def store(host, port, calling_ae_title, called_ae_title, filenames):
transfer_syntaxes = [
odil.registry.ExplicitVRLittleEndian,
odil.registry.ImplicitVRLittleEndian,
]
# Find all SOP classes to negotiate at association time. We don't need to
# read the whole data set for this
sop_classes = set()
for filename in filenames:
with odil.open(filename) as stream:
_, data_set = odil.Reader.read_file(
stream,
halt_condition=lambda tag: tag > odil.registry.SOPClassUID)
sop_classes.update(data_set.as_string("SOPClassUID"))
presentation_contexts = [
odil.AssociationParameters.PresentationContext(
2 * i + 1, sop_class, transfer_syntaxes,
odil.AssociationParameters.PresentationContext.Role.SCU)
for i, sop_class in enumerate(sop_classes)
]
# Create the association and the Store SCU
association = odil.Association()
association.set_peer_host(host)
association.set_peer_port(port)
association.update_parameters()\
.set_calling_ae_title(calling_ae_title)\
.set_called_ae_title(called_ae_title)\
.set_presentation_contexts(presentation_contexts)
association.associate()
negotiated_parameters = association.get_negotiated_parameters()
negotiated_pc = negotiated_parameters.get_presentation_contexts()
store = odil.StoreSCU(association)
for filename in filenames:
with odil.open(filename) as stream:
_, data_set = odil.Reader.read_file(stream)
try:
store.set_affected_sop_class(data_set)
store.store(data_set)
except Exception as e:
print("Could not store {}: {}".format(filename, e))
association.release()
def store(host, port, calling_ae_title, called_ae_title, filenames):
transfer_syntaxes = [
odil.registry.ExplicitVRLittleEndian,
odil.registry.ImplicitVRLittleEndian,
]
# Find all SOP classes to negotiate at association time. We don't need to
# read the whole data set for this
sop_classes = set()
for filename in filenames:
with odil.open(filename) as stream:
_, data_set = odil.Reader.read_file(
stream,
halt_condition=lambda tag: tag>odil.registry.SOPClassUID)
sop_classes.update(data_set.as_string("SOPClassUID"))
presentation_contexts = [
odil.AssociationParameters.PresentationContext(
2*i+1, sop_class, transfer_syntaxes, True, False)
for i, sop_class in enumerate(sop_classes)
]
# Create the association and the Store SCU
association = odil.Association()
association.set_peer_host(host)
association.set_peer_port(port)
association.update_parameters()\
.set_calling_ae_title(calling_ae_title)\
.set_called_ae_title(called_ae_title)\
.set_presentation_contexts(presentation_contexts)
association.associate()
negotiated_parameters = association.get_negotiated_parameters()
negotiated_pc = negotiated_parameters.get_presentation_contexts()
store = odil.StoreSCU(association)
for filename in filenames:
with odil.open(filename) as stream:
_, data_set = odil.Reader.read_file(stream)
try:
store.set_affected_sop_class(data_set)
store.store(data_set)
except Exception as e:
print("Could not store {}: {}".format(filename, e))
association.release()
def convert(input, output, transfer_syntax, item_length, use_group_length):
with odil.open(input) as stream:
header, data_set = odil.Reader.read_file(stream)
to_remove = [
"FileMetaInformationVersion",
"MediaStorageSOPClassUID", "MediaStorageSOPInstanceUID",
"TransferSyntaxUID",
"ImplementationClassUID", "ImplementationVersionName"
]
for name in to_remove:
header.remove(getattr(odil.registry, name))
odil.write(data_set, output, header, transfer_syntax, item_length, use_group_length)
def __call__(self, data_set):
if not os.path.isdir(self.root):
os.makedirs(self.root)
if self.iso_9660:
filename = "{:08d}.dcm".format(1 + len(os.listdir(self.root)))
else:
filename = data_set.as_string("SOPInstanceUID")[0].decode()
destination = os.path.join(self.root, filename)
with odil.open(destination, "wb") as fd:
odil.Writer.write_file(data_set, fd, odil.DataSet(),
self.transfer_syntax)
self.files.append(destination)
def convert(input, output, transfer_syntax, item_length, use_group_length):
with odil.open(input) as stream:
header, data_set = odil.Reader.read_file(stream)
to_remove = [
"FileMetaInformationVersion", "MediaStorageSOPClassUID",
"MediaStorageSOPInstanceUID", "TransferSyntaxUID",
"ImplementationClassUID", "ImplementationVersionName"
]
for name in to_remove:
header.remove(getattr(odil.registry, name))
odil.write(data_set, output, header, transfer_syntax, item_length,
use_group_length)
def print_(inputs, print_header, decode_uids):
for input in inputs:
logging.info("Printing {}".format(input))
with odil.open(input) as stream:
header, data_set = odil.Reader.read_file(stream)
max_length = find_max_name_length(data_set)
if print_header:
max_length = max(max_length, find_max_name_length(header))
if print_header:
print_data_set(header, decode_uids, "", max_length,
odil.Value.Strings())
print()
print_data_set(data_set, decode_uids, "", max_length,
odil.Value.Strings())
def print_(inputs, print_header, decode_uids):
for input in inputs:
logging.info("Printing {}".format(input))
with odil.open(input) as stream:
header, data_set = odil.Reader.read_file(stream)
max_length = find_max_name_length(data_set)
if print_header:
max_length = max(max_length, find_max_name_length(header))
if print_header:
print_data_set(
header, decode_uids, "", max_length, odil.Value.Strings())
print()
print_data_set(
data_set, decode_uids, "", max_length, odil.Value.Strings())
def test_open_context(self):
data = (128 * b"\x00" + b"DICM" + b"\x02\x00\x10\x00"
b"UI"
b"\x14\x00"
b"1.2.840.10008.1.2.1\x00"
b"\x10\x00\x10\x00"
b"PN"
b"\x08\x00"
b"Foo^Bar ")
fd, path = tempfile.mkstemp()
os.write(fd, data)
os.close(fd)
try:
with odil.open(path) as fd:
header, data_set = odil.Reader.read_file(fd)
finally:
os.remove(path)
def main():
parser = argparse.ArgumentParser(description="Print content of DICOM file")
parser.add_argument("file")
parser.add_argument("--header",
"-H",
action="store_true",
help="Print header")
parser.add_argument("--decode-uids",
"-D",
action="store_true",
help="Display UID names")
arguments = parser.parse_args()
with odil.open(arguments.file) as stream:
header, data_set = odil.Reader.read_file(stream)
if arguments.header:
print_data_set(header, arguments.decode_uids)
print
print_data_set(data_set, arguments.decode_uids)
def run_client(self):
command = [
"getscu", "-ll", "error", "-P", "-k", "QueryRetrieveLevel=PATIENT",
"-k", "PatientID=*", "-k", "PatientName", "+B", "localhost",
"11113"
]
retcode = subprocess.call(command)
if retcode != 0:
return []
files = sorted(glob.glob("{}*".format(odil.uid_prefix)))
data_sets = []
for file_ in files:
with odil.open(file_, "rb") as fd:
data_sets.append(odil.Reader.read_file(fd)[1])
for file_ in files:
os.remove(file_)
return data_sets
def run_client(self):
command = [
"findscu",
"-P", "-k", "QueryRetrieveLevel=PATIENT",
"-k", "PatientID=*", "-k", "PatientName",
"-q", "-X",
"localhost", "11113"]
retcode = subprocess.call(command)
if retcode != 0:
return []
files = sorted(glob.glob("rsp*"))
data_sets = []
for file_ in files:
with odil.open(file_, "rb") as fd:
data_sets.append(odil.Reader.read_file(fd)[1])
for file_ in files:
os.remove(file_)
return data_sets
def test_respondDICOM(self):
wado = odil.webservices.WADORSResponse()
wado.set_data_sets(self.data_sets)
wado.respond_dicom(odil.webservices.Utils.Representation.DICOM)
self.assertEqual(wado.get_type(), odil.webservices.Utils.Type.DICOM)
self.assertEqual(wado.get_representation(),
odil.webservices.Utils.Representation.DICOM)
http = wado.get_http_response()
msg = self._http_message_to_email_message(http)
self.assertTrue(msg.is_multipart())
i = 0
for part in msg.walk():
if part.get_content_type() == "application/dicom":
file = tempfile.mkstemp()
stream = io.FileIO(file[1], "wb")
stream.write(part.get_payload(decode=True))
stream.close()
with odil.open(file[1], "rb") as stream:
ds = odil.Reader.read_file(stream)[1]
self.assertEqual(self.data_sets[i], ds)
i = i + 1
self.assertEqual(i, len(self.data_sets))
def as_xml(input, output, pretty_print):
with odil.open(input) as stream:
_, data_set = odil.Reader.read_file(stream)
with open(output, "w") as fd:
xml = odil.as_xml(data_set, pretty_print)
fd.write(xml)
def as_binary(input, output, transfer_syntax):
with odil.open(input) as stream:
_, data_set = odil.Reader.read_file(stream)
with odil.open(output, "wb") as fd:
odil.Writer.write_file(data_set, fd, transfer_syntax=transfer_syntax)
def store(self, data_set):
specific_character_set = odil.Value.Strings()
if "SpecificCharacterSet" in data_set:
specific_character_set = data_set.as_string(
"SpecificCharacterSet")
as_unicode = lambda x: odil.as_unicode(x, specific_character_set)
if layout == "flat":
directory = ""
elif layout == "tree":
# Patient directory: <PatientName> or <PatientID>.
patient_directory = None
if "PatientName" in data_set and data_set.as_string(
"PatientName"):
patient_directory = data_set.as_string("PatientName")[0]
else:
patient_directory = data_set.as_string("PatientID")[0]
patient_directory = as_unicode(patient_directory)
# Study directory: <StudyID>_<StudyDescription>, both parts are
# optional. If both tags are missing or empty, default to a
# numeric index based on StudyInstanceUID.
study_directory = []
if "StudyID" in data_set and data_set.as_string("StudyID"):
study_directory.append(data_set.as_string("StudyID")[0])
if ("StudyDescription" in data_set
and data_set.as_string("StudyDescription")):
study_directory.append(
data_set.as_string("StudyDescription")[0])
if not study_directory:
study_instance_uid = data_set.as_string(
"StudyInstanceUID")[0]
study_directory.append(
self._study_ids.setdefault(study_instance_uid,
1 + len(self._study_ids)))
study_directory = "_".join(
as_unicode(x) for x in study_directory)
# Study directory: <SeriesNumber>_<SeriesDescription>, both
# parts are optional. If both tags are missing or empty, default
# to a numeric index based on SeriesInstanceUID.
series_directory = []
if "SeriesNumber" in data_set and data_set.as_int(
"SeriesNumber"):
series_directory.append(
str(data_set.as_int("SeriesNumber")[0]))
if ("SeriesDescription" in data_set
and data_set.as_string("SeriesDescription")):
series_directory.append(
data_set.as_string("SeriesDescription")[0])
if not series_directory:
series_instance_uid = data_set.as_string(
"series_instance_uid")[0]
series_directory.append(
self._series_ids.setdefault(series_instance_uid,
1 + len(self._series_ids)))
series_directory = "_".join(
as_unicode(x) for x in series_directory)
if iso_9660:
patient_directory = to_iso_9660(patient_directory)
study_directory = to_iso_9660(study_directory)
series_directory = to_iso_9660(series_directory)
directory = os.path.join(patient_directory, study_directory,
series_directory)
if not os.path.isdir(os.path.join(self.directory, directory)):
os.makedirs(os.path.join(self.directory, directory))
else:
raise NotImplementedError()
self.stored.setdefault(directory, 0)
if iso_9660:
filename = "IM{:06d}".format(1 + self.stored[directory])
else:
filename = as_unicode(data_set.as_string("SOPInstanceUID")[0])
with odil.open(os.path.join(self.directory, directory, filename),
"wb") as fd:
odil.Writer.write_file(data_set, fd)
self.stored[directory] += 1
self.files.append(os.path.join(directory, filename))
def as_xml(input, output, pretty_print):
with odil.open(input) as stream:
_, data_set = odil.Reader.read_file(stream)
with open(output, "w") as fd:
xml = odil.as_xml(data_set, pretty_print)
fd.write(xml)
def as_binary(input, output, transfer_syntax):
with odil.open(input) as stream:
_, data_set = odil.Reader.read_file(stream)
with odil.open(output, "wb") as fd:
odil.Writer.write_file(data_set, fd, transfer_syntax=transfer_syntax)
def store(self, data_set):
specific_character_set = odil.Value.Strings()
if "SpecificCharacterSet" in data_set:
specific_character_set = data_set.as_string(
"SpecificCharacterSet")
as_unicode = lambda x: odil.as_unicode(x, specific_character_set)
if layout == "flat":
directory = ""
elif layout == "tree":
# Patient directory: <PatientName> or <PatientID>.
patient_directory = None
if "PatientName" in data_set and data_set.as_string("PatientName"):
patient_directory = data_set.as_string("PatientName")[0]
else:
patient_directory = data_set.as_string("PatientID")[0]
patient_directory = as_unicode(patient_directory)
# Study directory: <StudyID>_<StudyDescription>, both parts are
# optional. If both tags are missing or empty, default to a
# numeric index based on StudyInstanceUID.
study_directory = []
if "StudyID" in data_set and data_set.as_string("StudyID"):
study_directory.append(data_set.as_string("StudyID")[0])
if ("StudyDescription" in data_set and
data_set.as_string("StudyDescription")):
study_directory.append(
data_set.as_string("StudyDescription")[0])
if not study_directory:
study_instance_uid = data_set.as_string("StudyInstanceUID")[0]
study_directory.append(
self._study_ids.setdefault(
study_instance_uid, 1+len(self._study_ids)))
study_directory = "_".join(as_unicode(x) for x in study_directory)
# Study directory: <SeriesNumber>_<SeriesDescription>, both
# parts are optional. If both tags are missing or empty, default
# to a numeric index based on SeriesInstanceUID.
series_directory = []
if "SeriesNumber" in data_set and data_set.as_int("SeriesNumber"):
series_directory.append(str(data_set.as_int("SeriesNumber")[0]))
if ("SeriesDescription" in data_set and
data_set.as_string("SeriesDescription")):
series_directory.append(
data_set.as_string("SeriesDescription")[0])
if not series_directory:
series_instance_uid = data_set.as_string("series_instance_uid")[0]
series_directory.append(
self._series_ids.setdefault(
series_instance_uid, 1+len(self._series_ids)))
series_directory = "_".join(as_unicode(x) for x in series_directory)
if iso_9660:
patient_directory = to_iso_9660(patient_directory)
study_directory = to_iso_9660(study_directory)
series_directory = to_iso_9660(series_directory)
directory = os.path.join(
patient_directory, study_directory, series_directory)
if not os.path.isdir(os.path.join(self.directory, directory)):
os.makedirs(os.path.join(self.directory, directory))
else:
raise NotImplementedError()
self.stored.setdefault(directory, 0)
if iso_9660:
filename = "IM{:06d}".format(1+self.stored[directory])
else:
filename = as_unicode(data_set.as_string("SOPInstanceUID")[0])
with odil.open(os.path.join(self.directory, directory, filename), "wb") as fd:
odil.Writer.write_file(data_set, fd)
self.stored[directory] += 1
self.files.append(os.path.join(directory, filename))