def pull_and_send(self,
items: Iterable,
source: Orthanc,
domain: str,
dest: Orthanc,
anonymize=False):
def mkq(d: Dixel):
return {"StudyInstanceUID": d.tags["StudyInstanceUID"]}
for d in items:
sham_oid = ShamDixel.sham_oid(d)
logging.debug(sham_oid)
if dest.exists(sham_oid):
logging.debug("SKIPPING {}".format(d.tags["PatientName"]))
continue
if not source.exists(d):
source.rfind(mkq(d),
domain,
level=DicomLevel.STUDIES,
retrieve=True)
else:
logging.debug("SKIPPING PULL for {}".format(
d.tags["PatientName"]))
replacement_map = ShamDixel.orthanc_sham_map(d)
anon_id = source.anonymize(d, replacement_map=replacement_map)
source.psend(anon_id, dest)
source.delete(anon_id)
source.delete(d)
def test_shams():
tags = {
"PatientName": "FOOABC^BAR^Z",
"PatientBirthDate": "20000101",
"StudyDate": "20180102",
"StudyTime": "120001",
"AccessionNumber": "12345678"
}
expected_meta = {
'ShamID': 'NTE3OTYH32XNES3LPNKR2U6CVOCZXDIL',
'ShamName': 'NADERMAN^TRACY^E',
'ShamBirthDate': "19991009",
'ShamStudyDateTime': datetime.datetime(2017, 10, 10, 12, 15, 3)
}
d = ShamDixel(tags=tags)
logging.debug(d)
assert (expected_meta.items() <= d.meta.items())
assert (d.meta["ShamName"] == "NADERMAN^TRACY^E")
assert (d.ShamStudyDate() == "20171010")
assert (
d.meta["ShamAccessionNumber"] == "25d55ad283aa400af464c76d713c07ad")
logging.debug(d.orthanc_sham_map())
expected_replacement_map = \
{'Replace': {'PatientName': 'NADERMAN^TRACY^E', 'PatientID': 'NTE3OTYH32XNES3LPNKR2U6CVOCZXDIL',
'PatientBirthDate': '19991009', 'AccessionNumber': '25d55ad283aa400af464c76d713c07ad',
'StudyInstanceUID': '1.2.826.0.1.3680043.10.43.62.716180617702.336145899646',
'StudyDate': '20171010', 'StudyTime': '121503'}, 'Keep': ['PatientSex', 'StudyDescription'],
'Force': True}
assert (d.orthanc_sham_map() == expected_replacement_map)
c = Dixel(tags=tags)
e = ShamDixel.from_dixel(c)
assert (d.meta["ShamName"] == e.meta["ShamName"])
f = ShamDixel.from_dixel(c, salt="FOO")
logging.debug(f.meta["ShamName"])
assert (d.meta["ShamName"] != f.meta["ShamName"])
def pull_and_save(self,
items: Iterable,
source: Orthanc,
domain: str,
dest: DcmDir,
anonymize=False):
def mkq(d: Dixel):
return {"StudyInstanceUID": d.tags["StudyInstanceUID"]}
for d in items:
working_level = DicomLevel.STUDIES
if anonymize:
if working_level == DicomLevel.SERIES:
d_fn = "{}-{}.zip".format(
d.meta["ShamAccessionNumber"][0:6],
d.meta["ShamSeriesDescription"])
else:
d_fn = "{}.zip".format(d.meta["ShamAccessionNumber"][0:16])
else:
if working_level == DicomLevel.SERIES:
d_fn = "{}-{}-{}.zip".format(
d.tags["PatientName"][0:6],
d.tags["AccessionNumber"][0:8],
d.tags["SeriesDescription"])
else:
d_fn = "{}-{}.zip".format(d.tags["PatientName"][0:6],
d.tags["AccessionNumber"][0:8])
if dest.exists(d_fn):
logging.debug("SKIPPING {}".format(d.tags["PatientName"]))
continue
if not source.exists(d):
source.rfind(mkq(d),
domain,
level=working_level,
retrieve=True)
else:
logging.debug("SKIPPING PULL for {}".format(
d.tags["PatientName"]))
if anonymize:
try:
replacement_map = ShamDixel.orthanc_sham_map(d)
anon_id = source.anonymize(d,
replacement_map=replacement_map)
e = source.get(anon_id,
level=working_level,
view=DixelView.FILE)
e.meta["FileName"] = d_fn
logging.debug(e)
dest.put(e)
source.delete(e)
except (HTTPError, GatewayConnectionError) as e:
logging.error("Failed to anonymize dixel")
logging.error(e)
with open("errors.txt", "a+") as f:
f.write(d.tags["AccessionNumber"] + "\n")
else:
d = source.get(d, level=working_level, view=DixelView.FILE)
dest.put(d)
try:
source.delete(d)
except GatewayConnectionError as e:
logging.error("Failed to delete dixel")
logging.error(e)
import logging
from diana.dixel import ShamDixel
from diana.apis import get_service
services_path = "my_services.yml"
oid = "802d6dcb-baf06419-375e594c-yyyyyyyy-xxxxxxxx"
logging.basicConfig(level=logging.DEBUG)
source = get_service(services_path, "internal", True)
dest = get_service(services_path, "external", True)
# q = {
# "PatientName": patient_name
# }
#
# result = source.find(q)
# for oid in result:
d = source.get(oid)
dd = ShamDixel.from_dixel(d)
map = ShamDixel.orthanc_sham_map(dd)
e = source.anonymize(d, replacement_map=map)
source.psend(e, dest)
source.delete(e)