projectpyrho/pyrho

A virtual optogenetics laboratory

pyrho's Issues

after using lmfit 1.0.3 isnt work

PyRhO/pyrho/parameters.py

Line 296 in f62af03

self.__setitem__(param.name, param)

Error while running modified example

Hello:-)

Thank you for a nice software package!

I tried to modify the code from the example notebook for my purposes but I get the following error:

BrianObjectException: Error encountered with object named "statemonitor_3".
Object was created here (most recent call only, full details in debug log):
File "", line 35, in
monitors={'states' : StateMonitor(neuron_rho, RhO.brianStateVars, record=0), 'I': StateMonitor(neuron_rho, 'I', record=0), # Record current

Here's my code

from brian2 import *
start=time.time()
defaultclock.dt = 0.1*ms
tau = 10*ms
vr = -70*mV
vt = -60*mV
eqs = '''
dv/dt = I_ampa/Cm : volt
I_ampa=-g_ext_ampa*s_ext*(v-E_ampa) : amp
ds_ext/dt=-s_ext/t_ampa : 1
'''
eqs_rho = '''
dv/dt = I_ampa/Cm +((-I*R_m)+E_m-v)/tau_m : volt
I_ampa=-g_ext_ampa*s_ext*(v-E_ampa) : amp
ds_ext/dt=-s_ext/t_ampa : 1
'''+ RhO.brian_phi_t
netParams = {'t_ampa':2*ms, 'Cm':0.5*nF, 'E_ampa':0.0*mV, 'g_ext_ampa':3.1*nS,'vt':-60*mV,'vr':-70*mV,'w':1,'E_m':-70*mV,'tau_m':10*ms, 'R_m':70*Mohm}
E_ampa=0.0*mV
neuron = NeuronGroup(100, eqs, threshold='v>vt', reset='v=vr')
neuron_rho=NeuronGroup(100,eqs_rho,threshold='v>vt',reset='v=vr',name='Inputs')
neuron.v = -10*mV
neuron.s_ext = 0
spikes_gen=SpikeGeneratorGroup(1000,list(cell_identity),spikes*1000*ms)
w = 1
S = Synapses(spikes_gen, neuron, on_pre='s_ext += w')
S.connect(p=0.1)
S = Synapses(spikes_gen, neuron_rho, on_pre='s_ext += w')
S.connect(p=0.1)
S = Synapses(neuron_rho, neuron, on_pre='s_ext += w')
S.connect(p=0.5)
# Record the spikes
Mgp = SpikeMonitor(neuron)
Mgp_rho = SpikeMonitor(neuron_rho)
Minput = SpikeMonitor(spikes_gen)
monitors={'states' : StateMonitor(neuron_rho, RhO.brianStateVars, record=0), 'I': StateMonitor(neuron_rho, 'I', record=0),                  # Record current
            'spikes':[Mgp,Mgp_rho,Minput]}
import time
start=time.time()
import brian2 as br
net = br.Network(br.collect())
net.add(monitors.values())
Sim = simulators['Brian'](Prot, RhO, simParams['Brian'], net, netParams, monitors)
Sim.run()
Sim.plot()
end=time.time()
print(end-start)

Any help would be appreciated! No idea really what's going on!

All the very best,
Maria

Spines and ticks are not drawn properly

This affects all photocurrent plots with centred axes except rectifier.
Either the ylims are not set properly (when max(pc.I) == 0) or the left (y-axis) spines and ticks are not drawn up to ymax.