def index_directory(self, rootp: PathLike):
D = DicomDirectory(root=rootp)
file_names = D.inventory()
# def check_bhashes(value):
# _value = value[:NUM_KEY_CHARS]
# return not (_value in self.bhashes) # True if its needed
for fn in file_names:
self.index_instance(D, fn)
#
# try:
# # May raise "InvalidDicomException" if not dicom
# # (or return None if ignore_errors flag is set)
# inst = D.get(fn, bhash_validator=check_bhashes)
# # Some instances are un-indexable
# if inst.dhash == None:
# print(f"No pixels found in {fn}")
# self.bhashes[self.t(inst, KTy.BHASH)] = inst.mhash
# continue
# self.put(inst)
# except FileExistsError:
# # print(f"Already indexed {fn}")
# continue
# except InvalidDicomException:
# print(f"Not a DICOM file {fn}")
# continue
# Safe to freeze after reading an entire dir
self.freeze()
def test_get():
D = DicomDirectory(root=rootp)
fn = "ibis1/01001_2.16.840.1.113669.632.21.1139687029.3025563835.31534914061935431.dcm"
d = D.get(fn)
assert d.tags["PatientID"] == "123456789"
fn = "ibis2/IM100"
d = D.get(fn)
assert d.tags[
"PatientID"] == "15.03.26-07:44:14-STD-1.3.12.2.1107.5.1.4.66502"
def test_status_and_exceptions():
with tempfile.TemporaryDirectory() as tmp:
D = DicomDirectory(root=tmp)
assert (D.status())
(pathlib.Path(tmp) / "test").touch()
with pytest.raises(InvalidDicomException):
D.get("test")
with pytest.raises(FileNotFoundError):
D.get("testtesttest")
assert D.get("test", ignore_errors=True) is None
assert D.get("testtesttest", ignore_errors=True) is None
assert not D.status()
def anonymize_and_upload(R: DicomRegistry, D: DicomDirectory, O: Orthanc):
for d in R.instances.values():
ser_mhash = Dixel.from_child(d).mhash
# Find the real ser
ser = R.get(ser_mhash, dlvl=DLv.SERIES)
stu_mhash = Dixel.from_child(d, DLv.STUDY).mhash
# Find the real stu
stu = R.get(stu_mhash, dlvl=DLv.STUDY)
m = orthanc_sham_map(
stu.mhash,
stu.dhash,
# Try patient id first, fall back to patient name, or use "UNKNOWN"
patient_id=stu.tags.get("PatientID",
stu.tags.get("PatientName", "UNKNOWN")),
stu_dt=stu.timestamp,
ser_mhash=ser.mhash,
ser_dhash=ser.dhash,
ser_dt=ser.timestamp,
inst_mhash=d.mhash,
inst_dhash=d.dhash,
inst_dt=d.timestamp)
dd = D.get(d.meta["fp"], binary=True)
r = O.put(dd) # If no Patient ID, need to use returned value
oid = r['ID']
print(f"Putting {dd.main_tags()} in {oid}")
O.anonymize(oid,
replacement_map=m) # Anon inst no longer returns image?
O.delete(oid, dlvl=DLv.INSTANCE)
def register_path(D: DicomDirectory,
H: HashRegistry,
O: Orthanc = None,
upload: bool = False):
print(f"Registering path {D.root}")
tic = time.time()
m, n, o = 0, 0, 0
for fn in D.inventory():
m += 1
if m % ANNOUNCEMENT_INTERVAL == 0:
print(f"Checked {m} files")
H.shelve()
dx = D.get(fn,
binary=True,
bhash_validator=lambda h: not H.exists(h),
ignore_errors=True)
if dx is not None:
if not H.exists(dx.mhash):
n += 1
if n % ANNOUNCEMENT_INTERVAL == 0:
print(f"Registered {n} files")
H.put(dx)
if upload and O is not None:
o += 1
if o % ANNOUNCEMENT_INTERVAL == 0:
print(f"Uploaded {o} files")
O.put(dx)
toc = time.time()
print(f"----------------------------")
print(f"Checked {m} files")
print(f"Registered new {n} instances")
print(f"Uploaded {o} instances")
print(f"Elapsed time: {toc-tic:.2f} ({max([n,1])/(toc-tic):.2f}dx/s)")
print(f"----------------------------")
H.shelve()
pprint(H.find(q={"dlvl": DLv.STUDY}))
def test_orthanc_upload():
O = Orthanc()
O.clear()
ROOTP = "~/data/dcm/ibis2"
D = DicomDirectory(ROOTP)
d = D.get("IM1", binary=True)
print(d.summary())
O.put(d)
g = O.get(d.oid(), dlvl=DLv.INSTANCE)
Dixel.comparator = CTy.METADATA
assert d == g
e = Dixel.from_child(d)
h = O.get(e.oid(), dlvl=DLv.SERIES)
assert e == h
f = Dixel.from_child(e)
i = O.get(f.oid(), dlvl=DLv.STUDY)
assert f == i
def index_instance(self, D: DicomDirectory, fn: str):
def check_bhashes(value):
_value = value[:NUM_KEY_CHARS]
return not (_value in self.bhashes) # True if its needed
try:
# May raise "InvalidDicomException" if not dicom
# (or return None if ignore_errors flag is set)
inst = D.get(fn, bhash_validator=check_bhashes)
# Some instances are un-indexable
if inst.dhash == None:
print(f"No pixels found in {fn}")
self.bhashes[self.t(inst, KTy.BHASH)] = inst.mhash
return
self.put(inst)
except FileExistsError:
# print(f"Already indexed {fn}")
pass
except InvalidDicomException:
print(f"Not a DICOM file {fn}")
return
def test_inventory():
D = DicomDirectory(root=rootp)
inv = D.inventory()
# Each has about 350+ studies
assert len(inv) > 700
print(f"Registered {n} files")
H.put(dx)
if upload and O is not None:
o += 1
if o % ANNOUNCEMENT_INTERVAL == 0:
print(f"Uploaded {o} files")
O.put(dx)
toc = time.time()
print(f"----------------------------")
print(f"Checked {m} files")
print(f"Registered new {n} instances")
print(f"Uploaded {o} instances")
print(f"Elapsed time: {toc-tic:.2f} ({max([n,1])/(toc-tic):.2f}dx/s)")
print(f"----------------------------")
H.shelve()
pprint(H.find(q={"dlvl": DLv.STUDY}))
if __name__ == "__main__":
D = DicomDirectory(root=ROOT_PATH)
H = HashRegistry(clear_cache=CLEAR_HASHES, cache_file=CACHE_FILE)
O = Orthanc(url=ORTHANC_URL)
if CLEAR_DICOM:
input("Are you sure that you want to clear the queue?")
O.clear()
register_path(D, H, O, upload=UPLOAD_DICOM)