def populate(infile, outfile):
dbmodel.db.connect()
dbmodel.create_db()
from dbmodel import Cells, Synapses
# load the individual neurons
indata = pickle.load(open(infile, 'r'))
neurons = indata['neurons']
for neuron_name, nd in neurons.iterrows():
nt = nd['neurotransmitters']
if type(nt) == float:
nt = None
role = nd['role']
if type(role)==float:
role = None
Cells.create(cell_name =neuron_name,
cell_class= nd['class'],
soma_pos = nd['soma_pos'],
neurotransmitters=nt,
role = role)
connections = indata['connections']
for n1 in neurons.index.values:
for n2 in neurons.index.values:
c1 = Cells.get(Cells.cell_name == n1)
c2 = Cells.get(Cells.cell_name == n2)
c = (n1, n2)
if c in connections:
for synapse_type, nbr in connections[c]:
code = synapse_type[0]
st_short = None
# note this dataset includes entries for both A sends to B (type S) and B receives from A (type R)
if code == "Sp" or code == 'S':
st_short = 'C'
elif code == 'E':
st_short = 'E'
elif code == 'R' or code == 'Rp':
pass
else:
raise Exception("code %s not understood" % code)
if st_short:
s = Synapses.select().where(Synapses.from_id == c1,
Synapses.to_id == c2,
Synapses.synapse_type == st_short).count()
if s == 0:
Synapses.create(from_id = c1,
to_id = c2,
synapse_type = st_short,
count = nbr)
else:
Synapses.update(count = Synapses.count + nbr).where(Synapses.from_id == c1,
Synapses.to_id == c2,
synapse_type == st_short)
dbmodel.db.close()
def populate(infile, outfile):
dbmodel.db.connect()
dbmodel.create_db()
from dbmodel import Cells, Synapses
# load the individual neurons
indata = pickle.load(open(infile, 'r'))
neurons = indata['neurons']
for neuron_name, nd in neurons.iterrows():
nt = nd['neurotransmitters']
if type(nt) == float:
nt = None
role = nd['role']
if type(role) == float:
role = None
Cells.create(cell_name=neuron_name,
cell_class=nd['class'],
soma_pos=nd['soma_pos'],
neurotransmitters=nt,
role=role)
connections = indata['connections']
for n1 in neurons.index.values:
for n2 in neurons.index.values:
c1 = Cells.get(Cells.cell_name == n1)
c2 = Cells.get(Cells.cell_name == n2)
c = (n1, n2)
if c in connections:
for synapse_type, nbr in connections[c]:
code = synapse_type[0]
st_short = None
# note this dataset includes entries for both A sends to B (type S) and B receives from A (type R)
if code == "Sp" or code == 'S':
st_short = 'C'
elif code == 'E':
st_short = 'E'
elif code == 'R' or code == 'Rp':
pass
else:
raise Exception("code %s not understood" % code)
if st_short:
s = Synapses.select().where(
Synapses.from_id == c1, Synapses.to_id == c2,
Synapses.synapse_type == st_short).count()
if s == 0:
Synapses.create(from_id=c1,
to_id=c2,
synapse_type=st_short,
count=nbr)
else:
Synapses.update(count=Synapses.count + nbr).where(
Synapses.from_id == c1, Synapses.to_id == c2,
synapse_type == st_short)
dbmodel.db.close()
def create_db(_, outfile):
dbmodel.db.connect()
dbmodel.create_db()