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 convert(nome_tiff, nome_dicom):
global ds
# Nomes do arquivo
filename_little_endian = nome_dicom
# Criando arquivos com informações minimas
print('Criando arquivo Dicom Image')
file_meta = FileMetaDataset()
file_meta.MediaStorageSOPClassUID = '1.2.840.10008.5.1.4.1.1.481.1' #http://dicom.nema.org/dicom/2013/output/chtml/part04/sect_I.4.html
file_meta.MediaStorageSOPInstanceUID = "1.2.246.352.81.3.273720375.51644.19651.179.0"
file_meta.ImplementationClassUID = "1.2.246.352.70.2.1.160.3"
#Criando um dataset "vazio" ==> https://pydicom.github.io/pydicom/dev/reference/generated/pydicom.dataset.FileDataset.html
ds = FileDataset(filename_little_endian, {}, file_meta = file_meta, preamble = b"\0"*128)
#Adicionando elementos
ds.PatientName = "Teste"
ds.PatientID = "123456789"
#Transfer Syntax
ds.file_meta.TransferSyntaxUID = pydicom.uid.ExplicitVRLittleEndian
ds.is_little_endian = True
ds.is_implicit_VR = False
#Adicionando data e hora de criação
dt = datetime.datetime.now()
ds.ContentDate = dt.strftime('%Y%m%d')
timeStr = dt.strftime('%H%M%S.%f') # formato longo com micro segundos
ds.ContentTime = timeStr
#Carregando arquivo TIFF
tiff_file = Image.open(nome_tiff)
tiff_rotacionada90 = tiff_file.rotate(90)
tiff_array = np.array(tiff_rotacionada90)
#Adicionando array e outras informações da imagem ao dataset
ds.PixelData = tiff_array.tobytes()
tiff_meta_dict = {TAGS[key] : tiff_file.tag[key] for key in tiff_file.tag.keys()}
ds.add_new([0x0008,0x0016], 'UI','1.2.840.10008.5.1.4.1.1.481.1') #SOP Class UID
ds.add_new([0x0008,0x0018], 'UI','1.2.246.352.81.3.273720375.51644.19651.179.0') #SOP Instance UID
ds.add_new([0x0028,0x0010], 'US',tiff_meta_dict['ImageLength'][0]) #rows
ds.add_new([0x0028,0x0011], 'US',tiff_meta_dict['ImageWidth'][0]) #columns
ds.add_new([0x0028,0x0100], 'US',tiff_meta_dict['BitsPerSample'][0]) #Bits Alocated
ds.add_new([0x0028,0x0103], 'US', 0) # PixelRepresentation
ds.add_new([0x0028,0x0002], 'US', tiff_meta_dict['SamplesPerPixel'][0]) # SamplesPerPixel
ds.add_new([0x0028,0x0004], 'CS', 'MONOCHROME2') # Photometric Interpretation ==> https://dicom.innolitics.com/ciods/enhanced-mr-image/enhanced-mr-image/00280103
ds.add_new([0x0008,0x0060], 'CS', 'RTIMAGE') #Modality
ds.add_new([0x0028,0x0101], 'US',tiff_meta_dict['BitsPerSample'][0]) #Bits Stored
ds.add_new([0x3002,0x0022], 'DS', 1000.0) # Radiation Machine SAD
ds.add_new([0x3002,0x0026], 'DS', 1600.0) # RT Image SID
ds.add_new([0x5000,0x0030], 'SH', ['PIXL', 'PIXL']) #Axis Units
x = tiff_meta_dict['XResolution'][0]
### Rever resolução IVIEW
x_res = 1/((x[0]/x[1])/40.25) # mm por pixel
ds.add_new([0x3002,0x0011], 'DS', [x_res,x_res]) #Image Plane Pixel Spacing
print('Pronto!')
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 create_ds():
# Populate required values for file meta information
file_meta = FileMetaDataset()
file_meta.MediaStorageSOPClassUID = '1.2.840.10008.5.1.4.1.1.2'
file_meta.MediaStorageSOPInstanceUID = "1.2.3"
file_meta.ImplementationClassUID = "1.2.3.4"
# Create the FileDataset instance (initially no data elements, but file_meta
# supplied)
ds = FileDataset(FILENAME_PATH, {},
file_meta=file_meta,
preamble=b"\0" * 128)
# Add the data elements -- not trying to set all required here. Check DICOM
# standard
ds.PatientName = "Test^Firstname"
ds.PatientID = "123456"
# Set the transfer syntax
ds.is_little_endian = True
ds.is_implicit_VR = True
# Set image position patient and image orientation patient
ds.PixelSpacing = ['3.0', '3.0']
slice_data = numpy.zeros((50, 50)).astype(numpy.uint16)
ds.ImagePositionPatient = [
'-74.87273061275482', '-147.24999237060547', '-147.1303328871727'
]
ds.ImageOrientationPatient = [
'0.9995653468771569', '0.027916281967051135', '-0.00947620828628687',
'-0.02835352390030065', '0.9983635539946439', '-0.04966177340388578'
]
# set the settings for this slice
ds.Rows = slice_data.shape[1]
ds.Columns = slice_data.shape[0]
ds.SamplesPerPixel = 1
ds.PhotometricInterpretation = 'MONOCHROME2'
ds.PlanarConfiguration = 0
ds.BitsAllocated = 16
ds.BitsStored = 16
ds.HighBit = 15
ds.PixelRepresentation = 1
ds.WindowCenter = 0
ds.WindowWidth = 100
# Set creation date/time
dt = datetime.datetime.now()
ds.ContentDate = dt.strftime('%Y%m%d')
timeStr = dt.strftime('%H%M%S.%f') # long format with micro seconds
ds.ContentTime = timeStr
return ds
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 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
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 _build_dummy_pydicom_header(fields=None):
"""Builds dummy pydicom-based header.
Note these headers are not dicom compliant and should not be used to write out DICOM
files.
Adapted from
https://pydicom.github.io/pydicom/dev/auto_examples/input_output/plot_write_dicom.html
"""
suffix = ".dcm"
filename_little_endian = tempfile.NamedTemporaryFile(suffix=suffix).name
file_meta = FileMetaDataset()
file_meta.MediaStorageSOPClassUID = "1.2.840.10008.5.1.4.1.1.2"
file_meta.MediaStorageSOPInstanceUID = "1.2.3"
file_meta.ImplementationClassUID = "1.2.3.4"
# Create the FileDataset instance (initially no data elements, but file_meta supplied).
ds = FileDataset(filename_little_endian, {}, file_meta=file_meta, preamble=b"\0" * 128)
# Add the data elements -- not trying to set all required here. Check DICOM standard.
ds.PatientName = "Test^Firstname"
ds.PatientID = "123456"
if fields is not None:
for k, v in fields.items():
setattr(ds, k, v)
# Set the transfer syntax
ds.is_little_endian = True
ds.is_implicit_VR = True
# Set creation date/time
dt = datetime.datetime.now()
ds.ContentDate = dt.strftime("%Y%m%d")
timeStr = dt.strftime("%H%M%S.%f") # long format with micro seconds
ds.ContentTime = timeStr
return ds
def _dicom(filename='image.dcm', **values):
filename = str(tmpdir.join(filename))
file_meta = FileMetaDataset()
file_meta.MediaStorageSOPClassUID = '1.2.840.10008.5.1.4.1.1.2'
file_meta.MediaStorageSOPInstanceUID = '1.2.3'
file_meta.ImplementationClassUID = '1.2.3.4'
ds = FileDataset(filename, {},
file_meta=file_meta,
preamble=b'\0' * 128)
ds.is_little_endian = True
ds.is_implicit_VR = False
ds.PatientName = 'Jonathan^Suever'
ds.SeriesDescription = 'Dicom Sort Test Series'
ds.SeriesNumber = 1
ds.update(values)
ds.save_as(filename)
return filename, ds
def dicom_from_image_layer(image_layer):
suffix = '.dcm'
filename_little_endian = tempfile.NamedTemporaryFile(suffix=suffix).name
filename_big_endian = tempfile.NamedTemporaryFile(suffix=suffix).name
file_meta = FileMetaDataset()
file_meta.MediaStorageSOPClassUID = '1.2.840.10008.5.1.4.1.1.2'
file_meta.MediaStorageSOPInstanceUID = "1.2.3"
file_meta.ImplementationClassUID = "1.2.3.4"
ds = FileDataset(filename_little_endian, {},
file_meta=file_meta,
preamble=b"\0" * 128)
ds.PatientName = "Test^Firstname"
ds.PatientID = "123456"
ds.PixelData = image_layer.data.tostring()
ds.is_little_endian = True
ds.is_implicit_VR = True
dt = datetime.datetime.now()
ds.ContentDate = dt.strftime('%Y%m%d')
timeStr = dt.strftime('%H%M%S.%f') # long format with micro seconds
ds.ContentTime = timeStr
return ds
import datetime
import pydicom
from pydicom.dataset import Dataset, FileDataset, FileMetaDataset
# Create some temporary filenames
suffix = '.dcm'
filename_little_endian = tempfile.NamedTemporaryFile(suffix=suffix).name
filename_big_endian = tempfile.NamedTemporaryFile(suffix=suffix).name
print("Setting file meta information...")
# Populate required values for file meta information
file_meta = FileMetaDataset()
file_meta.MediaStorageSOPClassUID = '1.2.840.10008.5.1.4.1.1.2'
file_meta.MediaStorageSOPInstanceUID = "1.2.3"
file_meta.ImplementationClassUID = "1.2.3.4"
print("Setting dataset values...")
# Create the FileDataset instance (initially no data elements, but file_meta
# supplied)
ds = FileDataset(filename_little_endian, {},
file_meta=file_meta, preamble=b"\0" * 128)
# Add the data elements -- not trying to set all required here. Check DICOM
# standard
ds.PatientName = "Test^Firstname"
ds.PatientID = "123456"
# Set the transfer syntax
ds.is_little_endian = True
ds.is_implicit_VR = True
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 anonymizeDicom(self, dcm, dict_study):
'''
Anonymize a dicom by pre-defined rules
dcm: loaded dicom file to anonymize
dict: additional information obtained outside the dicom, such as exam_id, series_id from directory
return an anonymized dicom by creating a new one
'''
# suffix = '.dcm'
# filename_little_endian = tempfile.NamedTemporaryFile(suffix=suffix).name
# print(dcm.file_meta)
file_meta = FileMetaDataset()
file_meta.MediaStorageSOPClassUID = '1.2.840.10008.5.1.4.1.1.2'
file_meta.MediaStorageSOPInstanceUID = "1.2.3"
file_meta.ImplementationClassUID = "1.2.3.4"
# anonyDcmObj = pydicom.dataset.Dataset()
anonyDcmObj = FileDataset([], {},
file_meta=file_meta,
preamble=b"\0" * 128)
# print(anonyDcmObj.file_meta)
# FileDataset(filename_little_endian, {},
# file_meta=file_meta, preamble=b"\0" * 128)
# copy pixel_array
arr = dcm.pixel_array
anonyDcmObj.PixelData = arr.tobytes()
# set the required fields
anonyDcmObj.preamble = dcm.preamble
anonyDcmObj.file_meta = file_meta #dcm.file_meta
anonyDcmObj.is_little_endian = dcm.is_little_endian
anonyDcmObj.is_implicit_VR = dcm.is_implicit_VR
# Test
#anonyDcmObj.file_meta.MediaStorageSOPClassUID = []
for sTag in self.tagsHandler:
vr = self.lookupTable["dictionary_vr"][sTag]
tag = self.str2tag(sTag)
if self.tagsHandler[sTag]["method"] == "keep":
if tag in dcm:
elem = dcm[tag]
anonyDcmObj.add(elem)
elif tag in dcm.file_meta:
elem = dcm.file_meta[tag]
# setattr(anonyDcmObj.file_meta, tag, elem)
anonyDcmObj.file_meta.add(elem)
# because file_meta has already been copied
pass
elif self.tagsHandler[sTag]["method"] == "const":
if tag in dcm or tag in dcm.file_meta:
if tag in dcm:
elem = dcm[tag]
elem.value = self.tagsHandler[sTag]["value"]
anonyDcmObj.add(elem)
else:
elem = dcm.file_meta[tag]
elem.value = self.tagsHandler[sTag]["value"]
# setattr(anonyDcmObj.file_meta, tag, elem.value)
anonyDcmObj.file_meta.add(elem)
# The tag belongs to file_meta
# anonyDcmObj.file_meta[tag].value = self.tagsHandler[sTag]["value"]
elif self.tagsHandler[sTag]["method"] == "lookup":
if tag in dcm:
tagName = self.lookupTable["Tag2Name"][str(tag).replace(
" ", "")]
elem = dcm[tag]
if tagName == 'PatientName':
tagVal = 'Lrm_' + str(
dcm[tag].value).split('_')[1] + '_assess'
else:
tagVal = str(dcm[tag].value)
elem.value = self.lookupTable[tagName][tagVal]
anonyDcmObj.add(elem)
elif self.tagsHandler[sTag]["method"] == "less_than":
if tag in dcm:
sVal = dcm[tag].value
iVal = int(self.extractDigits(sVal))
maxVal = int(self.tagsHandler[sTag]["value"])
if iVal > maxVal:
modifiedVal = maxVal
else:
modifiedVal = iVal
elem = dcm[tag]
elem.value = "{:03d}Y".format(modifiedVal)
anonyDcmObj.add(elem)
elif self.tagsHandler[sTag]["method"] == "random":
if tag in dcm or tag in dcm.file_meta:
if self.tagsHandler[sTag][
"tagID"] == "0020,000e": #SeriesInstanceUID
rand_str = '.'.join([
dict_study['rand_6_SeriesInstanceUID'],
dict_study['rand_5_SeriesInstanceUID'], '2.1.1',
dict_study['rand_tail_SeriesInstanceUID']
])
elif self.tagsHandler[sTag][
"tagID"] == "0008,0018": #SOPInstanceUID
rand_str = '.'.join([
dict_study['rand_6_SOPInstanceUID'],
dict_study['rand_5_SOPInstanceUID'], '2.1.3',
dict_study['rand_tail_SOPInstanceUID']
])
elif self.tagsHandler[sTag][
"tagID"] == "0020,000d": #StudyInstanceUID
rand_str = '.'.join([
dict_study['rand_6_StudyInstanceUID'],
dict_study['rand_5_StudyInstanceUID'], '2.1.1',
dict_study['rand_tail_StudyInstanceUID']
])
elif self.tagsHandler[sTag][
"tagID"] == "0002,0003": #MediaStorageSOPInstanceUID
rand_str = '.'.join([
dict_study['rand_6_MediaStorageSOPInstanceUID'],
dict_study['rand_5_MediaStorageSOPInstanceUID'],
'2.1.3',
dict_study['rand_tail_MediaStorageSOPInstanceUID']
])
if tag in dcm:
elem = dcm[tag]
elem.value = rand_str
anonyDcmObj.add(elem)
elif tag in dcm.file_meta:
elem = dcm.file_meta[tag]
elem.value = rand_str
anonyDcmObj.file_meta.add(elem)
else:
raise NameError('Unknown Method')
return anonyDcmObj
import pydicom
from pydicom.dataset import Dataset, FileDataset, FileMetaDataset
from PIL import Image
from PIL.TiffTags import TAGS
import numpy as np
import matplotlib.pyplot as plt
# Nomes do arquivo
filename_little_endian = 'testeDicom.dcm'
# Criando arquivos com informações minimas
print('Criando arquivo Dicom Image')
file_meta = FileMetaDataset()
file_meta.MediaStorageSOPClassUID = '1.2.840.10008.5.1.4.1.1.481.1' #http://dicom.nema.org/dicom/2013/output/chtml/part04/sect_I.4.html
file_meta.MediaStorageSOPInstanceUID = "1.2.246.352.81.3.273720375.51644.19651.179.0"
file_meta.ImplementationClassUID = "1.2.246.352.70.2.1.160.3"
#Criando um dataset "vazio"
ds = FileDataset(filename_little_endian, {},
file_meta=file_meta,
preamble=b"\0" * 128)
#Adicionando elementos
ds.PatientName = "Teste"
ds.PatientID = "123456789"
#Transfer Syntax
ds.file_meta.TransferSyntaxUID = pydicom.uid.ExplicitVRLittleEndian
ds.is_little_endian = True
ds.is_implicit_VR = 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)
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)
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
ds.SliceThickness = info.SliceThickness