ivec = h.Vector()
kc_solo_vvec = h.Vector()
ivec_solo = h.Vector()
tvec.record(h._ref_t)
kc_vvec.record(kc.soma(0.5)._ref_v)
ggn_ca_vvec.record(model['ggn_pre'][0][0](model['ggn_pre'][0][1])._ref_v)
ivec.record(inject._ref_i)
kc_solo_vvec.record(kc_solo.soma(0.5)._ref_v)
ivec_solo.record(inject_solo._ref_i)
fb_dict = {'t': tvec, 'i': ivec, 'kc': kc_vvec, 'ca': ggn_ca_vvec}
solo_dict = {'t': tvec, 'i': ivec_solo, 'kc': kc_solo_vvec}
outfile = '{}_UTC{}_PID{}_JID{}.h5'.format(
args.outprefix, timestamp.strftime('%Y_%m_%d__%H_%M_%S'), mypid,
myjobid)
logger.info('Starting simulation')
with h5.File(outfile, 'w') as fd:
fd.attrs['command_line'] = str(sys.argv)
fd.attrs['ggn_kc_syn'] = str(ggn_kc_syn_params)
syntype = np.dtype([('sec', h5.special_dtype(vlen=str)),
('pos', np.float32)])
ds_ca_syn = fd.create_dataset('ggn_pre', (len(model['ggn_pre']), ),
dtype=syntype)
ds_ca_syn[:] = [(sec.name(), pos) for sec, pos in model['ggn_pre']]
grp_feedback = fd.create_group('ggn_kc')
grp_solo = fd.create_group('kc')
grp_vec_inject = [(grp_feedback, fb_dict, inject),
(grp_solo, solo_dict, inject_solo)]
if len(args.freq) > 1:
def main():
parser = make_parser()
args = parser.parse_args()
logger.info('Command line args: {}'.format(str(sys.argv)))
print(args.ggn_vm_file)
# KCs with GGN inhibition
inhibited_vec = defaultdict(list)
solo_vec_list = []
tstart = Q_(args.tstart).to('ms').m
tend = Q_(args.tend).to('ms').m
istart = Q_(args.istart).to('nA').m
iend = Q_(args.iend).to('nA').m
di = Q_(args.di).to('nA').m
irange = np.arange(istart, iend + di / 2.0, di)
logger.info('Starting current: {} nA'.format(istart))
logger.info('End current: {} nA'.format(iend))
logger.info('Increment: {} nA'.format(di))
logger.info('current range: {}'.format(irange))
ggn_vm = {}
for input_file in args.ggn_vm_file:
ggn_vm[input_file] = np.loadtxt(input_file)
for inject in irange:
for input_file, vm in ggn_vm.items():
kc_vvec, ggn_gvec = make_kc_with_dynaclamp(args.kc, args.kc_file,
inject, tstart, tend,
vm)
inhibited_vec[input_file].append((kc_vvec, ggn_gvec))
# KC without any inhibition
kc_vvec, ggn_gvec = make_kc_with_dynaclamp(args.kc, args.kc_file,
inject, tstart, tend)
solo_vec_list.append(kc_vvec)
tvec = h.Vector()
tvec.record(h._ref_t)
h.tstop = tend
print('Init')
h.init()
print('Run')
h.run()
print('Finished simulation')
fig, ax = plt.subplots(nrows=len(irange) + 1,
ncols=len(ggn_vm) + 1,
sharex='all',
sharey='all')
t = np.array(tvec.x)
solo_data = []
for ii, vvec in enumerate(solo_vec_list):
ax[ii + 1, 0].plot(tvec, vvec, color='#e66101')
solo_data.append(np.array(vvec.x))
combined = np.vstack(solo_data)
prefix = 'UTC' + timestamp.strftime('%Y%m%d_%H%M%S')
fname = '{}_solo_kc.npz'.format(prefix)
np.savez(fname, t=t, vm=combined, inject=irange)
logger.info('Saved solo KC data in {}'.format(fname))
for jj, input_file in enumerate(args.ggn_vm_file):
fname = '{}_{}.npz'.format(prefix, os.path.basename(input_file))
data = []
kc_vm_list = inhibited_vec[input_file]
for ii, (vvec, gvec) in enumerate(kc_vm_list):
data.append(np.array(vvec.x))
ax[ii + 1, jj + 1].plot(tvec, vvec, color='#e66101')
ax[ii + 1, 0].set_ylabel('{} pA'.format(irange[ii] * 1e3))
# ax[ii+1, 0].set_ylabel('{} pA'.format(int(np.round(irange[ii]*1e3)))) # to avoid decimal point when integer values
# ax[0, jj+1].plot(tvec, gvec)
# ax[0, jj+1].plot(ggn_vm[input_file][:,0], ggn_vm[input_file][:,1])
ax[0, jj + 1].set_title(input_file)
combined = np.vstack(data)
np.savez(fname,
combined=combined,
irange=irange,
ggn_vm=ggn_vm[input_file])
logger.info(
'Saved data from dynamic clamp with input from {} in {}'.format(
input_file, fname))
for axis in ax.flat:
axis.set_xlim(250, 1750)
fig.set_size_inches(210 / 25.4, 290 / 25.4)
fig.tight_layout()
fig.savefig('{}_KC_dynamic_range_with_ggn_vm.svg'.format(prefix))
plt.show()
print('End')