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 populate_db(infile, outfile):
dbmodel.db.connect()
from dbmodel import Types, Cells, SomaPositions, Contacts
with dbmodel.db.transaction():
types_df = pickle.load(open('type_metadata.pickle', 'r'))['type_metadata']
for r_id, r in types_df.iterrows():
print "rid=", r_id
t = Types.create(type_id = int(r_id),
designation = r['desig'],
volgyi_type = r['volgyi'],
macneil_type = r['macneil'],
certainty = r['certainty'],
coarse = r['coarse'])
t.save()
# create the additional types, because... this data is noisy
for i in range(72, 79):
t = Types.create(type_id = i)
cell_types = pickle.load(open('xlsxdata.pickle', 'r'))['types']
for c_i, c_t in cell_types.iteritems():
c = Cells.create(cell_id = c_i,
type_id = Types.get(Types.type_id == c_t))
c.save()
pos = pickle.load(open("soma.positions.pickle", 'r'))
for k, v in pos['pos'].iteritems():
p = SomaPositions.create(cell_id = Cells.get(Cells.cell_id ==k),
x = v[0], y =v[1], z=v[2])
p.save()
s = pickle.load(open("synapses.pickle", 'r'))
for r_id, r in s['synapsedf'].iterrows():
for from_id in Cells.select().where(Cells.cell_id == r['from_id']):
for to_id in Cells.select().where(Cells.cell_id == r['to_id']):
# WE ARE INTENTIONALLY THROWING OUT ALL THE CONTACTS
# that have cell_ids that don't map to known cells.
Contacts.create(from_id = from_id, to_id = to_id,
x = r['x'], y=r['y'], z=r['z'],
area = r['area']).save()
dbmodel.db.close()
open(outfile, 'w').write(" ")
