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 test_csv(tmp_path):
fp = tmp_path / "tmp.csv"
ep0 = CsvFile(fp=fp)
ep0.fieldnames = ["_Age", "PatientName", "AccessionNumber"]
for i in range(10):
tags = {
"PatientName": "Subject {}".format(i),
"AccessionNumber": "Study {}".format(i)
}
meta = {
"Age": 20+i
}
ep0.dixels.add(Dixel(tags=tags, meta=meta))
ep0.write()
ep1 = CsvFile(fp=fp)
ep1.read()
d = ep1.dixels.pop()
logging.debug(d)
assert( d.meta['Age']>="20" )
assert( d.tags['PatientName'].startswith("Subject"))
logging.debug(ep1.fieldnames)
ep2 = CsvFile(fp=fp)
ep2.fieldnames = ['_ShamID', '_ShamBirthDate', '_ShamAccessionNumber', 'PatientName', 'AccessionNumber']
ShamDixel.REFERENCE_DATE = date(year=2018, month=1, day=1)
for d in ep0.dixels:
logging.debug(d)
ep2.dixels.add( ShamDixel.from_dixel(d) )
ep2.write()
ep2.fieldnames = "ALL"
ep2.write()
os.remove(fp)
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 test_anon(setup_orthanc0):
O = Orthanc()
dicom_dir = find_resource("resources/dcm")
D = DcmDir(path=dicom_dir)
d = D.get("IM2263", view=DixelView.TAGS_FILE)
O.put(d)
d.tags["AccessionNumber"] = "123456"
d.tags["PatientBirthDate"] = "20000101"
d.tags["PatientID"] = "ABC"
d.tags["PatientName"] = "XYZ"
d.level = DicomLevel.STUDIES
e = ShamDixel.from_dixel(d)
rep = e.orthanc_sham_map()
O.anonymize("959e4e9f-e954be4e-11917c87-09d0f98f-7cc39128",
level=DicomLevel.STUDIES,
replacement_map=rep)
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)
def test_dt_shams_at_levels():
tags = {
"PatientName": "FOOABC^BAR^Z",
"PatientBirthDate": "20000101",
"StudyDate": "20180102",
"StudyTime": "120001",
"AccessionNumber": "12345678"
}
expected_meta = {
'ShamAccessionNumber': '25d55ad283aa400af464c76d713c07ad',
'ShamBirthDate': '19991009',
'ShamID': 'NTE3OTYH32XNES3LPNKR2U6CVOCZXDIL',
'ShamName': 'NADERMAN^TRACY^E',
'StudyDateTime': datetime.datetime(2018, 1, 2, 12, 0, 1),
'ShamStudyDateTime': datetime.datetime(2017, 10, 10, 12, 15, 3)
}
d = ShamDixel(tags=tags, level=DicomLevel.STUDIES)
logging.debug(pformat(d.meta))
assert (expected_meta.items() <= d.meta.items())
# check for imputing missing series dt tags
d = ShamDixel(tags=tags, level=DicomLevel.SERIES)
logging.debug(pformat(d.meta))
assert d.meta["ShamStudyDateTime"] == d.meta["ShamSeriesDateTime"]
# check for imputing missing instance dt tags
d = ShamDixel(tags=tags, level=DicomLevel.INSTANCES)
logging.debug(pformat(d.meta))
assert d.meta["ShamInstanceCreationDateTime"] == d.meta[
"ShamSeriesDateTime"] == d.meta["ShamStudyDateTime"]
tags.update({"SeriesDate": "20180102", "SeriesTime": "120101"})
expected_meta.update({
'SeriesDateTime':
datetime.datetime(2018, 1, 2, 12, 1, 1),
'ShamSeriesDateTime':
datetime.datetime(2017, 10, 10, 12, 16, 3)
})
d = ShamDixel(tags=tags, level=DicomLevel.SERIES)
logging.debug(pformat(d.meta))
assert (expected_meta.items() <= d.meta.items())
tags.update({
"InstanceCreationDate": "20180102",
"InstanceCreationTime": "120101"
})
expected_meta.update({
'InstanceCreationDateTime':
datetime.datetime(2018, 1, 2, 12, 1, 1),
'ShamInstanceCreationDateTime':
datetime.datetime(2017, 10, 10, 12, 16, 3)
})
d = ShamDixel(tags=tags, level=DicomLevel.INSTANCES)
logging.debug(pformat(d.meta))
assert (expected_meta.items() <= d.meta.items())
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)