def createSpine(parentCompt, parentObj, index, frac, length, dia, theta):
"""Create spine of specified dimensions and index"""
RA = 1.0
RM = 1.0
CM = 0.01
shaftDia = dia / 5.0
sname = 'shaft' + str(index)
hname = 'head' + str(index)
shaft = moose.SymCompartment(parentObj.path + '/' + sname)
moose.connect(parentCompt, 'cylinder', shaft, 'proximalOnly', 'Single')
x = parentCompt.x0 + frac * (parentCompt.x - parentCompt.x0)
y = parentCompt.y0 + frac * (parentCompt.y - parentCompt.y0)
z = parentCompt.z0 + frac * (parentCompt.z - parentCompt.z0)
shaft.x0 = x
shaft.y0 = y
shaft.z0 = z
sy = y + length * math.cos(theta * math.pi / 180.0)
sz = z + length * math.sin(theta * math.pi / 180.0)
shaft.x = x
shaft.y = sy
shaft.z = sz
shaft.diameter = dia / 2.0
shaft.length = length
xa = math.pi * shaftDia * shaftDia / 4
circumference = math.pi * shaftDia
shaft.Ra = RA * length / xa
shaft.Rm = RM / (length * circumference)
shaft.Cm = CM * length * circumference
shaft.Em = EREST_ACT
shaft.initVm = EREST_ACT
head = moose.SymCompartment(parentObj.path + '/' + hname)
moose.connect(shaft, 'distal', head, 'proximal', 'Single')
head.x0 = x
head.y0 = sy
head.z0 = sz
hy = sy + length * math.cos(theta * math.pi / 180.0)
hz = sz + length * math.sin(theta * math.pi / 180.0)
head.x = x
head.y = hy
head.z = hz
head.diameter = dia
head.length = length
xa = math.pi * dia * dia / 4.0
circumference = math.pi * dia
head.Ra = RA * length / xa
head.Rm = RM / (length * circumference)
head.Cm = CM * length * circumference
head.Em = EREST_ACT
head.initVm = EREST_ACT
#print head.Rm, head.Ra, head.Cm, head.diameter, head.length
#print shaft.Rm, shaft.Ra, shaft.Cm, shaft.diameter, shaft.length
return head
def test_symcompartment():
"""This example demonstrates the use of SymCompartment class of MOOSE."""
model = moose.Neutral('model')
soma = moose.SymCompartment('%s/soma' % (model.path))
soma.Em = -60e-3
soma.Rm = 1000402560
soma.Cm = 2.375043912e-11
soma.Ra = 233957.7812
d1 = moose.SymCompartment('%s/d1' % (model.path))
d1.Rm = 397887392
d1.Cm = 2.261946489e-12
d1.Ra = 24867960
d2 = moose.SymCompartment('%s/d2' % (model.path))
d2.Rm = 2.877870285e+10
d2.Cm = 8.256105218e-13
d2.Ra = 20906072
moose.connect(d1, 'proximal', soma, 'distal')
moose.connect(d2, 'proximal', soma, 'distal')
moose.connect(d1, 'sibling', d2, 'sibling')
pg = moose.PulseGen('/model/pulse')
pg.delay[0] = 10e-3
pg.width[0] = 20e-3
pg.level[0] = 1e-6
pg.delay[1] = 1e9
moose.connect(pg, 'output', d1, 'injectMsg')
data = moose.Neutral('/data')
tab_soma = moose.Table('%s/soma_Vm' % (data.path))
tab_d1 = moose.Table('%s/d1_Vm' % (data.path))
tab_d2 = moose.Table('%s/d2_Vm' % (data.path))
moose.connect(tab_soma, 'requestOut', soma, 'getVm')
moose.connect(tab_d1, 'requestOut', d1, 'getVm')
moose.connect(tab_d2, 'requestOut', d2, 'getVm')
moose.setClock(0, simdt)
moose.setClock(1, simdt)
moose.setClock(2, simdt)
moose.useClock(
0, '/model/##[ISA=Compartment]', 'init'
) # This is allowed because SymCompartment is a subclass of Compartment
moose.useClock(1, '/model/##', 'process')
moose.useClock(2, '/data/##[ISA=Table]', 'process')
moose.reinit()
moose.start(simtime)
t = np.linspace(0, simtime, len(tab_soma.vector))
data_matrix = np.vstack((t, tab_soma.vector, tab_d1.vector, tab_d2.vector))
np.savetxt('symcompartment.txt', data_matrix.transpose())
pylab.plot(t, tab_soma.vector, label='Vm_soma')
pylab.plot(t, tab_d1.vector, label='Vm_d1')
pylab.plot(t, tab_d2.vector, label='Vm_d2')
pylab.show()
def test_symcompartment():
model = moose.Neutral('model')
soma = moose.SymCompartment('%s/soma' % (model.path))
soma.Em = -60e-3
soma.Rm = 1e9
soma.Cm = 1e-11
soma.Ra = 1e6
d1 = moose.SymCompartment('%s/d1' % (model.path))
d1.Rm = 1e8
d1.Cm = 1e-10
d1.Ra = 1e7
d2 = moose.SymCompartment('%s/d2' % (model.path))
d2.Rm = 1e8
d2.Cm = 1e-10
d2.Ra = 2e7
moose.connect(d1, 'proximal', soma, 'distal')
moose.connect(d2, 'proximal', soma, 'distal')
moose.connect(d1, 'sibling', d2, 'sibling')
pg = moose.PulseGen('/model/pulse')
pg.delay[0] = 10e-3
pg.width[0] = 20e-3
pg.level[0] = 1e-6
pg.delay[1] = 1e9
moose.connect(pg, 'output', d1, 'injectMsg')
data = moose.Neutral('/data')
tab_soma = moose.Table('%s/soma_Vm' % (data.path))
tab_d1 = moose.Table('%s/d1_Vm' % (data.path))
tab_d2 = moose.Table('%s/d2_Vm' % (data.path))
moose.connect(tab_soma, 'requestOut', soma, 'getVm')
moose.connect(tab_d1, 'requestOut', d1, 'getVm')
moose.connect(tab_d2, 'requestOut', d2, 'getVm')
moose.setClock(0, simdt)
moose.setClock(1, simdt)
moose.setClock(2, simdt)
moose.useClock(
0, '/model/##[ISA=Compartment]', 'init'
) # This is allowed because SymCompartment is a subclass of Compartment
moose.useClock(1, '/model/##', 'process')
moose.useClock(2, '/data/##[ISA=Table]', 'process')
moose.reinit()
moose.start(simtime)
t = np.linspace(0, simtime, len(tab_soma.vector))
data_matrix = np.vstack((t, tab_soma.vector, tab_d1.vector, tab_d2.vector))
np.savetxt('symcompartment.txt', data_matrix.transpose())
pylab.plot(t, tab_soma.vector, label='Vm_soma')
pylab.plot(t, tab_d1.vector, label='Vm_d1')
pylab.plot(t, tab_d2.vector, label='Vm_d2')
pylab.show()
def createSquid():
"""Create a single compartment squid model."""
parent = moose.Neutral('/n')
elec = moose.Neutral('/n/elec')
compt = moose.SymCompartment('/n/elec/compt')
Em = EREST_ACT + 10.613e-3
compt.Em = Em
compt.initVm = EREST_ACT
compt.Cm = 7.85e-9 * 0.5
compt.Rm = 4.2e5 * 5.0
compt.Ra = 7639.44e3
compt.length = 100e-6
compt.diameter = 4e-6
nachan = moose.HHChannel('/n/elec/compt/Na')
nachan.Xpower = 3
xGate = moose.HHGate(nachan.path + '/gateX')
xGate.setupAlpha(Na_m_params + [VDIVS, VMIN, VMAX])
xGate.useInterpolation = 1
nachan.Ypower = 1
yGate = moose.HHGate(nachan.path + '/gateY')
yGate.setupAlpha(Na_h_params + [VDIVS, VMIN, VMAX])
yGate.useInterpolation = 1
nachan.Gbar = 0.942e-3
nachan.Ek = 115e-3 + EREST_ACT
moose.connect(nachan, 'channel', compt, 'channel', 'OneToOne')
kchan = moose.HHChannel('/n/elec/compt/K')
kchan.Xpower = 4.0
xGate = moose.HHGate(kchan.path + '/gateX')
xGate.setupAlpha(K_n_params + [VDIVS, VMIN, VMAX])
xGate.useInterpolation = 1
kchan.Gbar = 0.2836e-3
kchan.Ek = -12e-3 + EREST_ACT
moose.connect(kchan, 'channel', compt, 'channel', 'OneToOne')
return compt
def makeChannelPrototypes():
"""Create channel prototypes for readcell."""
library = moose.Neutral('/library')
moose.setCwe('/library')
compt = moose.SymCompartment('/library/symcompartment')
Em = EREST_ACT + 10.613e-3
compt.Em = Em
compt.initVm = EREST_ACT
compt.Cm = 7.85e-9 * 0.5
compt.Rm = 4.2e5 * 5.0
compt.Ra = 7639.44e3
nachan = moose.HHChannel('/library/Na')
nachan.Xpower = 3
xGate = moose.HHGate(nachan.path + '/gateX')
xGate.setupAlpha(Na_m_params + [VDIVS, VMIN, VMAX])
xGate.useInterpolation = 1
nachan.Ypower = 1
yGate = moose.HHGate(nachan.path + '/gateY')
yGate.setupAlpha(Na_h_params + [VDIVS, VMIN, VMAX])
yGate.useInterpolation = 1
nachan.Gbar = 0.942e-3
nachan.Ek = 115e-3 + EREST_ACT
kchan = moose.HHChannel('/library/K')
kchan.Xpower = 4.0
xGate = moose.HHGate(kchan.path + '/gateX')
xGate.setupAlpha(K_n_params + [VDIVS, VMIN, VMAX])
xGate.useInterpolation = 1
kchan.Gbar = 0.2836e-3
kchan.Ek = -12e-3 + EREST_ACT
def create_squid():
"""Create a single compartment squid model."""
parent = moose.Neutral('/n')
compt = moose.SymCompartment('/n/compt')
Em = EREST_ACT + 10.613e-3
compt.Em = Em
compt.initVm = EREST_ACT
compt.Cm = 7.85e-9 * 0.5
compt.Rm = 4.2e5 * 5.0
compt.Ra = 7639.44e3
nachan = moose.HHChannel('/n/compt/Na')
nachan.Xpower = 3
xGate = moose.HHGate(nachan.path + '/gateX')
xGate.setupAlpha(Na_m_params + [VDIVS, VMIN, VMAX])
#This is important: one can run without it but the output will diverge.
xGate.useInterpolation = 1
nachan.Ypower = 1
yGate = moose.HHGate(nachan.path + '/gateY')
yGate.setupAlpha(Na_h_params + [VDIVS, VMIN, VMAX])
yGate.useInterpolation = 1
nachan.Gbar = 0.942e-3
nachan.Ek = 115e-3 + EREST_ACT
moose.connect(nachan, 'channel', compt, 'channel', 'OneToOne')
kchan = moose.HHChannel('/n/compt/K')
kchan.Xpower = 4.0
xGate = moose.HHGate(kchan.path + '/gateX')
xGate.setupAlpha(K_n_params + [VDIVS, VMIN, VMAX])
xGate.useInterpolation = 1
kchan.Gbar = 0.2836e-3
kchan.Ek = -12e-3 + EREST_ACT
moose.connect(kchan, 'channel', compt, 'channel', 'OneToOne')
return compt
