def test_view_classifier():
# These weights classify as AP (pos) or Lateral (neg)
fp = find_resource("resources/models/pose/view_classifier.h5")
_model = get_mobilenet(0, weights=None)
_model.load_weights(fp)
fp = find_resource("resources/scouts")
D = DcmDir(path=fp)
# This one is lateral
d = D.get("ct_scout_01.dcm", view=DixelView.PIXELS)
prediction = d.get_prediction(_model)
logging.debug("Prediction is {}".format(prediction))
assert (prediction < 0.5)
# prediction = get_prediction( model, image )
# positive = "AP"
# negative = "Lateral"
# if prediction >= 0.5:
# logging.debug("Predicted: {} ({})".format( positive, round(prediction, 2) ))
# else:
# logging.debug("Predicted: {} ({})".format( negative, round(1.0-prediction, 2) ))
# This one is an AP
d = D.get("ct_scout_02.dcm", view=DixelView.PIXELS)
prediction = d.get_prediction(_model)
logging.debug("Prediction is {}".format(prediction))
assert (prediction >= 0.5)
def test_reader():
dcm_file = find_resource("resources/dcm/IM2263")
json_file = find_resource("resources/reports/screening_rpt_anon.txt")
DcmFileHandler().get(dcm_file)
with pytest.raises(DicomFormatError):
DcmFileHandler().get(json_file)
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 test_orthanc_upload(setup_orthanc0):
logging.debug("Test Orthanc Upload")
O = Orthanc()
dicom_dir = find_resource("resources/dcm")
D = DcmDir(path=dicom_dir)
d = D.get("IM2263", view=DixelView.TAGS_FILE)
O.put(d)
q = {"PatientID": "AW15119516.678.1392297407"}
result = O.find(q)
if result:
id = result[0]
logging.debug(id)
result = O.exists(id)
logging.debug(result)
assert (result)
O.delete(d)
result = O.exists(id)
assert (not result)
def test_ba_estimator():
# These weights classify as AP (pos) or Lateral (neg)
model_path = find_resource("resources/models/bone_age")
image_path = "/Users/derek/Data/DICOM/bone_age"
predict_ba(dicom_folder=image_path, models_folder=model_path)
def test_zip_reader():
p = find_resource("resources")
D = DcmDir(path=p)
f = D.get("dcm/IM2263", view=DixelView.TAGS_FILE)
gs = D.get_zipped("dcm_zip/test.zip")
for _g in gs:
if "2263" in _g.meta["FileName"]:
g = _g
break
logging.debug(f)
logging.debug(g)
assert(f.tags["StudyInstanceUID"] == g.tags["StudyInstanceUID"])
from binascii import hexlify
logging.debug("f file:")
logging.debug( hexlify(f.file[1024:2048]) )
logging.debug("g file:")
logging.debug( hexlify(g.file[1024:2048]) )
assert f.file == g.file
def test_psend(setup_orthanc0, setup_orthanc1):
O = Orthanc(peername="peer0")
print(O)
O.check()
O2 = Orthanc(port=8043, peername="peer0")
print(O2)
O2.check()
dicom_dir = find_resource("resources/dcm")
D = DcmDir(path=dicom_dir)
d = D.get("IM2263", view=DixelView.TAGS_FILE)
O2.put(d)
logging.debug(O2.gateway._get("peers"))
O2.psend(d.oid(), O)
e = O.get(d.oid(), level=DicomLevel.INSTANCES)
logging.debug(e)
assert d.oid() == e.oid()
def orth_test_runner():
O = Orthanc()
dicom_dir = find_resource("resources/dcm")
D = DcmDir(path=dicom_dir)
print("Starting script")
time.sleep(1)
d = D.get("IM2263", view=DixelView.FILE)
O.put(d)
O.check()
print("Ending script")
def test_cfg_handler():
cfg_file = find_resource("resources/config/td_bridge.cfg.jdf")
with open(cfg_file) as f:
source = f.read()
data = SimpleConfigParser().loads(source)
logging.debug(pformat(data))
out = SimpleConfigParser().dumps(data)
assert out.strip() in source
def test_mock_svcs():
C.start_swarm()
C.clean_swarm()
c = C.api_client()
admin_stack = find_resource("platform/docker-stacks/admin/admin-stack.yml")
cmd = ["docker", "stack", "deploy", "-c", admin_stack, "admin"]
subprocess.run(cmd)
service_names = [x['Spec']['Name'] for x in c.services()]
assert ("admin_portainer" in service_names)
assert ("admin_traefik" in service_names)
mock_stack = find_resource(
"platform/docker-stacks/diana-workers/mock-stack.yml")
cmd = ["docker", "stack", "deploy", "-c", mock_stack, "mock"]
# Don't forget to set the password, or docker-compose will
# interpret it as empty rather than default
os.environ["ORTHANC_PASSWORD"] = "******"
subprocess.run(cmd)
service_names = [x['Spec']['Name'] for x in c.services()]
assert ("mock_diana-mock" in service_names)
assert ("mock_orthanc-mock" in service_names)
# Pause to generate some data
time.sleep(20)
O = Orthanc(path="orthanc-mock", port=80)
info = O.gateway._get("statistics")
# At least 100 new images in the PACS
assert (info['CountInstances'] > 100)
C.clean_swarm()
def test_cli_svc_check(setup_orthanc0, setup_redis):
runner = CliRunner()
services_file = find_resource("resources/test_services.yml")
result = runner.invoke(app, [
"-s", "{redis_bad2: {ctype: Redis, port: 9999}}", "-S", services_file,
"check"
])
print(result.output)
assert ("orthanc: Ready" in result.output)
assert ("orthanc_bad: Not Ready" in result.output)
assert ("redis: Ready" in result.output)
assert ("redis_bad: Not Ready" in result.output)
assert ("redis_bad2: Not Ready" in result.output)
def test_simplify():
dir = find_resource("resources/dose")
items = ["dose_tags_anon"]
for item in items:
fn = "{}.json".format(item)
fp = os.path.join(dir, fn)
with open(fp) as f:
tags = json.load(f)
tags = dicom_simplify(tags)
# Have to compare in dumped space b/c loader doesn't convert times back into times
tag_str = json.dumps(tags,
indent=3,
cls=SmartJSONEncoder,
sort_keys=True)
# logging.debug(pformat(tag_str))
fn = "{}.simple.json".format(item)
fp = os.path.join(dir, fn)
# with open(fp, 'w') as f:
# f.write(tag_str)
with open(fp) as f:
simple_str = f.read()
# logging.debug(tag_str)
# logging.debug(simple_str)
# a = tag_str
# b = simple_str
# for i, s in enumerate(difflib.ndiff(a, b)):
# if s[0] == ' ':
# continue
# elif s[0] == '-':
# print(u'Delete "{}" from position {}'.format(s[-1], i))
# elif s[0] == '+':
# print(u'Add "{}" to position {}'.format(s[-1], i))
assert tag_str == simple_str
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_measurement():
path = find_resource("resources/scouts")
D = DcmDir(path=path)
fn_s1 = "ct_scout_01.dcm"
d_s1 = D.get(fn_s1, view=DixelView.PIXELS)
ret = d_s1.measure_scout()
logging.debug(ret)
assert (ret[0] == 'AP' and round(ret[1]) == 28)
fn_s2 = "ct_scout_02.dcm"
d_s2 = D.get(fn_s2, view=DixelView.PIXELS)
ret = d_s2.measure_scout()
logging.debug(ret)
assert (ret[0] == 'LATERAL' and round(ret[1]) == 43)
def test_mock_dixel():
reset_mock_seed()
d = MockStudy(study_datetime=ref_dt)
inst = list(d.instances())[-1]
# Check reproducibility
reset_mock_seed()
e = MockStudy(study_datetime=ref_dt)
assert (inst.tags == list(e.instances())[-1].tags)
# Check correctness
logging.debug(inst.tags)
assert (inst.tags == ref_inst_tags)
logging.debug(len(list(d.instances())))
assert (len(list(d.instances())) == ref_n_instances)
for item in d.instances():
logging.debug("{!s}".format(item))
# Check file creation
inst.gen_file()
inst_dcm = find_resource("resources/mock/inst.dcm")
# Reset mock/inst.dcm with fresh data
with open(inst_dcm, "wb") as f:
f.write(inst.file)
with open(inst_dcm, "rb") as f:
data = f.read()
assert (inst.file == data)
# Test file legibility
ds = pydicom.dcmread(BytesIO(inst.file))
logging.debug(ds)
assert (ds.AccessionNumber == d.tags["AccessionNumber"])
# Test new item is unique
f = MockStudy(study_datetime=ref_dt)
for item in f.instances():
logging.debug("{!s}".format(item))
assert (d.tags["AccessionNumber"] != f.tags["AccessionNumber"])
def test_unzip(tmp_path):
resources_dir = find_resource("resources/dcm_zip")
fp = resources_dir / "test.zip"
E = ImageDir(path=tmp_path, anonymizing=True)
with open(fp, 'rb') as f:
E.put_zipped(f)
fn = "6ee6f414e4c779c8bb1f90baf45c000c-0004-0002.png"
fp = Path( tmp_path / fn )
assert( fp.is_file() )
os.remove(fp)
fn = "78496388f522585b71b90f374051f552-0016-0001.png"
fp = Path( tmp_path / fn )
assert( fp.is_file() )
os.remove(fp)
def test_reader():
path = find_resource("resources/reports")
with open(os.path.join(path, "screening_rpt_anon.txt"), "r") as f:
text = f.readlines()
r = LungScreeningReport(text=text)
logging.debug(r)
logging.debug(r.current_smoker())
logging.debug(r.lungrads())
logging.debug(r.radcat())
logging.debug(r.years_since_quit())
assert (r.current_smoker() == True)
assert (r.lungrads() == "2S")
assert (r.radcat() == ('3', True))
def test_subdirs():
D = DcmDir(recurse_style="ORTHANC")
# for fp in D.recurse():
# logging.debug(fp)
subdirs = list(D.subdirs())
assert (len(subdirs) == 256 * 256)
assert ("./ff/ff" in subdirs)
assert ("./00/00" in subdirs)
p = find_resource("resources")
D = DcmDir(path=p)
subdirs = list(D.subdirs())
logging.debug(subdirs)
assert (len(subdirs) >= 8)
def test_montage():
services_file = find_resource(".secrets/lifespan_services.yml")
with open(services_file) as f:
services = yaml.load(f)
kwargs = services['montage']
del kwargs['ctype']
source = Montage(**services['montage'])
assert (source.check())
qdict = {
"q": "cta",
"modality": 4,
"exam_type": [8683, 7713, 8766],
"start_date": "2016-11-17",
"end_date": "2016-11-19"
}
worklist = source.find(qdict)
assert (len(worklist) == 20)
def test_conversion(tmp_path):
resources_dir = find_resource("resources/dcm")
D = DcmDir(path=resources_dir)
logging.debug(D)
d = D.get("IM2263", view=DixelView.PIXELS)
E = ImageDir(path=tmp_path)
E.put(d)
fn = "1.2.840.113619.2.181.90581140298.2577.1392297407726.4-0004-0002.png"
fp = Path( tmp_path / fn )
assert( fp.is_file() )
os.remove(fp)
F = ImageDir(path=tmp_path, anonymizing=True)
F.put(d)
fn = "6ee6f414e4c779c8bb1f90baf45c000c-0004-0002.png"
fp = Path( tmp_path / fn )
assert( fp.is_file() )
os.remove(fp)
def mk_diana_rest():
service_path = find_resource("resources/test_services.yml")
app.app.load_services(service_path)
client = app.app.test_client()
return client
