import custom_params
custom_params.filename='g37e1i002'
from common import *
import granules
import misc
import params
from all2all import all2all
gdist_std = .1
doesn=0
''' convert the arc s to xyz pos '''
def xyz(sec, s):
sec.push()
n0 = int(h.n3d())
x = h.Vector(n0) ; y = h.Vector(n0) ; z = h.Vector(n0)
s0 = h.Vector(n0)
for i in range(n0):
x.x[i], y.x[i], z.x[i], s0.x[i] = (h.x3d(i), h.y3d(i), h.z3d(i), h.arc3d(i))
x.interpolate(s, s0)
y.interpolate(s, s0)
z.interpolate(s, s0)
h.pop_section()
return (x, y, z)
''' arc of connections position '''
def secden_connection_positions(sec, rng):
# Assume poisson distribution of positions of synapses on secondary dendrite.
rng.negexp(1.)
s = h.Vector()
x = 0
L = sec.L
while True:
x += params.mean_synapse_interval #* rng.repick()
if (x > L):
break
s.append(x)
return s
''' connect a dendrite '''
def determine_secden_target(mgid, isec, sec, rng):
s = secden_connection_positions(sec, rng) # arc positions
p = xyz(sec, s) # from arc to 3d pos
s.mul(1 / sec.L)
connection_info = []
for i, x in enumerate(s):
connection_info.append((mgid, isec, x, None, 0, None, 0, (p[0][i], p[1][i], p[2][i])))
return connection_info
''' determine all connections info '''
def determine_mitral_target(mgid, mitral):
connection_info = []
for i in range(int(mitral.nsecden)):
if h.section_exists('secden', i, mitral):
sec = mitral.secden[i]
rng = params.ranstream(mgid, params.stream_mitraldendconnect + i)
connection_info += determine_secden_target(mgid, i, sec, rng)
return connection_info
''' select the granules '''
def connect_to_granule(x, y, z, rng, gconnected=set()):
gpos = list(granules.get_below([x, y, z]).difference(gconnected))
eup = misc.Ellipsoid(params.bulbCenter, params.somaAxis[0])
edw = misc.Ellipsoid(params.bulbCenter, params.granAxisInf)
gi = int(rng.discunif(0, len(gpos) - 1)) # pick the random granules
while len(gpos) > 0:
if eup.normalRadius(gpos[gi]) < 1 and edw.normalRadius(gpos[gi]) > 1: # inside layer
break
del gpos[gi]
gi = int(rng.discunif(0, len(gpos) - 1)) # pick the random granules
# can't connect
if len(gpos) == 0:
return -1, -1, ()
gpos = gpos[gi]
ggid = granules.pos2ggid[gpos]
gprj = eup.project(gpos) # granule projected pos
u = misc.versor(gprj, params.bulbCenter)
gx = u[0]*(x-gprj[0])+u[1]*(y-gprj[1])+u[2]*(z-gprj[2]) # near pos. on line
# randomize
gx += rng.normal(0, gdist_std**2)
# convert to arc
gx /= params.granule_priden2_len
# force if out of segment
if gx > 1 or gx < 0: gx = rng.uniform(0, 1)
return ggid, gx, gpos
''' wait '''
def connections_wait():
iters = int(pc.allreduce(0, 2)) * params.Nmitral_per_glom
for i in range(iters): all2all({})
''' connect the target points to the granules '''
def determine_mitral_connections(mgid, mitral):
ctarget = determine_mitral_target(mgid, mitral) # mitral dendrite's segment
# to connect
rng = params.ranstream(mgid, params.stream_m2g)
gconnected = set() # granules within the same glom
ci = []
if params.m2g_multiple: # multiple conn. within glom
for i in range(len(ctarget)):
x, y, z = ctarget[i][-1]
ggid, gx, gpos = connect_to_granule(x, y, z, rng, gconnected)
if ggid > 0:
gconnected.add(gpos)
ci.append(ctarget[i][:3] + (ggid, 0, gx) + ctarget[i][6:]) # update conn. info
else:
iters = int(pc.allreduce(len(ctarget), 2)) # max iterations is the maximal number of connections
nmg = params.Nmitral_per_glom
rbase = (rank-mgid%nmg)
for i in range(iters):
for mi in range(nmg):
# no more connections needs
if i >= len(ctarget):
all2all({})
else:
newg = {}
# current mitral to connect
if mi == rank%nmg:
x, y, z = ctarget[i][-1]
ggid, gx, gpos = connect_to_granule(x, y, z, rng, gconnected)
if ggid > 0:
gconnected.add(gpos)
ci.append(ctarget[i][:3] + (ggid, 0, gx) + ctarget[i][6:])
# fill the message to sent
for r in range(nmg):
r += rbase
if r == rank:
continue
newg.update({ r:gpos })
# send it!
all2all(newg)
else:
# read new connection
newg = all2all({})
if newg.has_key(rank):
gconnected.add(newg[rank])
return ci
''' serial version of determine_mitral_connections '''
def determine_glom_connections(glomid):
global doesn
import mkmitral
mtarget = [ None ] * params.Nmitral_per_glom
rng = [ None ] * params.Nmitral_per_glom
gconnected = [ None ] * params.Nmitral_per_glom
for i in range(params.Nmitral_per_glom):
mgid = i + glomid * params.Nmitral_per_glom
mtarget[i] = determine_mitral_target(mgid, mkmitral.mkmitral(mgid))
rng[i] = params.ranstream(mgid, params.stream_m2g)
# connection
if params.m2g_multiple:
gconnected[i] = set()
else:
if i == 0:
gconnected[i] = set()
else:
gconnected[i] = gconnected[0]
ciout = []
hasmore = True
j = 0
while hasmore:
hasmore = False
for i in range(len(mtarget)):
if j < len(mtarget[i]):
hasmore = True
ci = mtarget[i][j]
pos = ci[-1]
ggid, gx, gpos = connect_to_granule(pos[0], pos[1], pos[2], rng[i], gconnected[i])
if ggid > 0:
gconnected[i].add(gpos)
ciout.append(ci[:3] + (ggid, 0, gx) + ci[6:])
else:
doesn+=1
print 'doesn',doesn
j += 1
return ciout
if __name__ == '__main__':
import mkmitral
if rank == 0:
m = mkmitral.mkmitral(0)
print 'rank:',rank
ci = determine_mitral_connections(0, m)
elif rank == 1:
m = mkmitral.mkmitral(1)
print 'rank:',rank
ci = determine_mitral_connections(1, m)
elif rank == 2:
m = mkmitral.mkmitral(2)
print 'rank:',rank
ci = determine_mitral_connections(2, m)
elif rank == 3:
m = mkmitral.mkmitral(3)
print 'rank:',rank
ci = determine_mitral_connections(3, m)
elif rank == 4:
m = mkmitral.mkmitral(4)
print 'rank:',rank
ci = determine_mitral_connections(4, m)
else:
connections_wait()
print 'finished', rank
#print ci
