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_orthanc_upload(setup_orthanc0):
logging.debug("Test Orthanc Upload")
O = Orthanc()
dicom_dir = find_resource("resources/dcm")
D = DcmDir(path=dicom_dir)
d = D.get("IM2263", view=DixelView.TAGS_FILE)
O.put(d)
q = {"PatientID": "AW15119516.678.1392297407"}
result = O.find(q)
if result:
id = result[0]
logging.debug(id)
result = O.exists(id)
logging.debug(result)
assert (result)
O.delete(d)
result = O.exists(id)
assert (not result)
def _handle_instance_in_dcm_dir(item: Dixel, orth: Orthanc, salt: str):
orth.put(item)
anon = ShamDixel.from_dixel(item, salt=salt)
afile = orth.anonymize(anon, replacement_map=anon.orthanc_sham_map())
anon.file = afile
orth.put(anon)
orth.delete(item)
anon_study_id = anon.sham_parent_oid(DCMLv.STUDIES)
logging.debug(anon_study_id)
logging.debug(tagged_studies)
if anon_study_id not in tagged_studies:
logging.debug("Tagging parent study: {}".format(anon_study_id))
siren_info = pack_siren_info(anon)
orth.gateway.put_metadata(anon_study_id, DCMLv.STUDIES, "siren_info",
siren_info)
tagged_studies.append(anon_study_id)
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)
