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randomise session for histology #687

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merged 2 commits into from
Dec 13, 2023
Merged

randomise session for histology #687

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9fbc0f2
randomise session for histology
mayofaulkner Dec 13, 2023
8454d8d
randomise all seeds
mayofaulkner Dec 13, 2023
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29 changes: 22 additions & 7 deletions ibllib/tests/qc/test_alignment_qc.py
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Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,6 @@
from ibllib.pipes.histology import register_track, register_chronic_track
from one.registration import RegistrationClient


EPHYS_SESSION = 'b1c968ad-4874-468d-b2e4-5ffa9b9964e9'
one = ONE(**TEST_DB)
brain_atlas = AllenAtlas(25)
Expand All @@ -35,9 +34,15 @@ class TestTracingQc(unittest.TestCase):

@classmethod
def setUpClass(cls) -> None:
rng = np.random.default_rng()
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,
date = str(datetime.date(2019, rng.integers(1, 12), rng.integers(1, 28)))
_, eid = RegistrationClient(one).create_new_session('ZM_1150', date=date)
cls.eid = str(eid)
# Currently the task protocol of a session must contain 'ephys' in order to create an insertion!
one.alyx.rest('sessions', 'partial_update', id=cls.eid, data={'task_protocol': 'ephys'})
ins = create_alyx_probe_insertions(session_path=cls.eid, 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.
Expand All @@ -64,21 +69,28 @@ def test_tracing_not_exists(self):
def tearDownClass(cls) -> None:
one.alyx.rest('insertions', 'delete', id=cls.probe01_id)
one.alyx.rest('insertions', 'delete', id=cls.probe00_id)
one.alyx.rest('sessions', 'delete', id=cls.eid)


class TestChronicTracingQC(unittest.TestCase):
@classmethod
def setUpClass(cls) -> None:
rng = np.random.default_rng()
probe = ''.join(random.choices(string.ascii_letters, k=5))
serial = ''.join(random.choices(string.ascii_letters, k=10))

# Make a chronic insertions
ref = one.eid2ref(EPHYS_SESSION)
insdict = {"subject": ref['subject'], "name": probe, "model": '3B2', "serial": serial}
date = str(datetime.date(2019, rng.integers(1, 12), rng.integers(1, 28)))
_, eid = RegistrationClient(one).create_new_session('ZM_1150', date=date)
cls.eid = str(eid)
# Currently the task protocol of a session must contain 'ephys' in order to create an insertion!
one.alyx.rest('sessions', 'partial_update', id=cls.eid, data={'task_protocol': 'ephys'})

insdict = {"subject": 'ZM_1150', "name": probe, "model": '3B2', "serial": serial}
ins = one.alyx.rest('chronic-insertions', 'create', data=insdict)
cls.chronic_id = ins['id']
# Make a probe insertions
insdict = {"session": EPHYS_SESSION, "name": probe, "model": '3B2', "serial": serial,
insdict = {"session": cls.eid, "name": probe, "model": '3B2', "serial": serial,
"chronic_insertion": cls.chronic_id}
ins = one.alyx.rest('insertions', 'create', data=insdict)
cls.probe_id = ins['id']
Expand Down Expand Up @@ -117,6 +129,7 @@ def test_tracing_not_exists(self):
def tearDownClass(cls) -> None:
one.alyx.rest('insertions', 'delete', id=cls.probe_id)
one.alyx.rest('chronic-insertions', 'delete', id=cls.chronic_id)
one.alyx.rest('sessions', 'delete', id=cls.eid)


class TestAlignmentQcExisting(unittest.TestCase):
Expand All @@ -125,6 +138,7 @@ class TestAlignmentQcExisting(unittest.TestCase):

@classmethod
def setUpClass(cls) -> None:
rng = np.random.default_rng()
data = np.load(Path(Path(__file__).parent.parent.
joinpath('fixtures', 'qc', 'data_alignmentqc_existing.npz')),
allow_pickle=True)
Expand All @@ -137,7 +151,7 @@ def setUpClass(cls) -> None:
insertion = data['insertion'].tolist()
insertion['name'] = ''.join(random.choices(string.ascii_letters, k=5))
insertion['json'] = {'xyz_picks': cls.xyz_picks}
date = str(datetime.date(2019, np.random.randint(1, 12), np.random.randint(1, 28)))
date = str(datetime.date(2019, rng.integers(1, 12), rng.integers(1, 28)))
_, eid = RegistrationClient(one).create_new_session('ZM_1150', date=date)
cls.eid = str(eid)
# Currently the task protocol of a session must contain 'ephys' in order to create an insertion!
Expand Down Expand Up @@ -243,6 +257,7 @@ class TestAlignmentQcManual(unittest.TestCase):

@classmethod
def setUpClass(cls) -> None:
rng = np.random.default_rng()
data = np.load(Path(Path(__file__).parent.parent.
joinpath('fixtures', 'qc', 'data_alignmentqc_manual.npz')),
allow_pickle=True)
Expand All @@ -257,7 +272,7 @@ def setUpClass(cls) -> None:
insertion['name'] = ''.join(random.choices(string.ascii_letters, k=5))
insertion['json'] = {'xyz_picks': cls.xyz_picks}

date = str(datetime.date(2018, np.random.randint(1, 12), np.random.randint(1, 28)))
date = str(datetime.date(2018, rng.integers(1, 12), rng.integers(1, 28)))
_, eid = RegistrationClient(one).create_new_session('ZM_1150', date=date)
cls.eid = str(eid)
insertion['session'] = cls.eid
Expand Down
3 changes: 2 additions & 1 deletion ibllib/tests/qc/test_critical_reasons.py
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Original file line number Diff line number Diff line change
Expand Up @@ -28,10 +28,11 @@ def mock_input(prompt):
class TestUserPmtSess(unittest.TestCase):

def setUp(self) -> None:
rng = np.random.default_rng()
# Make sure tests use correct session ID
one.alyx.clear_rest_cache()
# Create new session on database with a random date to avoid race conditions
date = str(datetime.date(2022, np.random.randint(1, 12), np.random.randint(1, 28)))
date = str(datetime.date(2022, rng.integers(1, 12), rng.integers(1, 28)))
from one.registration import RegistrationClient
_, eid = RegistrationClient(one).create_new_session('ZM_1150', date=date)
eid = str(eid)
Expand Down
3 changes: 2 additions & 1 deletion ibllib/tests/test_oneibl.py
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Expand Up @@ -267,6 +267,7 @@ def test_task_names_extractors(self):
class TestRegistration(unittest.TestCase):

def setUp(self) -> None:
rng = np.random.default_rng()
self.one = ONE(**TEST_DB, cache_rest=None)
# makes sure tests start without session created
eid = self.one.search(subject=SUBJECT, date_range='2018-04-01', query_type='remote')
Expand All @@ -292,7 +293,7 @@ def setUp(self) -> None:
except HTTPError:
self.rev = self.one.alyx.rest('revisions', 'create', data={'name': self.revision})
# Create a new tag
tag_data = {'name': f'test_tag_{np.random.randint(0, 1e3)}', 'protected': True}
tag_data = {'name': f'test_tag_{rng.integers(0, 1e3)}', 'protected': True}
self.tag = self.one.alyx.rest('tags', 'create', data=tag_data)

def test_registration_datasets(self):
Expand Down
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