStorage)
file_meta.MediaStorageSOPInstanceUID = pydicom.uid.generate_uid(
root_uid) # TODO Generate this properly
file_meta.TransferSyntaxUID = pydicom.uid.ImplicitVRLittleEndian
# From dicom imaging file
imaging_meta = [
"FileMetaInformationVersion",
"ImplementationClassUID",
"ImplementationVersionName",
]
copy_attrs(dcm.file_meta, file_meta, imaging_meta)
# file_meta.FileMetaInformationVersion = dcm.file_meta.FileMetaInformationVersion
# file_meta.ImplementationClassUID = (
# dcm.file_meta.ImplementationClassUID
# ) # TODO Check this is true on non-anon data
# file_meta.ImplementationVersionName = dcm.file_meta.ImplementationVersionName
return file_meta
def handle(event):
meta = FileMetaDataset()
meta.TransferSyntaxUID = event.context.transfer_syntax
event.dataset.file_meta = meta
event_out.append(event.dataset)
return 0x0000
def _basic_file_meta(class_UID):
"""Create basic file meta for DICOM dataset."""
# File meta info data elements
file_meta = FileMetaDataset()
file_meta.FileMetaInformationVersion = b'\x00\x01'
file_meta.MediaStorageSOPClassUID = class_UID
file_meta.MediaStorageSOPInstanceUID = generate_uid()
file_meta.TransferSyntaxUID = '1.2.840.10008.1.2'
return file_meta
def get_file_meta() -> FileMetaDataset:
file_meta = FileMetaDataset()
file_meta.FileMetaInformationGroupLength = 202
file_meta.FileMetaInformationVersion = b'\x00\x01'
file_meta.TransferSyntaxUID = ImplicitVRLittleEndian
file_meta.MediaStorageSOPClassUID = SOPClassUID.RTSTRUCT
file_meta.MediaStorageSOPInstanceUID = generate_uid() # TODO find out random generation is fine
file_meta.ImplementationClassUID = SOPClassUID.RTSTRUCT_IMPLEMENTATION_CLASS
return file_meta
def get_file_meta(dcms):
dcm = dcms[0]
file_meta = FileMetaDataset()
file_meta.FileMetaInformationVersion = dcm.file_meta.FileMetaInformationVersion
file_meta.MediaStorageSOPClassUID = "RT Structure Set Storage"
file_meta.MediaStorageSOPInstanceUID = "Anonymous" # TODO
file_meta.TransferSyntaxUID = dcm.file_meta.TransferSyntaxUID
file_meta.ImplementationClassUID = dcm.file_meta.ImplementationClassUID
file_meta.ImplementationVersionName = dcm.file_meta.ImplementationVersionName
return file_meta
def set_file_meta(instance: Dataset):
meta = FileMetaDataset()
# meta.FileMetaInformationGroupLength = ??
# meta.FileMetaInformationVersion = b'\x00\x01'
meta.MediaStorageSOPClassUID = instance.SOPClassUID
meta.MediaStorageSOPInstanceUID = instance.SOPInstanceUID
meta.TransferSyntaxUID = ImplicitVRLittleEndian
instance.is_implicit_VR = instance.is_little_endian = True
# meta.ImplementationClassUID = ??
# meta.ImplementationVersionName = ??
instance.file_meta = meta
instance.preamble = b'\x00' * 128
def DICOM_File_Meta_Information(ds):
# File meta info data elements
file_meta = FileMetaDataset()
# file_meta.FileMetaInformationGroupLength = 210
# file_meta.FileMetaInformationVersion = b'\x00\x01'
file_meta.MediaStorageSOPClassUID = ds.SOPClassUID
file_meta.MediaStorageSOPInstanceUID = ds.SOPInstanceUID
file_meta.TransferSyntaxUID = '1.2.840.10008.1.2.1'
file_meta.ImplementationClassUID = '1.2.276.0.20.1.1.33.6.1.0'
file_meta.ImplementationVersionName = 'PatientSelect6.1'
file_meta.SourceApplicationEntityTitle = 'kESI'
return file_meta
def handle_store(event):
"""Store the pydicom Dataset `ds`.
Parameters
----------
event : pydicom.event
Returns
-------
status : int or pydicom.dataset.Dataset
The status returned to the peer AE in the C-STORE response. Must be
a valid C-STORE status value for the applicable Service Class as
either an ``int`` or a ``Dataset`` object containing (at a
minimum) a (0000,0900) *Status* element.
"""
global scpdir
ds = event.dataset
context = event.context
# logging.debug('on_c_store: info {}'.format(info))
# calling_aet = info['requestor']['ae_title']
# called_aet = info['acceptor']['ae_title']
# logging.debug('on_c_store: calling_aet {}'.format(calling_aet))
# logging.debug('on_c_store: called_aet {}'.format(called_aet))
# Add the DICOM File Meta Information
meta = FileMetaDataset()
meta.MediaStorageSOPClassUID = ds.SOPClassUID
meta.MediaStorageSOPInstanceUID = ds.SOPInstanceUID
meta.ImplementationClassUID = PYNETDICOM_IMPLEMENTATION_UID
meta.ImplementationVersionName = PYNETDICOM_IMPLEMENTATION_VERSION
meta.TransferSyntaxUID = context.transfer_syntax
# Add the file meta to the dataset
ds.file_meta = meta
# Set the transfer syntax attributes of the dataset
ds.is_little_endian = context.transfer_syntax.is_little_endian
ds.is_implicit_VR = context.transfer_syntax.is_implicit_VR
# Save the dataset using the SOP Instance UID as the filename
ds.save_as(
os.path.join(scpdir.name, ds.SOPInstanceUID),
write_like_original=False)
# Return a 'Success' status
return 0x0000
def create_file_meta(
*,
sop_class_uid: UID,
sop_instance_uid: UID,
transfer_syntax: UID,
implementation_uid: UID = PYNETDICOM_IMPLEMENTATION_UID,
implementation_version: str = PYNETDICOM_IMPLEMENTATION_VERSION,
) -> FileMetaDataset:
"""Return a new file meta dataset
.. versionadded:: 2.0
Parameters
----------
sop_class_uid : pydicom.uid.UID
The value for the *Media Storage SOP Class UID*.
sop_instance_uid : pydicom.uid.UID
The value for the *Media Storage SOP Instance UID*.
transfer_syntax : pydicom.uid.UID
The value for the *Transfer Syntax UID*.
implementation_uid : pydicom.uid.UID, optional
The value for the *Implementation Class UID*.
implementation_version : str, optional
The value for the *Implementation Version Name*.
Returns
-------
pydicom.dataset.FileMetaDataset
The File Meta dataset
"""
file_meta = FileMetaDataset()
file_meta.FileMetaInformationGroupLength = 0
file_meta.FileMetaInformationVersion = b'\x00\x01'
file_meta.MediaStorageSOPClassUID = sop_class_uid
file_meta.MediaStorageSOPInstanceUID = sop_instance_uid
file_meta.TransferSyntaxUID = transfer_syntax
file_meta.ImplementationClassUID = implementation_uid
file_meta.ImplementationVersionName = implementation_version
# File Meta Information is always encoded as Explicit VR Little Endian
file_meta.is_little_endian = True
file_meta.is_implicit_VR = False
return file_meta
def generate_dicom_sr(file_path, img_ds, data, series_description):
"""
Generates DICOM Structured Report files for the given file path.
:param file_path: the file name and directory to save the DICOM
SR file in.
:param img_ds: A CT or MR image from the dataset used to pull
general information for the DICOM SR.
:param data: Text data to be written to the DICOM SR file.
:param series_description: Description of text data written to SR.
:return: dicom_sr, a dataset for the new DICOM SR file.
"""
if img_ds is None:
raise ValueError("No CT data to initialize RT SS")
# Create file meta
file_meta = FileMetaDataset()
file_meta.FileMetaInformationGroupLength = 238
file_meta.FileMetaInformationVersion = b'\x00\x01'
file_meta.MediaStorageSOPClassUID = '1.2.840.10008.5.1.4.1.1.88.33'
file_meta.MediaStorageSOPInstanceUID = pydicom.uid.generate_uid()
file_meta.TransferSyntaxUID = ImplicitVRLittleEndian
validate_file_meta(file_meta)
# Create dataset
dicom_sr = pydicom.dataset.FileDataset(file_path, {},
preamble=b"\0" * 128,
file_meta=file_meta)
dicom_sr.fix_meta_info()
# Get current date and time
now = datetime.datetime.now()
dicom_date = now.strftime("%Y%m%d")
dicom_time = now.strftime("%H%M")
# List of tags to copy from CT/MR image
top_level_tags_to_copy: list = [
Tag("PatientName"),
Tag("PatientID"),
Tag("PatientBirthDate"),
Tag("PatientSex"),
Tag("StudyDate"),
Tag("StudyTime"),
Tag("ReferringPhysicianName"),
Tag("StudyDescription"),
Tag("StudyInstanceUID"),
Tag("StudyID"),
Tag("RequestingService"),
Tag("PatientAge"),
Tag("PatientSize"),
Tag("PatientWeight"),
Tag("MedicalAlerts"),
Tag("Allergies"),
Tag("PregnancyStatus"),
Tag("InstitutionName"),
Tag("InstitutionAddress")
]
# Copy tags from CT/MR image
for tag in top_level_tags_to_copy:
if tag in img_ds:
dicom_sr[tag] = deepcopy(img_ds[tag])
dicom_sr.AccessionNumber = ""
# == SR Document Series Module
dicom_sr.SeriesDate = dicom_date
dicom_sr.SeriesTime = dicom_time
dicom_sr.Modality = "SR"
dicom_sr.SeriesDescription = series_description
# Can be empty
referenced_performed_procedure_step_sequence = Sequence()
dicom_sr.ReferencedPerformedProcedureStepSequence = \
referenced_performed_procedure_step_sequence
dicom_sr.SeriesInstanceUID = pydicom.uid.generate_uid()
dicom_sr.SeriesNumber = 1
# == General Equipment Module
dicom_sr.Manufacturer = "OnkoDICOM"
dicom_sr.ManufacturersModelName = "OnkoDICOM"
# TODO: Pull this off build information in some way
dicom_sr.SoftwareVersions = "2021"
# == SR Document General Module
dicom_sr.ContentDate = dicom_date
dicom_sr.ContentTime = dicom_time
dicom_sr.InstanceNumber = 1
# Empty if unknown
performed_procedure_code_sequence = Sequence()
dicom_sr.PerformedProcedureCodeSequence = performed_procedure_code_sequence
# Do not want to mark as complete in case it isn't!
dicom_sr.CompletionFlag = "PARTIAL"
dicom_sr.VerificationFlag = "UNVERIFIED"
# == SR Document Content Module
referenced_sop_sequence = Sequence([Dataset()])
referenced_sop_sequence[0].ReferencedSOPClassUID = ''
referenced_sop_sequence[0].ReferencedSOPInstanceUID = ''
dicom_sr.ReferencedSOPSequence = referenced_sop_sequence
dicom_sr.ValueType = "CONTAINER"
dicom_sr.ContinuityOfContent = "CONTINUOUS"
dicom_sr.TemporalRangeTime = ""
dicom_sr.ReferencedTimeOffsets = ""
dicom_sr.ReferencedDateTime = ""
dicom_sr.MeasuredValueSequence = Sequence()
og_frame_of_reference_UID = \
deepcopy(img_ds[Tag("FrameOfReferenceUID")].value)
dicom_sr.ReferencedFrameOfReferenceUID = og_frame_of_reference_UID
# == Content Sequence
content_sequence = Sequence([Dataset()])
content_sequence[0].RelationshipType = 'CONTAINS'
content_sequence[0].ValueType = 'TEXT'
concept_name_code_sequence = Sequence([Dataset()])
concept_name_code_sequence[0].CodeValue = ''
concept_name_code_sequence[0].CodingSchemeDesignator = ''
concept_name_code_sequence[0].CodeMeaning = ''
content_sequence[0].ConceptNameCodeSequence = concept_name_code_sequence
content_sequence[0].TextValue = data
dicom_sr.ContentSequence = content_sequence
# == SOP Common Module
dicom_sr.SOPClassUID = '1.2.840.10008.5.1.4.1.1.88.33'
dicom_sr.SOPInstanceUID = file_meta.MediaStorageSOPInstanceUID
dicom_sr.is_little_endian = True
dicom_sr.is_implicit_VR = True
return dicom_sr
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
for r in range(seg_mask.shape[0]):
for c in range(seg_mask.shape[1]):
smask[r][c][z - startIndex] = seg_mask[r][c][z]
print("Seg_mask array created")
stop = timeit.default_timer()
print("Runtime (mask creation): " + str(stop-start) + "s")
file_meta = FileMetaDataset()
file_meta.MediaStorageSOPClassUID='1.2.840.10008.5.1.4.1.1.66.4'
dicomuid = generate_uid()
instanceuid=dicomuid
file_meta.MediaStorageSOPInstanceUID=instanceuid
file_meta.TransferSyntaxUID=ExplicitVRLittleEndian
file_meta.ImplementationClassUID='1.2.840.10008.5.1.4.1.1.66.4'
file_meta.ImplementationVersionName='ePAD_matlab_1.0'
suffix = '.dcm'
info = seriesDCM[0]
info_mask = FileDataset('output/' + str(name) + str(suffix), {},
file_meta=file_meta, preamble=b"\0" * 128)
info_mask.StudyDescription=info.StudyDescription
info_mask.is_little_endian = False
info_mask.is_explicit_VR = False
if 'ImageOrientationPatient' in info:
ds = Dataset()
ds2 = Dataset()
ds2.ImageOrientationPatient = info.ImageOrientationPatient
def create_initial_rtss_from_ct(img_ds: pydicom.dataset.Dataset,
filepath: Path,
uid_list: list) -> pydicom.dataset.FileDataset:
"""
Pre-populate an RT Structure Set based on a single CT (or MR) and a
list of image UIDs The caller should update the Structure Set Label,
Name, and Description, which are set to "OnkoDICOM" plus the StudyID
from the CT, and must add Structure Set ROI Sequence, ROI Contour
Sequence, and RT ROI Observations Sequence
Parameters
----------
img_ds : pydicom.dataset.Dataset
A CT or MR image that the RT Structure Set will be "drawn" on
uid_list : list
list of UIDs (as strings) of the entire image volume that the
RT SS references
filepath: str
A path where the RTStruct will be saved
Returns
-------
pydicom.dataset.FileDataset
the half-baked RT SS, ready for Structure Set ROI Sequence,
ROI Contour Sequence, and RT ROI Observations Sequence
Raises
------
ValueError
[description]
"""
if img_ds is None:
raise ValueError("No CT data to initialize RT SS")
now = datetime.datetime.now()
dicom_date = now.strftime("%Y%m%d")
dicom_time = now.strftime("%H%M")
# File Meta module
file_meta = FileMetaDataset()
file_meta.FileMetaInformationGroupLength = 238
file_meta.FileMetaInformationVersion = b'\x00\x01'
file_meta.MediaStorageSOPClassUID = '1.2.840.10008.5.1.4.1.1.481.3'
file_meta.MediaStorageSOPInstanceUID = generate_uid()
file_meta.TransferSyntaxUID = ImplicitVRLittleEndian
validate_file_meta(file_meta)
rt_ss = pydicom.dataset.FileDataset(filepath, {},
preamble=b"\0" * 128,
file_meta=file_meta)
rt_ss.fix_meta_info()
top_level_tags_to_copy: list = [
Tag("PatientName"),
Tag("PatientID"),
Tag("PatientBirthDate"),
Tag("PatientSex"),
Tag("StudyDate"),
Tag("StudyTime"),
Tag("AccessionNumber"),
Tag("ReferringPhysicianName"),
Tag("StudyDescription"),
Tag("StudyInstanceUID"),
Tag("StudyID"),
Tag("RequestingService"),
Tag("PatientAge"),
Tag("PatientSize"),
Tag("PatientWeight"),
Tag("MedicalAlerts"),
Tag("Allergies"),
Tag("PregnancyStatus"),
Tag("FrameOfReferenceUID"),
Tag("PositionReferenceIndicator"),
Tag("InstitutionName"),
Tag("InstitutionAddress"),
Tag("OperatorsName")
]
for tag in top_level_tags_to_copy:
if tag in img_ds:
rt_ss[tag] = deepcopy(img_ds[tag])
if rt_ss.StudyInstanceUID == "":
raise ValueError(
"The given dataset is missing a required tag 'StudyInstanceUID'")
# RT Series Module
rt_ss.SeriesDate = dicom_date
rt_ss.SeriesTime = dicom_time
rt_ss.Modality = "RTSTRUCT"
rt_ss.OperatorsName = ""
rt_ss.SeriesInstanceUID = pydicom.uid.generate_uid()
rt_ss.SeriesNumber = "1"
# General Equipment Module
rt_ss.Manufacturer = "OnkoDICOM"
rt_ss.ManufacturerModelName = "OnkoDICOM"
# TODO: Pull this off build information in some way
rt_ss.SoftwareVersions = "2021"
# Frame of Reference module
rt_ss.FrameOfReferenceUID = img_ds.FrameOfReferenceUID
rt_ss.PositionReferenceIndicator = ""
# Structure Set module
# Best to modify the Structure Set Label with something more
# interesting in the application. and populate the Name and
# Description from the application also.
rt_ss.StructureSetLabel = "OnkoDICOM rtss"
rt_ss.StructureSetName = rt_ss.StructureSetLabel
rt_ss.StructureSetDescription = "OnkoDICOM rtss of " + rt_ss.StudyID
rt_ss.StructureSetDate = dicom_date
rt_ss.StructureSetTime = dicom_time
# Contour Image Sequence
contour_image_sequence = []
for uid in uid_list:
contour_image_sequence_item = pydicom.dataset.Dataset()
contour_image_sequence_item.ReferencedSOPClassUID = img_ds.SOPClassUID
contour_image_sequence_item.ReferencedSOPInstanceUID = uid
contour_image_sequence.append(contour_image_sequence_item)
# RT Referenced Series Sequence
rt_referenced_series = pydicom.dataset.Dataset()
rt_referenced_series.SeriesInstanceUID = img_ds.SeriesInstanceUID
rt_referenced_series.ContourImageSequence = contour_image_sequence
rt_referenced_series_sequence = [rt_referenced_series]
# RT Referenced Study Sequence
rt_referenced_study = pydicom.dataset.Dataset()
rt_referenced_study.ReferencedSOPClassUID = "1.2.840.10008.3.1.2.3.1"
rt_referenced_study.ReferencedSOPInstanceUID = img_ds.StudyInstanceUID
rt_referenced_study.RTReferencedSeriesSequence = \
rt_referenced_series_sequence
rt_referenced_study_sequence = [rt_referenced_study]
# RT Referenced Frame Of Reference Sequence, Structure Set Module
referenced_frame_of_reference = pydicom.dataset.Dataset()
referenced_frame_of_reference.FrameOfReferenceUID = \
img_ds.FrameOfReferenceUID
referenced_frame_of_reference.RTReferencedStudySequence = \
rt_referenced_study_sequence
rt_ss.ReferencedFrameOfReferenceSequence = [referenced_frame_of_reference]
# Sequence modules
rt_ss.StructureSetROISequence = []
rt_ss.ROIContourSequence = []
rt_ss.RTROIObservationsSequence = []
# SOP Common module
rt_ss.SOPClassUID = rt_ss.file_meta.MediaStorageSOPClassUID
rt_ss.SOPInstanceUID = rt_ss.file_meta.MediaStorageSOPInstanceUID
# Add required elements
rt_ss.InstanceCreationDate = dicom_date
rt_ss.InstanceCreationTime = dicom_time
rt_ss.is_little_endian = True
rt_ss.is_implicit_VR = True
return rt_ss
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_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)