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 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 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)