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 make_key(self, ids, source: Orthanc, domain: str) -> set:
print("Making key")
# Minimal data for oid and sham plus study and series desc
def mkq(accession_num):
return {
"PatientName": "",
"PatientID": "",
"PatientBirthDate": "",
"PatientSex": "",
"AccessionNumber": accession_num,
"StudyDescription": "",
"StudyInstanceUID": "",
"StudyDate": "",
"StudyTime": "",
}
items = set()
for id in ids:
q = mkq(id)
try:
r = source.rfind(q, domain, level=DicomLevel.STUDIES)
except:
r = None
if not r:
print("Failed to collect an id")
continue
tags = {
"PatientName": r[0]["PatientName"],
"PatientID": r[0]["PatientID"],
"PatientBirthDate": r[0]["PatientBirthDate"],
"PatientSex": r[0]["PatientSex"],
"AccessionNumber": r[0]["AccessionNumber"],
"StudyDescription": r[0]["StudyDescription"],
"StudyInstanceUID": r[0]["StudyInstanceUID"],
"StudyDate": r[0]["StudyDate"],
"StudyTime": r[0]["StudyTime"]
}
d = Dixel(tags=tags)
e = ShamDixel.from_dixel(d)
items.add(e)
print("Found {} items".format(len(items)))
logging.debug(e)
return items
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)
