[['soma', '0.5', 'kap', 'gbar']],
[['soma', '0.5', 'na8st', 'gbar']]
]
errfun = 'rms'
fitfun = 'get_v'
fitnessweights = [1]
model_dir = '../../../model/cells/dapmodel0.json'
mechanism_dir = '../../../model/channels/schmidthieber'
data_dir = '../../../data/2015_08_26b/rampIV/3.0(nA).csv'
fitter = HodgkinHuxleyFitter(variable_keys, errfun, fitfun, fitnessweights,
model_dir, mechanism_dir, data_dir, simulation_params={'celsius': 35})
# create cell
candidate = np.ones(len(variable_keys)) # gbars should be 1
fitter.update_cell(candidate)
# extract parameter
channel_list = get_channel_list(fitter.cell, 'soma')
ion_list = get_ionlist(channel_list)
v_exp = fitter.data.v.values
t_exp = fitter.data.t.values
i_exp = fitter.data.i.values
dt_exp = t_exp[1] - t_exp[0]
dvdt_exp = np.concatenate((np.array([(v_exp[1]-v_exp[0])/dt_exp]), np.diff(v_exp)/dt_exp))
celsius = fitter.simulation_params['celsius']
# convert units
dvdt_sc, i_inj_sc, _, _, cell_area = convert_units(fitter.cell.soma.L, fitter.cell.soma.diam,
