def parse_prediction(db_credentials, predict_config_path):
predict_cfg = read_predict_config(predict_config_path)
db = SynisterDb(db_credentials, predict_cfg["db_name_data"])
predictions = db.get_predictions(predict_cfg["split_name"],
predict_cfg["experiment"],
predict_cfg["train_number"],
predict_cfg["predict_number"])
synapses = db.get_synapses()
skeletons = db.get_skeletons()
predicted_synapses =\
{
synapse_id:
{
**{"prediction": prediction["prediction"]},
**synapses[synapse_id],
**skeletons[synapses[synapse_id]["skeleton_id"]]
}
for synapse_id, prediction in predictions.items()
}
return predicted_synapses, predict_cfg
class SynapseSourceMongoTestCase(unittest.TestCase):
def setUp(self):
self.db_credentials = os.path.join(os.path.abspath(os.path.dirname(__file__)) + "/../../db_credentials.ini")
self.db_name = "synister_v2_refactor"
self.split_name = "neuron"
self.points = PointsKey('SYNAPSES')
self.db = SynisterDb(self.db_credentials, self.db_name)
self.neurotransmitters = [
('gaba',),
#('acetylcholine',), TODO: Fix position query for large number of objects. DB hangs for this.
('glutamate',),
('dopamine',),
('octopamine',),
('serotonin',),
]
def runTest(self):
for synapse_type in self.neurotransmitters:
source = SynapseSourceMongo(self.db_credentials,
self.db_name,
self.split_name,
synapse_type,
self.points)
source.setup()
points = source.data
print("query pos...")
synapses = self.db.get_synapses(positions=points)
print("get skeletons...")
skeletons = self.db.get_skeletons()
n = 1
for synapse in synapses.values():
self.assertTrue(synapse["splits"][self.split_name] == "train")
nt = skeletons[synapse["skeleton_id"]]["nt_known"]
self.assertTrue(nt == synapse_type)
n += 1
synapses_in_split = self.db.get_synapses(split_name=self.split_name, neurotransmitters=synapse_type)
all_synapse_ids_in_train = [id_ for id_, s in synapses_in_split.items() if s["splits"][self.split_name] == "train"]
synapse_ids_retrieved = [s for s in synapses]
self.assertTrue(sorted(all_synapse_ids_in_train) == sorted(synapse_ids_retrieved))