def get_spont(nFiles):
spikeFreq = np.zeros(nFiles)
for fid in range(nFiles):
fname = format(fid, '05d')
v = np.genfromtxt('sim_gocnet_GoC_{}.v.dat'.format(fname))
spikes = np.genfromtxt('sim_gocnet_GoC_{}.v.spikes'.format(fname))
if not np.isnan(v[-1, 1]):
spikeFreq[fid] = analysis.mean_spike_frequency(spikes[:, 1] * 1e3)
else:
spikeFreq[fid] = np.nan
temp = spikeFreq
temp[np.isnan(temp)] = 0
useParams = np.where(abs(temp - 7) <= 2)
print(useParams, spikeFreq[useParams])
return spikeFreq
def generate_current_vs_frequency_curve(nml2_file,
cell_id,
start_amp_nA=-0.1,
end_amp_nA=0.1,
step_nA=0.01,
custom_amps_nA=[],
analysis_duration=1000,
analysis_delay=0,
pre_zero_pulse=0,
post_zero_pulse=0,
dt=0.05,
temperature="32degC",
spike_threshold_mV=0.,
plot_voltage_traces=False,
plot_if=True,
plot_iv=False,
xlim_if=None,
ylim_if=None,
xlim_iv=None,
ylim_iv=None,
label_xaxis=True,
label_yaxis=True,
show_volts_label=True,
grid=True,
font_size=12,
if_iv_color='k',
linewidth=1,
bottom_left_spines_only=False,
show_plot_already=True,
save_voltage_traces_to=None,
save_if_figure_to=None,
save_iv_figure_to=None,
save_if_data_to=None,
save_iv_data_to=None,
simulator="jNeuroML",
num_processors=1,
include_included=True,
title_above_plot=False,
return_axes=False,
verbose=False):
print_comment(
"Running generate_current_vs_frequency_curve() on %s (%s)" %
(nml2_file, os.path.abspath(nml2_file)), verbose)
from pyelectro.analysis import max_min
from pyelectro.analysis import mean_spike_frequency
import numpy as np
traces_ax = None
if_ax = None
iv_ax = None
sim_id = 'iv_%s' % cell_id
total_duration = pre_zero_pulse + analysis_duration + analysis_delay + post_zero_pulse
pulse_duration = analysis_duration + analysis_delay
end_stim = pre_zero_pulse + analysis_duration + analysis_delay
ls = LEMSSimulation(sim_id, total_duration, dt)
ls.include_neuroml2_file(nml2_file, include_included=include_included)
stims = []
if len(custom_amps_nA) > 0:
stims = [float(a) for a in custom_amps_nA]
stim_info = ['%snA' % float(a) for a in custom_amps_nA]
else:
amp = start_amp_nA
while amp <= end_amp_nA:
stims.append(amp)
amp += step_nA
stim_info = '(%snA->%snA; %s steps of %snA; %sms)' % (
start_amp_nA, end_amp_nA, len(stims), step_nA, total_duration)
print_comment_v("Generating an IF curve for cell %s in %s using %s %s" %
(cell_id, nml2_file, simulator, stim_info))
number_cells = len(stims)
pop = nml.Population(id="population_of_%s" % cell_id,
component=cell_id,
size=number_cells)
# create network and add populations
net_id = "network_of_%s" % cell_id
net = nml.Network(id=net_id,
type="networkWithTemperature",
temperature=temperature)
ls.assign_simulation_target(net_id)
net_doc = nml.NeuroMLDocument(id=net.id)
net_doc.networks.append(net)
net_doc.includes.append(nml.IncludeType(nml2_file))
net.populations.append(pop)
for i in range(number_cells):
stim_amp = "%snA" % stims[i]
input_id = ("input_%s" % stim_amp).replace('.',
'_').replace('-', 'min')
pg = nml.PulseGenerator(id=input_id,
delay="%sms" % pre_zero_pulse,
duration="%sms" % pulse_duration,
amplitude=stim_amp)
net_doc.pulse_generators.append(pg)
# Add these to cells
input_list = nml.InputList(id=input_id,
component=pg.id,
populations=pop.id)
input = nml.Input(id='0',
target="../%s[%i]" % (pop.id, i),
destination="synapses")
input_list.input.append(input)
net.input_lists.append(input_list)
net_file_name = '%s.net.nml' % sim_id
pynml.write_neuroml2_file(net_doc, net_file_name)
ls.include_neuroml2_file(net_file_name)
disp0 = 'Voltage_display'
ls.create_display(disp0, "Voltages", "-90", "50")
of0 = 'Volts_file'
ls.create_output_file(of0, "%s.v.dat" % sim_id)
for i in range(number_cells):
ref = "v_cell%i" % i
quantity = "%s[%i]/v" % (pop.id, i)
ls.add_line_to_display(disp0, ref, quantity, "1mV",
pynml.get_next_hex_color())
ls.add_column_to_output_file(of0, ref, quantity)
lems_file_name = ls.save_to_file()
print_comment(
"Written LEMS file %s (%s)" %
(lems_file_name, os.path.abspath(lems_file_name)), verbose)
if simulator == "jNeuroML":
results = pynml.run_lems_with_jneuroml(lems_file_name,
nogui=True,
load_saved_data=True,
plot=False,
show_plot_already=False,
verbose=verbose)
elif simulator == "jNeuroML_NEURON":
results = pynml.run_lems_with_jneuroml_neuron(lems_file_name,
nogui=True,
load_saved_data=True,
plot=False,
show_plot_already=False,
verbose=verbose)
elif simulator == "jNeuroML_NetPyNE":
results = pynml.run_lems_with_jneuroml_netpyne(
lems_file_name,
nogui=True,
load_saved_data=True,
plot=False,
show_plot_already=False,
num_processors=num_processors,
verbose=verbose)
else:
raise Exception(
"Sorry, cannot yet run current vs frequency analysis using simulator %s"
% simulator)
print_comment(
"Completed run in simulator %s (results: %s)" %
(simulator, results.keys()), verbose)
#print(results.keys())
times_results = []
volts_results = []
volts_labels = []
if_results = {}
iv_results = {}
for i in range(number_cells):
t = np.array(results['t']) * 1000
v = np.array(results["%s[%i]/v" % (pop.id, i)]) * 1000
if plot_voltage_traces:
times_results.append(t)
volts_results.append(v)
volts_labels.append("%s nA" % stims[i])
mm = max_min(v, t, delta=0, peak_threshold=spike_threshold_mV)
spike_times = mm['maxima_times']
freq = 0
if len(spike_times) > 2:
count = 0
for s in spike_times:
if s >= pre_zero_pulse + analysis_delay and s < (
pre_zero_pulse + analysis_duration + analysis_delay):
count += 1
freq = 1000 * count / float(analysis_duration)
mean_freq = mean_spike_frequency(spike_times)
#print("--- %s nA, spike times: %s, mean_spike_frequency: %f, freq (%fms -> %fms): %f"%(stims[i],spike_times, mean_freq, analysis_delay, analysis_duration+analysis_delay, freq))
if_results[stims[i]] = freq
if freq == 0:
if post_zero_pulse == 0:
iv_results[stims[i]] = v[-1]
else:
v_end = None
for j in range(len(t)):
if v_end == None and t[j] >= end_stim:
v_end = v[j]
iv_results[stims[i]] = v_end
if plot_voltage_traces:
traces_ax = pynml.generate_plot(
times_results,
volts_results,
"Membrane potential traces for: %s" % nml2_file,
xaxis='Time (ms)' if label_xaxis else ' ',
yaxis='Membrane potential (mV)' if label_yaxis else '',
xlim=[total_duration * -0.05, total_duration * 1.05],
show_xticklabels=label_xaxis,
font_size=font_size,
bottom_left_spines_only=bottom_left_spines_only,
grid=False,
labels=volts_labels if show_volts_label else [],
show_plot_already=False,
save_figure_to=save_voltage_traces_to,
title_above_plot=title_above_plot,
verbose=verbose)
if plot_if:
stims = sorted(if_results.keys())
stims_pA = [ii * 1000 for ii in stims]
freqs = [if_results[s] for s in stims]
if_ax = pynml.generate_plot(
[stims_pA], [freqs],
"Firing frequency versus injected current for: %s" % nml2_file,
colors=[if_iv_color],
linestyles=['-'],
markers=['o'],
linewidths=[linewidth],
xaxis='Input current (pA)' if label_xaxis else ' ',
yaxis='Firing frequency (Hz)' if label_yaxis else '',
xlim=xlim_if,
ylim=ylim_if,
show_xticklabels=label_xaxis,
show_yticklabels=label_yaxis,
font_size=font_size,
bottom_left_spines_only=bottom_left_spines_only,
grid=grid,
show_plot_already=False,
save_figure_to=save_if_figure_to,
title_above_plot=title_above_plot,
verbose=verbose)
if save_if_data_to:
with open(save_if_data_to, 'w') as if_file:
for i in range(len(stims_pA)):
if_file.write("%s\t%s\n" % (stims_pA[i], freqs[i]))
if plot_iv:
stims = sorted(iv_results.keys())
stims_pA = [ii * 1000 for ii in sorted(iv_results.keys())]
vs = [iv_results[s] for s in stims]
xs = []
ys = []
xs.append([])
ys.append([])
for si in range(len(stims)):
stim = stims[si]
if len(custom_amps_nA) == 0 and si > 1 and (
stims[si] - stims[si - 1]) > step_nA * 1.01:
xs.append([])
ys.append([])
xs[-1].append(stim * 1000)
ys[-1].append(iv_results[stim])
iv_ax = pynml.generate_plot(
xs,
ys,
"V at %sms versus I below threshold for: %s" %
(end_stim, nml2_file),
colors=[if_iv_color for s in xs],
linestyles=['-' for s in xs],
markers=['o' for s in xs],
xaxis='Input current (pA)' if label_xaxis else '',
yaxis='Membrane potential (mV)' if label_yaxis else '',
xlim=xlim_iv,
ylim=ylim_iv,
show_xticklabels=label_xaxis,
show_yticklabels=label_yaxis,
font_size=font_size,
linewidths=[linewidth for s in xs],
bottom_left_spines_only=bottom_left_spines_only,
grid=grid,
show_plot_already=False,
save_figure_to=save_iv_figure_to,
title_above_plot=title_above_plot,
verbose=verbose)
if save_iv_data_to:
with open(save_iv_data_to, 'w') as iv_file:
for i in range(len(stims_pA)):
iv_file.write("%s\t%s\n" % (stims_pA[i], vs[i]))
if show_plot_already:
from matplotlib import pyplot as plt
plt.show()
if return_axes:
return traces_ax, if_ax, iv_ax
return if_results
def generate_current_vs_frequency_curve(nml2_file,
cell_id,
start_amp_nA,
end_amp_nA,
step_nA,
analysis_duration,
analysis_delay,
dt=0.05,
temperature="32degC",
spike_threshold_mV=0.,
plot_voltage_traces=False,
plot_if=True,
plot_iv=False,
xlim_if=None,
ylim_if=None,
xlim_iv=None,
ylim_iv=None,
show_plot_already=True,
save_if_figure_to=None,
save_iv_figure_to=None,
simulator="jNeuroML",
include_included=True):
from pyelectro.analysis import max_min
from pyelectro.analysis import mean_spike_frequency
import numpy as np
print_comment_v(
"Generating FI curve for cell %s in %s using %s (%snA->%snA; %snA steps)"
% (cell_id, nml2_file, simulator, start_amp_nA, end_amp_nA, step_nA))
sim_id = 'iv_%s' % cell_id
duration = analysis_duration + analysis_delay
ls = LEMSSimulation(sim_id, duration, dt)
ls.include_neuroml2_file(nml2_file, include_included=include_included)
stims = []
amp = start_amp_nA
while amp <= end_amp_nA:
stims.append(amp)
amp += step_nA
number_cells = len(stims)
pop = nml.Population(id="population_of_%s" % cell_id,
component=cell_id,
size=number_cells)
# create network and add populations
net_id = "network_of_%s" % cell_id
net = nml.Network(id=net_id,
type="networkWithTemperature",
temperature=temperature)
ls.assign_simulation_target(net_id)
net_doc = nml.NeuroMLDocument(id=net.id)
net_doc.networks.append(net)
net_doc.includes.append(nml.IncludeType(nml2_file))
net.populations.append(pop)
for i in range(number_cells):
stim_amp = "%snA" % stims[i]
input_id = ("input_%s" % stim_amp).replace('.',
'_').replace('-', 'min')
pg = nml.PulseGenerator(id=input_id,
delay="0ms",
duration="%sms" % duration,
amplitude=stim_amp)
net_doc.pulse_generators.append(pg)
# Add these to cells
input_list = nml.InputList(id=input_id,
component=pg.id,
populations=pop.id)
input = nml.Input(id='0',
target="../%s[%i]" % (pop.id, i),
destination="synapses")
input_list.input.append(input)
net.input_lists.append(input_list)
net_file_name = '%s.net.nml' % sim_id
pynml.write_neuroml2_file(net_doc, net_file_name)
ls.include_neuroml2_file(net_file_name)
disp0 = 'Voltage_display'
ls.create_display(disp0, "Voltages", "-90", "50")
of0 = 'Volts_file'
ls.create_output_file(of0, "%s.v.dat" % sim_id)
for i in range(number_cells):
ref = "v_cell%i" % i
quantity = "%s[%i]/v" % (pop.id, i)
ls.add_line_to_display(disp0, ref, quantity, "1mV",
pynml.get_next_hex_color())
ls.add_column_to_output_file(of0, ref, quantity)
lems_file_name = ls.save_to_file()
if simulator == "jNeuroML":
results = pynml.run_lems_with_jneuroml(lems_file_name,
nogui=True,
load_saved_data=True,
plot=plot_voltage_traces,
show_plot_already=False)
elif simulator == "jNeuroML_NEURON":
results = pynml.run_lems_with_jneuroml_neuron(lems_file_name,
nogui=True,
load_saved_data=True,
plot=plot_voltage_traces,
show_plot_already=False)
#print(results.keys())
if_results = {}
iv_results = {}
for i in range(number_cells):
t = np.array(results['t']) * 1000
v = np.array(results["%s[%i]/v" % (pop.id, i)]) * 1000
mm = max_min(v, t, delta=0, peak_threshold=spike_threshold_mV)
spike_times = mm['maxima_times']
freq = 0
if len(spike_times) > 2:
count = 0
for s in spike_times:
if s >= analysis_delay and s < (analysis_duration +
analysis_delay):
count += 1
freq = 1000 * count / float(analysis_duration)
mean_freq = mean_spike_frequency(spike_times)
# print("--- %s nA, spike times: %s, mean_spike_frequency: %f, freq (%fms -> %fms): %f"%(stims[i],spike_times, mean_freq, analysis_delay, analysis_duration+analysis_delay, freq))
if_results[stims[i]] = freq
if freq == 0:
iv_results[stims[i]] = v[-1]
if plot_if:
stims = sorted(if_results.keys())
stims_pA = [ii * 1000 for ii in stims]
freqs = [if_results[s] for s in stims]
pynml.generate_plot([stims_pA], [freqs],
"Frequency versus injected current for: %s" %
nml2_file,
colors=['k'],
linestyles=['-'],
markers=['o'],
xaxis='Input current (pA)',
yaxis='Firing frequency (Hz)',
xlim=xlim_if,
ylim=ylim_if,
grid=True,
show_plot_already=False,
save_figure_to=save_if_figure_to)
if plot_iv:
stims = sorted(iv_results.keys())
stims_pA = [ii * 1000 for ii in sorted(iv_results.keys())]
vs = [iv_results[s] for s in stims]
pynml.generate_plot(
[stims_pA], [vs],
"Final membrane potential versus injected current for: %s" %
nml2_file,
colors=['k'],
linestyles=['-'],
markers=['o'],
xaxis='Input current (pA)',
yaxis='Membrane potential (mV)',
xlim=xlim_iv,
ylim=ylim_iv,
grid=True,
show_plot_already=False,
save_figure_to=save_iv_figure_to)
if show_plot_already:
from matplotlib import pyplot as plt
plt.show()
return if_results
def generate_current_vs_frequency_curve(
nml2_file,
cell_id,
start_amp_nA,
end_amp_nA,
step_nA,
analysis_duration,
analysis_delay,
dt=0.05,
temperature="32degC",
spike_threshold_mV=0.0,
plot_voltage_traces=False,
plot_if=True,
simulator="jNeuroML",
):
from pyelectro.analysis import max_min
from pyelectro.analysis import mean_spike_frequency
import numpy as np
sim_id = "iv_%s" % cell_id
duration = analysis_duration + analysis_delay
ls = LEMSSimulation(sim_id, duration, dt)
ls.include_neuroml2_file(nml2_file)
stims = []
amp = start_amp_nA
while amp <= end_amp_nA:
stims.append(amp)
amp += step_nA
number_cells = len(stims)
pop = nml.Population(id="population_of_%s" % cell_id, component=cell_id, size=number_cells)
# create network and add populations
net_id = "network_of_%s" % cell_id
net = nml.Network(id=net_id, type="networkWithTemperature", temperature=temperature)
ls.assign_simulation_target(net_id)
net_doc = nml.NeuroMLDocument(id=net.id)
net_doc.networks.append(net)
net.populations.append(pop)
for i in range(number_cells):
stim_amp = "%snA" % stims[i]
input_id = ("input_%s" % stim_amp).replace(".", "_")
pg = nml.PulseGenerator(id=input_id, delay="0ms", duration="%sms" % duration, amplitude=stim_amp)
net_doc.pulse_generators.append(pg)
# Add these to cells
input_list = nml.InputList(id=input_id, component=pg.id, populations=pop.id)
input = nml.Input(id="0", target="../%s[%i]" % (pop.id, i), destination="synapses")
input_list.input.append(input)
net.input_lists.append(input_list)
net_file_name = "%s.net.nml" % sim_id
pynml.write_neuroml2_file(net_doc, net_file_name)
ls.include_neuroml2_file(net_file_name)
disp0 = "Voltage_display"
ls.create_display(disp0, "Voltages", "-90", "50")
of0 = "Volts_file"
ls.create_output_file(of0, "%s.v.dat" % sim_id)
for i in range(number_cells):
ref = "v_cell%i" % i
quantity = "%s[%i]/v" % (pop.id, i)
ls.add_line_to_display(disp0, ref, quantity, "1mV", pynml.get_next_hex_color())
ls.add_column_to_output_file(of0, ref, quantity)
lems_file_name = ls.save_to_file()
if simulator == "jNeuroML":
results = pynml.run_lems_with_jneuroml(
lems_file_name, nogui=True, load_saved_data=True, plot=plot_voltage_traces
)
elif simulator == "jNeuroML_NEURON":
results = pynml.run_lems_with_jneuroml_neuron(
lems_file_name, nogui=True, load_saved_data=True, plot=plot_voltage_traces
)
# print(results.keys())
if_results = {}
for i in range(number_cells):
t = np.array(results["t"]) * 1000
v = np.array(results["%s[%i]/v" % (pop.id, i)]) * 1000
mm = max_min(v, t, delta=0, peak_threshold=spike_threshold_mV)
spike_times = mm["maxima_times"]
freq = 0
if len(spike_times) > 2:
count = 0
for s in spike_times:
if s >= analysis_delay and s < (analysis_duration + analysis_delay):
count += 1
freq = 1000 * count / float(analysis_duration)
mean_freq = mean_spike_frequency(spike_times)
# print("--- %s nA, spike times: %s, mean_spike_frequency: %f, freq (%fms -> %fms): %f"%(stims[i],spike_times, mean_freq, analysis_delay, analysis_duration+analysis_delay, freq))
if_results[stims[i]] = freq
if plot_if:
from matplotlib import pyplot as plt
plt.xlabel("Input current (nA)")
plt.ylabel("Firing frequency (Hz)")
plt.grid("on")
stims = sorted(if_results.keys())
freqs = []
for s in stims:
freqs.append(if_results[s])
plt.plot(stims, freqs, "o")
plt.show()
return if_results
def generate_current_vs_frequency_curve(nml2_file,
cell_id,
start_amp_nA,
end_amp_nA,
step_nA,
analysis_duration,
analysis_delay,
dt = 0.05,
temperature = "32degC",
spike_threshold_mV=0.,
plot_voltage_traces=False,
plot_if=True,
plot_iv=False,
xlim_if = None,
ylim_if = None,
xlim_iv = None,
ylim_iv = None,
show_plot_already=True,
save_if_figure_to=None,
save_iv_figure_to=None,
simulator="jNeuroML",
include_included=True):
from pyelectro.analysis import max_min
from pyelectro.analysis import mean_spike_frequency
import numpy as np
print_comment_v("Generating FI curve for cell %s in %s using %s (%snA->%snA; %snA steps)"%
(cell_id, nml2_file, simulator, start_amp_nA, end_amp_nA, step_nA))
sim_id = 'iv_%s'%cell_id
duration = analysis_duration+analysis_delay
ls = LEMSSimulation(sim_id, duration, dt)
ls.include_neuroml2_file(nml2_file, include_included=include_included)
stims = []
amp = start_amp_nA
while amp<=end_amp_nA :
stims.append(amp)
amp+=step_nA
number_cells = len(stims)
pop = nml.Population(id="population_of_%s"%cell_id,
component=cell_id,
size=number_cells)
# create network and add populations
net_id = "network_of_%s"%cell_id
net = nml.Network(id=net_id, type="networkWithTemperature", temperature=temperature)
ls.assign_simulation_target(net_id)
net_doc = nml.NeuroMLDocument(id=net.id)
net_doc.networks.append(net)
net_doc.includes.append(nml.IncludeType(nml2_file))
net.populations.append(pop)
for i in range(number_cells):
stim_amp = "%snA"%stims[i]
input_id = ("input_%s"%stim_amp).replace('.','_').replace('-','min')
pg = nml.PulseGenerator(id=input_id,
delay="0ms",
duration="%sms"%duration,
amplitude=stim_amp)
net_doc.pulse_generators.append(pg)
# Add these to cells
input_list = nml.InputList(id=input_id,
component=pg.id,
populations=pop.id)
input = nml.Input(id='0',
target="../%s[%i]"%(pop.id, i),
destination="synapses")
input_list.input.append(input)
net.input_lists.append(input_list)
net_file_name = '%s.net.nml'%sim_id
pynml.write_neuroml2_file(net_doc, net_file_name)
ls.include_neuroml2_file(net_file_name)
disp0 = 'Voltage_display'
ls.create_display(disp0,"Voltages", "-90", "50")
of0 = 'Volts_file'
ls.create_output_file(of0, "%s.v.dat"%sim_id)
for i in range(number_cells):
ref = "v_cell%i"%i
quantity = "%s[%i]/v"%(pop.id, i)
ls.add_line_to_display(disp0, ref, quantity, "1mV", pynml.get_next_hex_color())
ls.add_column_to_output_file(of0, ref, quantity)
lems_file_name = ls.save_to_file()
if simulator == "jNeuroML":
results = pynml.run_lems_with_jneuroml(lems_file_name,
nogui=True,
load_saved_data=True,
plot=plot_voltage_traces,
show_plot_already=False)
elif simulator == "jNeuroML_NEURON":
results = pynml.run_lems_with_jneuroml_neuron(lems_file_name,
nogui=True,
load_saved_data=True,
plot=plot_voltage_traces,
show_plot_already=False)
#print(results.keys())
if_results = {}
iv_results = {}
for i in range(number_cells):
t = np.array(results['t'])*1000
v = np.array(results["%s[%i]/v"%(pop.id, i)])*1000
mm = max_min(v, t, delta=0, peak_threshold=spike_threshold_mV)
spike_times = mm['maxima_times']
freq = 0
if len(spike_times) > 2:
count = 0
for s in spike_times:
if s >= analysis_delay and s < (analysis_duration+analysis_delay):
count+=1
freq = 1000 * count/float(analysis_duration)
mean_freq = mean_spike_frequency(spike_times)
# print("--- %s nA, spike times: %s, mean_spike_frequency: %f, freq (%fms -> %fms): %f"%(stims[i],spike_times, mean_freq, analysis_delay, analysis_duration+analysis_delay, freq))
if_results[stims[i]] = freq
if freq == 0:
iv_results[stims[i]] = v[-1]
if plot_if:
stims = sorted(if_results.keys())
stims_pA = [ii*1000 for ii in stims]
freqs = [if_results[s] for s in stims]
pynml.generate_plot([stims_pA],
[freqs],
"Frequency versus injected current for: %s"%nml2_file,
colors = ['k'],
linestyles=['-'],
markers=['o'],
xaxis = 'Input current (pA)',
yaxis = 'Firing frequency (Hz)',
xlim = xlim_if,
ylim = ylim_if,
grid = True,
show_plot_already=False,
save_figure_to = save_if_figure_to)
if plot_iv:
stims = sorted(iv_results.keys())
stims_pA = [ii*1000 for ii in sorted(iv_results.keys())]
vs = [iv_results[s] for s in stims]
pynml.generate_plot([stims_pA],
[vs],
"Final membrane potential versus injected current for: %s"%nml2_file,
colors = ['k'],
linestyles=['-'],
markers=['o'],
xaxis = 'Input current (pA)',
yaxis = 'Membrane potential (mV)',
xlim = xlim_iv,
ylim = ylim_iv,
grid = True,
show_plot_already=False,
save_figure_to = save_iv_figure_to)
if show_plot_already:
from matplotlib import pyplot as plt
plt.show()
return if_results
def generate_current_vs_frequency_curve(nml2_file,
cell_id,
start_amp_nA = -0.1,
end_amp_nA = 0.1,
step_nA = 0.01,
custom_amps_nA = [],
analysis_duration = 1000,
analysis_delay = 0,
pre_zero_pulse = 0,
post_zero_pulse = 0,
dt = 0.05,
temperature = "32degC",
spike_threshold_mV = 0.,
plot_voltage_traces = False,
plot_if = True,
plot_iv = False,
xlim_if = None,
ylim_if = None,
xlim_iv = None,
ylim_iv = None,
label_xaxis = True,
label_yaxis = True,
show_volts_label = True,
grid = True,
font_size = 12,
if_iv_color = 'k',
linewidth = 1,
bottom_left_spines_only = False,
show_plot_already = True,
save_voltage_traces_to = None,
save_if_figure_to = None,
save_iv_figure_to = None,
save_if_data_to = None,
save_iv_data_to = None,
simulator = "jNeuroML",
num_processors = 1,
include_included = True,
title_above_plot = False,
return_axes = False,
verbose = False):
print_comment("Running generate_current_vs_frequency_curve() on %s (%s)"%(nml2_file,os.path.abspath(nml2_file)), verbose)
from pyelectro.analysis import max_min
from pyelectro.analysis import mean_spike_frequency
import numpy as np
traces_ax = None
if_ax = None
iv_ax = None
sim_id = 'iv_%s'%cell_id
total_duration = pre_zero_pulse+analysis_duration+analysis_delay+post_zero_pulse
pulse_duration = analysis_duration+analysis_delay
end_stim = pre_zero_pulse+analysis_duration+analysis_delay
ls = LEMSSimulation(sim_id, total_duration, dt)
ls.include_neuroml2_file(nml2_file, include_included=include_included)
stims = []
if len(custom_amps_nA)>0:
stims = [float(a) for a in custom_amps_nA]
stim_info = ['%snA'%float(a) for a in custom_amps_nA]
else:
amp = start_amp_nA
while amp<=end_amp_nA :
stims.append(amp)
amp+=step_nA
stim_info = '(%snA->%snA; %s steps of %snA; %sms)'%(start_amp_nA, end_amp_nA, len(stims), step_nA, total_duration)
print_comment_v("Generating an IF curve for cell %s in %s using %s %s"%
(cell_id, nml2_file, simulator, stim_info))
number_cells = len(stims)
pop = nml.Population(id="population_of_%s"%cell_id,
component=cell_id,
size=number_cells)
# create network and add populations
net_id = "network_of_%s"%cell_id
net = nml.Network(id=net_id, type="networkWithTemperature", temperature=temperature)
ls.assign_simulation_target(net_id)
net_doc = nml.NeuroMLDocument(id=net.id)
net_doc.networks.append(net)
net_doc.includes.append(nml.IncludeType(nml2_file))
net.populations.append(pop)
for i in range(number_cells):
stim_amp = "%snA"%stims[i]
input_id = ("input_%s"%stim_amp).replace('.','_').replace('-','min')
pg = nml.PulseGenerator(id=input_id,
delay="%sms"%pre_zero_pulse,
duration="%sms"%pulse_duration,
amplitude=stim_amp)
net_doc.pulse_generators.append(pg)
# Add these to cells
input_list = nml.InputList(id=input_id,
component=pg.id,
populations=pop.id)
input = nml.Input(id='0',
target="../%s[%i]"%(pop.id, i),
destination="synapses")
input_list.input.append(input)
net.input_lists.append(input_list)
net_file_name = '%s.net.nml'%sim_id
pynml.write_neuroml2_file(net_doc, net_file_name)
ls.include_neuroml2_file(net_file_name)
disp0 = 'Voltage_display'
ls.create_display(disp0,"Voltages", "-90", "50")
of0 = 'Volts_file'
ls.create_output_file(of0, "%s.v.dat"%sim_id)
for i in range(number_cells):
ref = "v_cell%i"%i
quantity = "%s[%i]/v"%(pop.id, i)
ls.add_line_to_display(disp0, ref, quantity, "1mV", pynml.get_next_hex_color())
ls.add_column_to_output_file(of0, ref, quantity)
lems_file_name = ls.save_to_file()
print_comment("Written LEMS file %s (%s)"%(lems_file_name,os.path.abspath(lems_file_name)), verbose)
if simulator == "jNeuroML":
results = pynml.run_lems_with_jneuroml(lems_file_name,
nogui=True,
load_saved_data=True,
plot=False,
show_plot_already=False,
verbose=verbose)
elif simulator == "jNeuroML_NEURON":
results = pynml.run_lems_with_jneuroml_neuron(lems_file_name,
nogui=True,
load_saved_data=True,
plot=False,
show_plot_already=False,
verbose=verbose)
elif simulator == "jNeuroML_NetPyNE":
results = pynml.run_lems_with_jneuroml_netpyne(lems_file_name,
nogui=True,
load_saved_data=True,
plot=False,
show_plot_already=False,
num_processors = num_processors,
verbose=verbose)
else:
raise Exception("Sorry, cannot yet run current vs frequency analysis using simulator %s"%simulator)
print_comment("Completed run in simulator %s (results: %s)"%(simulator,results.keys()), verbose)
#print(results.keys())
times_results = []
volts_results = []
volts_labels = []
if_results = {}
iv_results = {}
for i in range(number_cells):
t = np.array(results['t'])*1000
v = np.array(results["%s[%i]/v"%(pop.id, i)])*1000
if plot_voltage_traces:
times_results.append(t)
volts_results.append(v)
volts_labels.append("%s nA"%stims[i])
mm = max_min(v, t, delta=0, peak_threshold=spike_threshold_mV)
spike_times = mm['maxima_times']
freq = 0
if len(spike_times) > 2:
count = 0
for s in spike_times:
if s >= pre_zero_pulse + analysis_delay and s < (pre_zero_pulse + analysis_duration+analysis_delay):
count+=1
freq = 1000 * count/float(analysis_duration)
mean_freq = mean_spike_frequency(spike_times)
#print("--- %s nA, spike times: %s, mean_spike_frequency: %f, freq (%fms -> %fms): %f"%(stims[i],spike_times, mean_freq, analysis_delay, analysis_duration+analysis_delay, freq))
if_results[stims[i]] = freq
if freq == 0:
if post_zero_pulse==0:
iv_results[stims[i]] = v[-1]
else:
v_end = None
for j in range(len(t)):
if v_end==None and t[j]>=end_stim:
v_end = v[j]
iv_results[stims[i]] = v_end
if plot_voltage_traces:
traces_ax = pynml.generate_plot(times_results,
volts_results,
"Membrane potential traces for: %s"%nml2_file,
xaxis = 'Time (ms)' if label_xaxis else ' ',
yaxis = 'Membrane potential (mV)' if label_yaxis else '',
xlim = [total_duration*-0.05,total_duration*1.05],
show_xticklabels = label_xaxis,
font_size = font_size,
bottom_left_spines_only = bottom_left_spines_only,
grid = False,
labels = volts_labels if show_volts_label else [],
show_plot_already=False,
save_figure_to = save_voltage_traces_to,
title_above_plot = title_above_plot,
verbose=verbose)
if plot_if:
stims = sorted(if_results.keys())
stims_pA = [ii*1000 for ii in stims]
freqs = [if_results[s] for s in stims]
if_ax = pynml.generate_plot([stims_pA],
[freqs],
"Firing frequency versus injected current for: %s"%nml2_file,
colors = [if_iv_color],
linestyles=['-'],
markers=['o'],
linewidths = [linewidth],
xaxis = 'Input current (pA)' if label_xaxis else ' ',
yaxis = 'Firing frequency (Hz)' if label_yaxis else '',
xlim = xlim_if,
ylim = ylim_if,
show_xticklabels = label_xaxis,
show_yticklabels = label_yaxis,
font_size = font_size,
bottom_left_spines_only = bottom_left_spines_only,
grid = grid,
show_plot_already=False,
save_figure_to = save_if_figure_to,
title_above_plot = title_above_plot,
verbose=verbose)
if save_if_data_to:
with open(save_if_data_to,'w') as if_file:
for i in range(len(stims_pA)):
if_file.write("%s\t%s\n"%(stims_pA[i],freqs[i]))
if plot_iv:
stims = sorted(iv_results.keys())
stims_pA = [ii*1000 for ii in sorted(iv_results.keys())]
vs = [iv_results[s] for s in stims]
xs = []
ys = []
xs.append([])
ys.append([])
for si in range(len(stims)):
stim = stims[si]
if len(custom_amps_nA)==0 and si>1 and (stims[si]-stims[si-1])>step_nA*1.01:
xs.append([])
ys.append([])
xs[-1].append(stim*1000)
ys[-1].append(iv_results[stim])
iv_ax = pynml.generate_plot(xs,
ys,
"V at %sms versus I below threshold for: %s"%(end_stim,nml2_file),
colors = [if_iv_color for s in xs],
linestyles=['-' for s in xs],
markers=['o' for s in xs],
xaxis = 'Input current (pA)' if label_xaxis else '',
yaxis = 'Membrane potential (mV)' if label_yaxis else '',
xlim = xlim_iv,
ylim = ylim_iv,
show_xticklabels = label_xaxis,
show_yticklabels = label_yaxis,
font_size = font_size,
linewidths = [linewidth for s in xs],
bottom_left_spines_only = bottom_left_spines_only,
grid = grid,
show_plot_already=False,
save_figure_to = save_iv_figure_to,
title_above_plot = title_above_plot,
verbose=verbose)
if save_iv_data_to:
with open(save_iv_data_to,'w') as iv_file:
for i in range(len(stims_pA)):
iv_file.write("%s\t%s\n"%(stims_pA[i],vs[i]))
if show_plot_already:
from matplotlib import pyplot as plt
plt.show()
if return_axes:
return traces_ax, if_ax, iv_ax
return if_results