Secure your code as it's written. Use Snyk Code to scan source code in minutes - no build needed - and fix issues immediately.
def test():
from blenderneuron.quick import bn
with Blender(keep=False):
from neuron import h
h.load_file(test_hoc_file)
tc1 = h.TestCell()
tc2 = h.TestCell()
ic = h.IClamp(0.5, sec=tc1.soma)
ic.delay = 1
ic.dur = 3
ic.amp = 0.5
bn.prepare_for_collection()
bn.groups["all"]["3d_data"]["interaction_level"] = "Cell"
bn.groups["all"]["3d_data"]["color_level"] = "Segment"
h.run()
bn.to_blender()
self.assertTrue(bn.run_command("return_value = 'TestCell[0]' in bpy.data.objects"))
self.assertTrue(bn.run_command("return_value = 'TestCell[1]' in bpy.data.objects"))
self.assertTrue(bn.run_command("return_value = 'TestCell[0].soma[0]' in bpy.data.materials"))
def test():
from blenderneuron.quick import bn
with Blender(keep=False):
from neuron import h
h.load_file(test_hoc_file)
tc1 = h.TestCell()
tc2 = h.TestCell()
ic = h.IClamp(0.5, sec=tc1.soma)
ic.delay = 1
ic.dur = 3
ic.amp = 0.5
bn.prepare_for_collection()
bn.groups["all"]["3d_data"]["interaction_level"] = "Cell"
bn.groups["all"]["3d_data"]["color_level"] = "Section"
h.run()
bn.to_blender()
self.assertTrue(bn.run_command("return_value = 'TestCell[0]' in bpy.data.objects"))
self.assertTrue(bn.run_command("return_value = 'TestCell[1]' in bpy.data.objects"))
self.assertTrue(bn.run_command("return_value = 'TestCell[0].soma' in bpy.data.materials"))
from neuron import h, gui
import sys
h('''create soma''')
h.soma.L=5.6419
h.soma.diam=5.6419
h.soma.insert("hh")
ic = h.IClamp(h.soma(.5))
ic.delay = .5
ic.dur = 0.1
ic.amp = 0.3
h.cvode.use_fast_imem(1)
h.cvode.cache_efficient(1)
v = h.Vector()
v.record(h.soma(.5)._ref_v, sec = h.soma)
i_mem = h.Vector()
i_mem.record(h.soma(.5)._ref_i_membrane_, sec = h.soma)
tv = h.Vector()
tv.record(h._ref_t, sec=h.soma)
h.run()
vstd = v.cl()
tvstd = tv.cl()
Evaluate a neuron model with parameters e_pas and g_pas, extracts
features from resulting traces and returns a tuple with
abs(voltage_base-target_voltage1) and
abs(steady_state_voltage-target_voltage2)
"""
neuron.h.v_init = target_voltage1
soma = neuron.h.Section()
soma.insert('pas')
soma.g_pas = individual[0]
soma.e_pas = individual[1]
clamp = neuron.h.IClamp(0.5, sec=soma)
stim_start = 500
stim_end = 1000
clamp.amp = 1.0
clamp.delay = stim_start
clamp.dur = 100000
voltage = neuron.h.Vector()
voltage.record(soma(0.5)._ref_v)
time = neuron.h.Vector()
time.record(neuron.h._ref_t)
neuron.h.tstop = stim_end
neuron.h.run()
def inject_into(self, cell_list):
"""Inject this current source into some cells."""
for id in cell_list:
if id.local:
if not id.celltype.injectable:
raise TypeError("Can't inject current into a spike source.")
iclamp = h.IClamp(0.5, sec=id._cell.source_section)
iclamp.delay = 0.0
iclamp.dur = 1e12
iclamp.amp = 0.0
self._devices.append(iclamp)
self.amplitudes.play(iclamp._ref_amp, self.times)
def add_current_stim(self, delay):
self.stim = h.IClamp(self.dend(1.0))
self.stim.amp = 0.3 # input current in nA
self.stim.delay = delay # turn on after this time in ms
self.stim.dur = 1 # duration of 1 ms
def attach_current(self, cell):
self._stim = h.IClamp(cell.hobj.soma[0](0.5))
self._stim.delay = self._iclamp_del
self._stim.dur = self._iclamp_dur
self._stim.amp = self._iclamp_amp
return self._stim
import nrnVisio
controls = nrnVisio.Controls()
# Importing hoc interpreter
from neuron import h
# loading the model
# importing the interview so the GUI does not freeze
# Uncomment this if you use the interview GUI
import neuron.gui
# Load the script
h.load_file("demo.hoc")
## Insert an IClamp
st = h.IClamp(0.5, sec=h.soma)
st.amp = 0.25
st.delay = 3
st.dur = 40
controls.join() # Join the thread to have a clean exit.
controls = Controls()
# Importing hoc interpreter
from neuron import h
# loading the model
# importing the interview so the GUI does not freeze
# Uncomment this if you want to use also the interview GUI
#import neuron.gui
# Load the script
h.load_file("demo.hoc")
## Insert an IClamp
st = h.IClamp(0.5, sec=h.soma)
st.amp = 0.25
st.delay = 3
st.dur = 40