def init_run_save(group_vec_list, dsname, tstop, attrs):
"""init, run and save the data in fd, creating the dataset `dsname`.
vec_dict: {field name: Vector recording the field}
tstop: stop time of simulation
attrs: dict containing additional attributes for the dataset.
"""
h.tstop = tend
logger.info('Init: saving in dataset {}'.format(dsname))
h.init()
h.run()
print('Finished run: saving in dataset {}'.format(dsname))
for group, vec_dict in group_vec_list:
data = np.vstack([np.asarray(vec.x) for vec in vec_dict.values()])
ds = group.create_dataset(dsname, data=data)
ds.attrs['fields'] = list(vec_dict.keys())
for k, v in attrs.items():
ds.attrs[k] = v
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')