def _set_gap_junc_preselected(self, edge_prop, src_node, syn_weight, gj_ids):
if edge_prop.nsyns < 1:
return 1
sec_x = edge_prop['sec_x']
sec_id = edge_prop['sec_id']
section = self._secs_by_id[sec_id]
#Sets up the section to be connected to the gap junction.
pc.source_var(section(0.5)._ref_v, gj_ids[1], sec=section)
#Creates gap junction.
try:
gap_junc = h.Gap(0.5, sec=section)
except:
raise Exception("You need the gap.mod file to create gap junctions.")
#Attaches the source section to the gap junction.
pc.target_var(gap_junc, gap_junc._ref_vgap, gj_ids[0])
gap_junc.g = syn_weight
self._connections.append(ConnectionStruct(edge_prop, src_node, gap_junc, gap_junc, False, True))
self._gap_juncs.append(gap_junc)
self._edge_type_ids.append(edge_prop.edge_type_id)
if self._save_conn:
self._save_connection(src_gid=src_node.gid, src_net=src_node.network, sec_x=sec_x, seg_ix=sec_id,
edge_type_id=edge_prop.edge_type_id)
return 1
def init_gap_junctions():
# initialize source
for mgid in range(params.Nmitral):
mpriden = split.mpriden(mgid)
if mpriden:
mpriden.push()
pc.source_var(mpriden(0.99)._ref_v, mgid)
h.pop_section()
pc.barrier()
# initialize targets
for mgid in range(params.Nmitral):
mpriden = split.mpriden(mgid)
if mpriden:
glomid = mgid/nmxg
for sistermgid in range(glomid * nmxg, mgid)+range(mgid+1, (glomid+1)*nmxg):
if pc.gid_exists(sistermgid) > 0:
gap = h.Gap(mpriden(0.99))
if sistermgid != 189:
getmodel().gj[(mgid, sistermgid)] = gap
glomid = mgid / nmxg
pc.target_var(gap, gap._ref_vgap, sistermgid)
util.elapsed('Gap junctions builden')
def _set_gap_junc(self, edge_prop, src_node, syn_weight, gj_ids):
if edge_prop.nsyns < 1:
return 1
tar_seg_ix, tar_seg_prob = self._morph.get_target_segments(edge_prop)
nsyns = 1
# choose nsyn elements from seg_ix with probability proportional to segment area
seg_ix = self.prng.choice(tar_seg_ix, nsyns, p=tar_seg_prob)[0]
sec = self._secs[seg_ix] # section where synapases connect
x = self._morph.seg_prop['x'][
seg_ix] # distance along the section where synapse connects, i.e., seg_x
if edge_prop.nsyns > 1:
print(
"Warning: The number of synapses passed in was greater than 1, but only one gap junction will be made."
)
#Sets up the section to be connected to the gap junction.
pc.source_var(sec(0.5)._ref_v, gj_ids[1], sec=sec)
#Creates gap junction.
try:
gap_junc = h.Gap(0.5, sec=sec)
except:
raise Exception(
"You need the gap.mod file to create gap junctions.")
#Attaches the source section to the gap junction.
pc.target_var(gap_junc, gap_junc._ref_vgap, gj_ids[0])
gap_junc.g = syn_weight
self._connections.append(
ConnectionStruct(edge_prop, src_node, gap_junc, gap_junc, False,
True))
self._gap_juncs.append(gap_junc)
self._edge_type_ids.append(edge_prop.edge_type_id)
if self._save_conn:
self._save_connection(src_gid=src_node.gid,
src_net=src_node.network,
sec_x=x,
seg_ix=sec_ix,
edge_type_id=edge_prop.edge_type_id)
def _make_connection(self, segment, weight, local_to_remote_vargid, remote_to_local_vargid,
local_gid, remote_gid):
logger.debug("Setting source_var on local cell {} to connect to target_var on remote "
"cell {} with vargid {} on process {}"
.format(local_gid, remote_gid, local_to_remote_vargid,
state.mpi_rank))
# Set up the source reference for the local->remote connection
state.parallel_context.source_var(segment(0.5)._ref_v, local_to_remote_vargid)
# Create the gap_junction and set its weight
self.gap = h.Gap(0.5, sec=segment)
self.gap.g = weight
# Connect the gap junction with the source_var
logger.debug("Setting target_var on local cell {} to connect to source_var on remote "
"cell {} with vargid {} on process {}"
.format(local_gid, remote_gid, remote_to_local_vargid,
state.mpi_rank))
# set up the target reference for the remote->local connection
state.parallel_context.target_var(self.gap._ref_vgap, remote_to_local_vargid)
def init():
data = {}
for uid in range(nhost):
data.update({ uid:(getmodel().mitrals.keys()) })
data = a2a.all2all(data)
mgids = []
for _mgids in data.values(): mgids += _mgids
mgids = set(mgids)
# initialize source
for mgid in getmodel().mitrals.keys():
mpriden = split.mpriden(mgid)
if not mpriden:
continue
rgj = params.ranstream(mgid, params.stream_gap_junction)
mpriden.push()
secref = h.SectionRef()
h.pop_section()
h.mk_gj_src(pc, mgid, secref)
glomid = mgid2glom(mgid)
sistergids = []
# no longer all to all, only a chain
if not (ismtufted(mgid) and (mgid - nmi) % nmt == (nmt - 1)):
if ismitral(mgid) and mgid % nmxg == (nmxg - 1):
sistergids += [glomid * nmt + nmi]
else:
sistergids += [mgid + 1]
if not (ismitral(mgid) and mgid % nmxg == 0):
if ismtufted(mgid) and (mgid - nmi) % nmt == 0:
sistergids += [(glomid + 1) * nmxg - 1]
else:
sistergids += [mgid - 1]
sistergids = mgids.intersection(range(glomid * nmxg, glomid * nmxg + nmxg) + range(glomid * nmt + nmi, glomid * nmt + nmt + nmi)).difference([ mgid ])
for sistermgid in sistergids:
gap = h.Gap(mpriden(0.99))
if ismitral(mgid) and ismitral(sistermgid):
gap.g = rgj.uniform(gj_min_g1, gj_max_g1)
elif ismtufted(mgid) and ismtufted(sistermgid):
gap.g = rgj.uniform(gj_min_g3, gj_max_g3)
else:
gap.g = rgj.uniform(gj_min_g2, gj_max_g2)
getmodel().gj[(mgid, sistermgid)] = gap
pc.barrier()
# initialize targets
for key, gap in getmodel().gj.items():
mgid, sistermgid = key
pc.target_var(gap, gap._ref_vgap, sistermgid)
util.elapsed('Gap junctions built')