def test_create_alyx_probe_insertions(self):
# Connect to test DB
one = ONE(username='******',
password='******',
base_url='https://test.alyx.internationalbrainlab.org')
# Use existing session on test database
eid = 'b1c968ad-4874-468d-b2e4-5ffa9b9964e9'
# Force probe insertion 3A
misc.create_alyx_probe_insertions(eid,
one=one,
model='3A',
labels=['probe00', 'probe01'])
# Verify it's been inserted
alyx_insertion = one.alyx.rest('insertions', 'list', session=eid)
self.assertTrue(alyx_insertion[0]['model'] == '3A')
self.assertTrue(alyx_insertion[0]['name'] in ['probe00', 'probe01'])
self.assertTrue(alyx_insertion[1]['model'] == '3A')
self.assertTrue(alyx_insertion[1]['name'] in ['probe00', 'probe01'])
# Cleanup DB
one.alyx.rest('insertions', 'delete', id=alyx_insertion[0]['id'])
one.alyx.rest('insertions', 'delete', id=alyx_insertion[1]['id'])
# Force probe insertion 3B
misc.create_alyx_probe_insertions(eid,
one=one,
model='3B2',
labels=['probe00', 'probe01'])
# Verify it's been inserted
alyx_insertion = one.alyx.rest('insertions', 'list', session=eid)
self.assertTrue(alyx_insertion[0]['model'] == '3B2')
self.assertTrue(alyx_insertion[0]['name'] in ['probe00', 'probe01'])
self.assertTrue(alyx_insertion[1]['model'] == '3B2')
self.assertTrue(alyx_insertion[1]['name'] in ['probe00', 'probe01'])
# Cleanup DB
one.alyx.rest('insertions', 'delete', id=alyx_insertion[0]['id'])
one.alyx.rest('insertions', 'delete', id=alyx_insertion[1]['id'])
def test_create_alyx_probe_insertions(self):
# Connect to test DB
one = ONE(
username="******",
password="******",
base_url="https://test.alyx.internationalbrainlab.org",
)
# Use existing session on test database
eid = "b1c968ad-4874-468d-b2e4-5ffa9b9964e9"
# Force probe insertion 3A
misc.create_alyx_probe_insertions(
eid, one=one, model="3A", labels=["probe00", "probe01"], force=True
)
# Verify it's been inserted
alyx_insertion = one.alyx.rest("insertions", "list", session=eid)
self.assertTrue(alyx_insertion[0]["model"] == "3A")
self.assertTrue(alyx_insertion[0]["name"] in ["probe00", "probe01"])
self.assertTrue(alyx_insertion[1]["model"] == "3A")
self.assertTrue(alyx_insertion[1]["name"] in ["probe00", "probe01"])
# Cleanup DB
one.alyx.rest("insertions", "delete", id=alyx_insertion[0]["id"])
one.alyx.rest("insertions", "delete", id=alyx_insertion[1]["id"])
# Force probe insertion 3B
misc.create_alyx_probe_insertions(eid, one=one, model="3B2", labels=["probe00", "probe01"])
# Verify it's been inserted
alyx_insertion = one.alyx.rest("insertions", "list", session=eid)
self.assertTrue(alyx_insertion[0]["model"] == "3B2")
self.assertTrue(alyx_insertion[0]["name"] in ["probe00", "probe01"])
self.assertTrue(alyx_insertion[1]["model"] == "3B2")
self.assertTrue(alyx_insertion[1]["name"] in ["probe00", "probe01"])
# Cleanup DB
one.alyx.rest("insertions", "delete", id=alyx_insertion[0]["id"])
one.alyx.rest("insertions", "delete", id=alyx_insertion[1]["id"])
def setUpClass(cls) -> None:
probe = ['probe00', 'probe01']
create_alyx_probe_insertions(session_path=EPHYS_SESSION,
model='3B2',
labels=probe,
one=one,
force=True)
cls.probe_id = one.alyx.rest('insertions',
'list',
session=EPHYS_SESSION,
name='probe00')[0]['id']
cls.probe_id2 = one.alyx.rest('insertions',
'list',
session=EPHYS_SESSION,
name='probe01')[0]['id']
data = np.load(Path(
Path(__file__).parent.joinpath('fixtures',
'data_alignmentqc_gui.npz')),
allow_pickle=True)
cls.xyz_picks = data['xyz_picks']
cls.alignments = data['alignments'].tolist()
cls.cluster_chns = data['cluster_chns']
register_track(cls.probe_id,
picks=cls.xyz_picks,
one=one,
overwrite=True,
channels=False)
register_track(cls.probe_id2,
picks=cls.xyz_picks,
one=one,
overwrite=True,
channels=False)
def test_creation(self):
probe = ['probe00', 'probe01']
create_alyx_probe_insertions(session_path=EPHYS_SESSION, model='3B2', labels=probe,
one=one, force=True)
insertion = one.alyx.rest('insertions', 'list', session=EPHYS_SESSION)
assert(len(insertion) == 2)
assert (insertion[0]['json']['qc'] == 'NOT_SET')
assert (len(insertion[0]['json']['extended_qc']) == 0)
one.alyx.rest('insertions', 'delete', id=insertion[0]['id'])
one.alyx.rest('insertions', 'delete', id=insertion[1]['id'])
def setUpClass(cls) -> None:
probe = ['probe00', 'probe01']
create_alyx_probe_insertions(session_path=EPHYS_SESSION, model='3B2', labels=probe,
one=one, force=True)
cls.probe00_id = one.alyx.rest('insertions', 'list', session=EPHYS_SESSION,
name='probe00')[0]['id']
cls.probe01_id = one.alyx.rest('insertions', 'list', session=EPHYS_SESSION,
name='probe01')[0]['id']
data = np.load(Path(Path(__file__).parent.parent.
joinpath('fixtures', 'qc', 'data_alignmentqc_existing.npz')),
allow_pickle=True)
cls.xyz_picks = np.array(data['xyz_picks']) / 1e6
def test_create_alyx_probe_insertions(self):
# Connect to test DB
one = ONE(**TEST_DB)
# Use existing session on test database
eid = "b1c968ad-4874-468d-b2e4-5ffa9b9964e9"
# Force probe insertion 3A
misc.create_alyx_probe_insertions(eid,
one=one,
model="3A",
labels=["probe00", "probe01"],
force=True)
# Verify it's been inserted
alyx_insertion = one.alyx.rest("insertions",
"list",
session=eid,
no_cache=True)
alyx_insertion = [x for x in alyx_insertion if x["model"] == "3A"]
self.assertTrue(alyx_insertion[0]["model"] == "3A")
self.assertTrue(alyx_insertion[0]["name"] in ["probe00", "probe01"])
self.assertTrue(alyx_insertion[1]["model"] == "3A")
self.assertTrue(alyx_insertion[1]["name"] in ["probe00", "probe01"])
# Cleanup DB
one.alyx.rest("insertions", "delete", id=alyx_insertion[0]["id"])
one.alyx.rest("insertions", "delete", id=alyx_insertion[1]["id"])
# Force probe insertion 3B
misc.create_alyx_probe_insertions(eid,
one=one,
model="3B2",
labels=["probe00", "probe01"])
# Verify it's been inserted
alyx_insertion = one.alyx.rest("insertions",
"list",
session=eid,
no_cache=True)
self.assertTrue(alyx_insertion[0]["model"] == "3B2")
self.assertTrue(alyx_insertion[0]["name"] in ["probe00", "probe01"])
self.assertTrue(alyx_insertion[1]["model"] == "3B2")
self.assertTrue(alyx_insertion[1]["name"] in ["probe00", "probe01"])
# Cleanup DB
one.alyx.rest("insertions", "delete", id=alyx_insertion[0]["id"])
one.alyx.rest("insertions", "delete", id=alyx_insertion[1]["id"])
def setUpClass(cls) -> None:
probe = [
''.join(random.choices(string.ascii_letters, k=5)),
''.join(random.choices(string.ascii_letters, k=5))
]
ins = create_alyx_probe_insertions(session_path=EPHYS_SESSION,
model='3B2',
labels=probe,
one=one,
force=True)
cls.probe00_id, cls.probe01_id = (x['id'] for x in ins)
data = np.load(Path(
Path(__file__).parent.parent.joinpath(
'fixtures', 'qc', 'data_alignmentqc_existing.npz')),
allow_pickle=True)
cls.xyz_picks = np.array(data['xyz_picks']) / 1e6
