def _add_comp(self, parent, level_no, dia=15e-6, length=40e-6):
SpinyStellate.comp_cnt += 1
comp = MyCompartment('comp_' + str(SpinyStellate.comp_cnt), parent)
self.level[level_no].add(comp)
comp.diameter = dia
comp.length = length
return comp
def _add_comp(self, parent, level_no, dia=15e-6, length=40e-6):
SpinyStellate.comp_cnt += 1
comp = MyCompartment('comp_' + str(SpinyStellate.comp_cnt), parent)
self.level[level_no].add(comp)
comp.diameter = dia
comp.length = length
return comp
def _create_dtree(self, name_prefix, parent, tree, level, default_length=40e-6, radius_dict=radius):
"""Create the dendritic tree structure with compartments.
Returns the root."""
if not tree:
return
comp = MyCompartment(name_prefix + str(tree[0]), parent)
self.comp.append(comp)
comp.length = default_length
comp.diameter = radius_dict[tree[0]] * 2e-6
self.levels[level].add(comp)
self.dendrites.add(comp)
for subtree in tree[1:]:
self._create_dtree(name_prefix, comp, subtree, level+1, default_length, radius_dict)
def _create_cell(self):
"""Create the compartmental structure and set the geometry."""
if not hasattr(self, 'levels'):
self.levels = defaultdict(set)
comp = MyCompartment('soma', self)
self.comp.append(comp)
comp.length = 20e-6
comp.diameter = 7.5 * 2e-6
self.soma = comp
self.levels[1].add(comp)
t1 = datetime.now()
for i in range(4):
self. _create_dtree('d_' + str(i) + '_', comp, SpinyStellate.dendritic_tree, 2)
t2 = datetime.now()
delta = t2 - t1
print 'create_dtree took: ', delta.seconds + 1e-6 * delta.microseconds
self._create_axon()
def _create_cell(self):
"""Create the compartmental structure and set the geometry."""
if not hasattr(self, 'levels'):
self.levels = defaultdict(set)
comp = MyCompartment('soma', self)
self.comp.append(comp)
comp.length = 20e-6
comp.diameter = 7.5 * 2e-6
self.soma = comp
self.levels[1].add(comp)
t1 = datetime.now()
for i in range(4):
self._create_dtree('d_' + str(i) + '_', comp,
SpinyStellate.dendritic_tree, 2)
t2 = datetime.now()
delta = t2 - t1
print 'create_dtree took: ', delta.seconds + 1e-6 * delta.microseconds
self._create_axon()
def get_comp(cell, index):
"""Return a wrapper over compartment specified by index. None if
no such compartment exists."""
if index <= 0: return None
path = cell.path + '/comp_' + str(index)
# print 'get_comp', path
if config.context.exists(path):
return MyCompartment(path)
else:
raise Exception('Cell: %s , index: %d - no such compartment.' %
(cell.path, index))
def _create_dtree(self,
name_prefix,
parent,
tree,
level,
default_length=40e-6,
radius_dict=radius):
"""Create the dendritic tree structure with compartments.
Returns the root."""
if not tree:
return
comp = MyCompartment(name_prefix + str(tree[0]), parent)
self.comp.append(comp)
comp.length = default_length
comp.diameter = radius_dict[tree[0]] * 2e-6
self.levels[level].add(comp)
self.dendrites.add(comp)
for subtree in tree[1:]:
self._create_dtree(name_prefix, comp, subtree, level + 1,
default_length, radius_dict)
def _create_axon(self):
"""Create the axonal structure.
It is like:
a_0_0 -- a_0_1
/
/
soma -- a_0 -- a_1
\
\
a_1_0 -- a_1_1
"""
self.axon.append(MyCompartment('a_0', self.soma))
self.axon[-1].diameter = 0.7 * 2e-6
self.axon.append(MyCompartment('a_1', self.axon[0]))
self.axon[-1].diameter = 0.6 * 2e-6
self.axon.append(MyCompartment('a_0_0', self.axon[1]))
self.axon.append(MyCompartment('a_1_0', self.axon[1]))
self.axon.append(MyCompartment('a_0_1', self.axon[2]))
self.axon.append(MyCompartment('a_1_1', self.axon[3]))
for comp in self.axon[2:]:
comp.diameter = 0.5 * 2e-6
for comp in self.axon:
self.levels[0].add(comp)
comp.length = 50e-6
self.comp += self.axon
def test_twocomp(sim):
"""Pass a simulation object as parameter"""
spine_area_mult = 2.0
cell = moose.Cell('mycell', sim.model)
soma = MyCompartment('soma', cell)
soma.length = 20e-6
soma.diameter = 2 * 7.5e-6
soma.Em = -65e-3
soma.initVm = -65e-3
soma.setSpecificCm(9e-3)
soma.setSpecificRm(5.0)
soma.setSpecificRa(2.5)
dend = MyCompartment('dend', cell)
dend.length = 40e-6
dend.diameter = 2 * 1.06e-6
dend.Em = -65e-3
dend.initVm = -65e-3
dend.setSpecificCm(9e-3 * spine_area_mult)
dend.setSpecificRm(5.0 / spine_area_mult)
dend.setSpecificRa(2.5)
soma.traubConnect(dend)
vm_table = dend.insertRecorder("Vm1", "Vm", sim.data)
dend.insertPulseGen("pulsegen1", sim.model, firstLevel=3e-10, firstDelay=20e-3, firstWidth=100e-3)
# sim.schedule()
# sim.run(100e-3)
# sim.dump_data("data")
return cell
from simulation import Simulation
#import timeit
from datetime import datetime
import pylab
if __name__ == '__main__':
sim = Simulation()
t1 = datetime.now()
s = SpinyStellate('ss', sim.model)
t2 = datetime.now()
delta_t = t2 - t1
print '### TIME SPENT IN CELL CREATION: ', delta_t.seconds + delta_t.microseconds * 1e-6
# pymoose.printtree(s.soma)
dump_cell(s, 'ss.p')
path = s.soma.path + '/a_0/a_1/a_0_0/a_0_1'
a2 = MyCompartment(path)
vm_table = s.soma.insertRecorder('Vm_spinstell', 'Vm', sim.data)
s.soma.insertPulseGen('pulsegen',
sim.model,
firstLevel=3e-10,
firstDelay=20e-3,
firstWidth=100e-3)
sim.schedule()
t1 = datetime.now()
sim.run(100e-3)
t2 = datetime.now()
delta_t = t2 - t1
print '#### TIME TO SIMULATE:', delta_t.seconds + delta_t.microseconds * 1e-6
sim.dump_data('data')
pylab.plot(vm_table)
pylab.show()
#
# Code:
from subprocess import call
call(['/home/subha/neuron/nrn/x86_64/bin/nrngui', 'test_suppyrRS_1comp.hoc'], cwd='../nrn')
from datetime import datetime
import moose
import config
from cell import *
from capool import CaPool
from compartment import MyCompartment
from simulation import Simulation
sim = Simulation()
cell = moose.Cell('cell', sim.model)
soma = MyCompartment('soma', cell)
soma.diameter = 16e-6
soma.length = 15e-6
soma.Em = -70e-3
soma.initVm = -65e-3
soma.setSpecificRm(5.0)
soma.setSpecificRa(2.5)
soma.setSpecificCm(9e-3)
soma.insertChannel('NaF', specificGbar=1875.0, Ek=50e-3, shift=-3.5e-3)
soma.insertChannel('CaL', specificGbar=10.0, Ek=125e-3)
soma.insertCaPool(2600000.0, 100e-3)
vmTable = soma.insertRecorder('Vm', 'Vm', sim.data)
caTable = moose.Table('ca', sim.data)
caTable.stepMode = 3
soma.ca_pool.connect('Ca', caTable, 'inputRequest')
sim.schedule()
channel = moose.HHChannel(channel_class, lib)
else:
class_obj = eval(channel_class)
if channel_class == 'NaF2':
channel = class_obj(channel_class, lib, shift=-2.5e-3)
else:
channel = class_obj(channel_class, lib)
channel.X = 0.0
channel_lib[channel_class] = channel
channels_inited = True
return channel_lib
if __name__ == '__main__':
sim = Simulation('test_ss_soma')
soma = MyCompartment('soma', sim.model)
soma.length = 20e-6
soma.diameter = 2e-6 * 7.5
soma.setSpecificCm(9e-3)
soma.setSpecificRm(5.0)
soma.setSpecificRa(1.0)
soma.Em = -65e-3
soma.initVm = -65e-3
channel_lib = init_channels()
gk = {}
for channel, density in channel_density.items():
chan = channel_lib[channel]
new_chan = moose.HHChannel(chan, chan.name, soma)
chan = soma.insertChannel(new_chan, density)
chan.X = 0.0
gk[channel] = moose.Table(channel, sim.data)
channel = moose.HHChannel(channel_class, lib)
else:
class_obj = eval(channel_class)
if channel_class == 'NaF2':
channel = class_obj(channel_class, lib, shift=-2.5e-3)
else:
channel = class_obj(channel_class, lib)
channel.X = 0.0
channel_lib[channel_class] = channel
channels_inited = True
return channel_lib
if __name__ == '__main__':
sim = Simulation('test_ss_soma')
soma = MyCompartment('soma', sim.model)
soma.length = 20e-6
soma.diameter = 2e-6 * 7.5
soma.setSpecificCm(9e-3)
soma.setSpecificRm(5.0)
soma.setSpecificRa(1.0)
soma.Em = -65e-3
soma.initVm = -65e-3
channel_lib = init_channels()
gk = {}
chandict = {}
for channel, density in channel_density.items():
chan = channel_lib[channel]
new_chan = moose.HHChannel(chan, chan.name, soma)
chan = soma.insertChannel(new_chan, density)
chan.X = 0.0
if config.context.exists('/library/' + channel_class):
channel = moose.HHChannel(channel_class, lib)
else:
class_obj = eval(channel_class)
if channel_class == 'NaF2':
channel = class_obj(channel_class, lib, shift=-2.5e-3)
else:
channel = class_obj(channel_class, lib)
channel.X = 0.0
channel_lib[channel_class] = channel
channels_inited = True
return channel_lib
if __name__ == '__main__':
sim = Simulation('test_ss_soma')
soma = MyCompartment('soma', sim.model)
soma.length = 20e-6
soma.diameter = 2e-6 * 7.5
soma.setSpecificCm(9e-3)
soma.setSpecificRm(5.0)
soma.setSpecificRa(1.0)
soma.Em = -65e-3
soma.initVm = -65e-3
channel_lib = init_channels()
gk = {}
for channel, density in channel_density.items():
chan = channel_lib[channel]
new_chan = moose.HHChannel(chan, chan.name, soma)
chan = soma.insertChannel(new_chan, density)
chan.X = 0.0
gk[channel] = moose.Table(channel, sim.data)