def synapse_group_test(env,
presyn_name,
gid,
cell,
syn_ids,
syn_mech_dict,
group_size,
v_init,
tstart=200.):
syn_attrs = env.synapse_attributes
vv = h.Vector()
vv.append(0, 0, 0, 0, 0, 0)
ranstream = np.random.RandomState(0)
if len(syn_ids) == 0:
return
selected = ranstream.choice(np.arange(0, len(syn_ids)),
size=group_size,
replace=False)
selected_ids = [syn_ids[i] for i in selected]
for syn_name in syn_mech_dict:
nclst = []
print('synapse_group_test: %s %s synapses: %i out of %i' %
(presyn_name, syn_name, len(selected_ids), len(syn_ids)))
ns = h.NetStim()
ns.interval = 1000
ns.number = 1
ns.start = 200
ns.noise = 0
nclst = []
first_syn_id = None
for syn_id in selected_ids:
if syn_attrs.has_netcon(gid, syn_id, syn_name):
syn_index = syn_attrs.syn_name_index_dict[syn_name]
del (syn_attrs.pps_dict[gid][syn_id].netcon[syn_index])
syn = syn_attrs.get_pps(gid, syn_id, syn_name)
this_nc = h.NetCon(ns, syn)
syn_attrs.add_netcon(gid, syn_id, syn_name, this_nc)
synapses.config_syn(syn_name=syn_name,
rules=syn_attrs.syn_param_rules,
mech_names=syn_attrs.syn_mech_names,
nc=this_nc,
**syn_mech_dict[syn_name])
nclst.append(this_nc)
if first_syn_id is None:
first_syn_id = syn_id
print("%s netcon: %s" %
(syn_name,
str([
this_nc.weight[i]
for i in range(int(this_nc.wcnt()))
])))
for sec in list(cell.all):
h.psection(sec=sec)
v_holding_exc = -75
v_holding_inh = -45
if syn_name in ['NMDA', 'SatAMPA', 'AMPA']:
v_holding = v_holding_exc
v = cell.syntest_exc(
tstart, v_holding, v_init,
"MossyCell_%s_%s_synapse_trace_%i.dat" %
(presyn_name, syn_name, group_size))
elif syn_name in [
'SatGABA', 'GABA', 'SatGABA_A', 'GABA_A', 'SatGABA_B', 'GABA_B'
]:
v_holding = v_holding_inh
v = cell.syntest_inh(
tstart, v_holding, v_init,
"MossyCell_%s_%s_synapse_trace_%i.dat" %
(presyn_name, syn_name, group_size))
else:
raise RuntimeError('Unknown synapse mechanism type %s' % syn_name)
vv = vv.add(v)
amp = vv.x[0]
t_10_90 = vv.x[1]
t_20_80 = vv.x[2]
t_all = vv.x[3]
t_50 = vv.x[4]
t_decay = vv.x[5]
f = open(
"MossyCell_%s_%s_synapse_results_%i.dat" %
(presyn_name, syn_name, group_size), 'w')
f.write("%s synapses: \n" % syn_name)
f.write(" Amplitude %f\n" % amp)
f.write(" 10-90 Rise Time %f\n" % t_10_90)
f.write(" 20-80 Rise Time %f\n" % t_20_80)
f.write(" Decay Time Constant %f\n" % t_decay)
f.close()
def synapse_group_rate_test(env,
presyn_name,
gid,
cell,
syn_obj_dict,
syn_params_dict,
group_size,
rate,
tstart=200.):
syn_attrs = env.synapse_attributes
ranstream = np.random.RandomState(0)
syn_ids = list(syn_obj_dict.keys())
if group_size > len(syn_ids):
return
selected = ranstream.choice(np.arange(0, len(syn_ids)),
size=group_size,
replace=False)
selected_ids = [syn_ids[i] for i in selected]
for section_name, sec_syn_params_dict in utils.viewitems(syn_params_dict):
for syn_name in sec_syn_params_dict:
synlst = []
for syn_id in selected_ids:
synlst.append(syn_attrs.get_pps(gid, syn_id, syn_name))
print('synapse_group_rate_test: %s %s synapses: %i out of %i ' %
(presyn_name, syn_name, len(synlst), len(syn_ids)))
ns = h.NetStim()
ns.interval = 1000. / rate
ns.number = rate
ns.start = 200
ns.noise = 0
nclst = []
for syn_id, syn in zip(selected_ids, synlst):
syn_attrs.del_netcon(gid, syn_id, syn_name, throw_error=False)
this_nc = h.NetCon(ns, syn)
syn_attrs.add_netcon(gid, syn_id, syn_name, this_nc)
synapses.config_syn(syn_name=syn_name,
rules=syn_attrs.syn_param_rules,
mech_names=syn_attrs.syn_mech_names,
nc=this_nc,
**sec_syn_params_dict[syn_name])
nclst.append(this_nc)
if syn_name == 'SatAMPA':
v_init = -65
elif syn_name == 'AMPA':
v_init = -65
elif syn_name == 'SatGABA':
v_init = 0
elif syn_name == 'GABA':
v_init = 0
elif syn_name == 'SatGABA_A':
v_init = 0
elif syn_name == 'GABA_A':
v_init = 0
elif syn_name == 'SatGABA_B':
v_init = 0
elif syn_name == 'GABA_B':
v_init = 0
else:
raise RuntimeError('Unknown synapse mechanism type %s' %
syn_name)
hoc_cell = cell.hoc_cell
res = hoc_cell.syntest_rate(tstart, rate, v_init)
tlog = res.o(0)
vlog = res.o(1)
f = open(
"HIPPCell_%s_%s_synapse_rate_%i.dat" %
(presyn_name, syn_name, group_size), 'w')
for i in range(0, int(tlog.size())):
f.write('%g %g\n' % (tlog.x[i], vlog.x[i]))
f.close()
def synapse_group_rate_test(env,
presyn_name,
gid,
cell,
syn_ids,
syn_mech_dict,
group_size,
rate,
tstart=200.):
syn_attrs = env.synapse_attributes
syn_attrs = env.synapse_attributes
ranstream = np.random.RandomState(0)
if len(syn_ids) == 0:
return
selected = ranstream.choice(np.arange(0, len(syn_ids)),
size=group_size,
replace=False)
selected_ids = [syn_ids[i] for i in selected]
for syn_name in syn_mech_dict:
print('synapse_group_rate_test: %s %s synapses: %i out of %i ' %
(presyn_name, syn_name, len(selected_ids), len(syn_ids)))
ns = h.NetStim()
ns.interval = 1000. / rate
ns.number = rate
ns.start = 200
ns.noise = 0
nclst = []
first_syn_id = None
for syn_id in selected_ids:
for syn_name in syn_mech_dict:
if syn_attrs.has_netcon(gid, syn_id, syn_name):
syn_index = syn_attrs.syn_name_index_dict[syn_name]
del (syn_attrs.pps_dict[gid][syn_id].netcon[syn_index])
syn = syn_attrs.get_pps(gid, syn_id, syn_name)
this_nc = h.NetCon(ns, syn)
syn_attrs.add_netcon(gid, syn_id, syn_name, this_nc)
synapses.config_syn(syn_name=syn_name,
rules=syn_attrs.syn_param_rules,
mech_names=syn_attrs.syn_mech_names,
nc=this_nc,
**syn_mech_dict[syn_name])
nclst.append(this_nc)
if first_syn_id is None:
print("%s netcon: %s" %
(syn_name,
str([
this_nc.weight[i]
for i in range(int(this_nc.wcnt()))
])))
if first_syn_id is None:
first_syn_id = syn_id
for sec in list(cell.all):
h.psection(sec=sec)
print('synapse_group_rate_test: %s %s synapses: %i netcons ' %
(presyn_name, syn_name, len(nclst)))
v_init_exc = -75
v_init_inh = 0
if syn_name in ['NMDA', 'SatAMPA', 'AMPA']:
v_init = v_init_exc
elif syn_name in [
'SatGABA', 'GABA', 'SatGABA_A', 'GABA_A', 'SatGABA_B', 'GABA_B'
]:
v_init = v_init_inh
else:
raise RuntimeError('Unknown synapse mechanism type %s' % syn_name)
res = cell.syntest_rate(tstart, rate, v_init)
tlog = res.o(0)
vlog = res.o(1)
f = open(
"MossyCell_%s_%s_synapse_rate_%i.dat" %
(presyn_name, syn_name, group_size), 'w')
for i in range(0, int(tlog.size())):
f.write('%g %g\n' % (tlog.x[i], vlog.x[i]))
f.close()
def synapse_group_test(env,
presyn_name,
gid,
cell,
syn_obj_dict,
syn_params_dict,
group_size,
v_holding,
v_init,
tstart=200.):
syn_attrs = env.synapse_attributes
vv = h.Vector()
vv.append(0, 0, 0, 0, 0, 0)
ranstream = np.random.RandomState(0)
syn_ids = list(syn_obj_dict.keys())
if group_size > len(syn_ids):
print(
"synapse_group_test: gid %d: group size %d is greater than number of synapses %d"
% (gid, group_size, len(syn_ids)))
return
selected = ranstream.choice(np.arange(0, len(syn_ids)),
size=group_size,
replace=False)
selected_ids = [syn_ids[i] for i in selected]
for section_name, sec_syn_params_dict in utils.viewitems(syn_params_dict):
for syn_name in sec_syn_params_dict:
synlst = []
for syn_id in selected_ids:
synlst.append(syn_attrs.get_pps(gid, syn_id, syn_name))
print('synapse_group_test: %s %s synapses: %i out of %i' %
(presyn_name, syn_name, len(synlst), len(syn_ids)))
ns = h.NetStim()
ns.interval = 1000
ns.number = 1
ns.start = 200
ns.noise = 0
nclst = []
for syn_id, syn in zip(selected_ids, synlst):
syn_attrs.del_netcon(gid, syn_id, syn_name, throw_error=False)
this_nc = h.NetCon(ns, syn)
syn_attrs.add_netcon(gid, syn_id, syn_name, this_nc)
synapses.config_syn(syn_name=syn_name,
rules=syn_attrs.syn_param_rules,
mech_names=syn_attrs.syn_mech_names,
nc=this_nc,
**sec_syn_params_dict[syn_name])
nclst.append(this_nc)
hoc_cell = cell.hoc_cell
if syn_name == 'SatAMPA':
v = hoc_cell.syntest_exc(
tstart, v_holding, v_init,
"HIPPCell_%s_%s_synapse_trace_%i.dat" %
(presyn_name, syn_name, group_size))
elif syn_name == 'AMPA':
v = hoc_cell.syntest_exc(
tstart, v_holding, v_init,
"HIPPCell_%s_%s_synapse_trace_%i.dat" %
(presyn_name, syn_name, group_size))
elif syn_name == 'SatGABA':
v = hoc_cell.syntest_inh(
tstart, v_holding, v_init,
"HIPPCell_%s_%s_synapse_trace_%i.dat" %
(presyn_name, syn_name, group_size))
elif syn_name == 'GABA':
v = hoc_cell.syntest_inh(
tstart, v_holding, v_init,
"HIPPCell_%s_%s_synapse_trace_%i.dat" %
(presyn_name, syn_name, group_size))
elif syn_name == 'SatGABA_A':
v = hoc_cell.syntest_inh(
tstart, v_holding, v_init,
"HIPPCell_%s_%s_synapse_trace_%i.dat" %
(presyn_name, syn_name, group_size))
elif syn_name == 'GABA_A':
v = hoc_cell.syntest_inh(
tstart, v_holding, v_init,
"HIPPCell_%s_%s_synapse_trace_%i.dat" %
(presyn_name, syn_name, group_size))
elif syn_name == 'SatGABA_B':
v = hoc_cell.syntest_inh(
tstart, v_holding, v_init,
"HIPPCell_%s_%s_synapse_trace_%i.dat" %
(presyn_name, syn_name, group_size))
elif syn_name == 'GABA_B':
v = hoc_cell.syntest_inh(
tstart, v_holding, v_init,
"HIPPCell_%s_%s_synapse_trace_%i.dat" %
(presyn_name, syn_name, group_size))
else:
raise RuntimeError('Unknown synapse mechanism type %s' %
syn_name)
vv = vv.add(v)
amp = vv.x[0]
t_10_90 = vv.x[1]
t_20_80 = vv.x[2]
t_all = vv.x[3]
t_50 = vv.x[4]
t_decay = vv.x[5]
f = open(
"HIPPCell_%s_%s_synapse_results_%i.dat" %
(presyn_name, syn_name, group_size), 'w')
f.write("%s synapses: \n" % syn_name)
f.write(" Amplitude %f\n" % amp)
f.write(" 10-90 Rise Time %f\n" % t_10_90)
f.write(" 20-80 Rise Time %f\n" % t_20_80)
f.write(" Decay Time Constant %f\n" % t_decay)
f.close()