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() -> 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 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 write_file_meta_info(fp: DicomIO,
file_meta: FileMetaDataset,
enforce_standard: bool = True) -> None:
"""Write the File Meta Information elements in `file_meta` to `fp`.
If `enforce_standard` is ``True`` then the file-like `fp` should be
positioned past the 128 byte preamble + 4 byte prefix (which should
already have been written).
**DICOM File Meta Information Group Elements**
From the DICOM standard, Part 10,
:dcm:`Section 7.1<part10/chapter_7.html#sect_7.1>`, any DICOM file shall
contain a 128-byte preamble, a 4-byte DICOM prefix 'DICM' and (at a
minimum) the following Type 1 DICOM Elements (from
:dcm:`Table 7.1-1<part10/chapter_7.html#table_7.1-1>`):
* (0002,0000) *File Meta Information Group Length*, UL, 4
* (0002,0001) *File Meta Information Version*, OB, 2
* (0002,0002) *Media Storage SOP Class UID*, UI, N
* (0002,0003) *Media Storage SOP Instance UID*, UI, N
* (0002,0010) *Transfer Syntax UID*, UI, N
* (0002,0012) *Implementation Class UID*, UI, N
If `enforce_standard` is ``True`` then (0002,0000) will be added/updated,
(0002,0001) and (0002,0012) will be added if not already present and the
other required elements will be checked to see if they exist. If
`enforce_standard` is ``False`` then `file_meta` will be written as is
after minimal validation checking.
The following Type 3/1C Elements may also be present:
* (0002,0013) *Implementation Version Name*, SH, N
* (0002,0016) *Source Application Entity Title*, AE, N
* (0002,0017) *Sending Application Entity Title*, AE, N
* (0002,0018) *Receiving Application Entity Title*, AE, N
* (0002,0102) *Private Information*, OB, N
* (0002,0100) *Private Information Creator UID*, UI, N
If `enforce_standard` is ``True`` then (0002,0013) will be added/updated.
*Encoding*
The encoding of the *File Meta Information* shall be *Explicit VR Little
Endian*.
Parameters
----------
fp : file-like
The file-like to write the File Meta Information to.
file_meta : pydicom.dataset.Dataset
The File Meta Information elements.
enforce_standard : bool
If ``False``, then only the *File Meta Information* elements already in
`file_meta` will be written to `fp`. If ``True`` (default) then a DICOM
Standards conformant File Meta will be written to `fp`.
Raises
------
ValueError
If `enforce_standard` is ``True`` and any of the required *File Meta
Information* elements are missing from `file_meta`, with the
exception of (0002,0000), (0002,0001) and (0002,0012).
ValueError
If any non-Group 2 Elements are present in `file_meta`.
"""
validate_file_meta(file_meta, enforce_standard)
if enforce_standard and 'FileMetaInformationGroupLength' not in file_meta:
# Will be updated with the actual length later
file_meta.FileMetaInformationGroupLength = 0
# Write the File Meta Information Group elements
# first write into a buffer to avoid seeking back, that can be
# expansive and is not allowed if writing into a zip file
buffer = DicomBytesIO()
buffer.is_little_endian = True
buffer.is_implicit_VR = False
write_dataset(buffer, file_meta)
# If FileMetaInformationGroupLength is present it will be the first written
# element and we must update its value to the correct length.
if 'FileMetaInformationGroupLength' in file_meta:
# Update the FileMetaInformationGroupLength value, which is the number
# of bytes from the end of the FileMetaInformationGroupLength element
# to the end of all the File Meta Information elements.
# FileMetaInformationGroupLength has a VR of 'UL' and so has a value
# that is 4 bytes fixed. The total length of when encoded as
# Explicit VR must therefore be 12 bytes.
file_meta.FileMetaInformationGroupLength = buffer.tell() - 12
buffer.seek(0)
write_data_element(buffer, file_meta[0x00020000])
fp.write(buffer.getvalue())
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
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)
