def test_exists():
resources_dir = find_resource("resources/dcm")
D = DcmDir(path=resources_dir)
logging.debug(D)
assert (D.check())
assert (D.exists("IM2263"))
assert (not D.exists("abcd"))
D = DcmDir(path=resources_dir, subpath_width=3, subpath_depth=2)
assert (D.check())
assert (D.exists("IM2263"))
assert (not D.exists("abcd"))
logging.debug("Checking round-trip")
d = D.get("IM2263")
logging.debug(pformat(d.tags))
dd = d.json()
ee = json.loads(dd)
e = Serializable.Factory.create(**ee)
logging.debug(d)
logging.debug(e)
assert (d.tags == e.tags)
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)