def addMMPump(dShell, pumpparams, Vmax, surface):
shellName = ''
for s in dShell.path.split('[0]'):
shellName += s
pump = moose.MMPump(shellName + '_' + pumpparams.Name)
pump.Vmax = Vmax * surface
pump.Kd = pumpparams.Kd
moose.connect(pump, "PumpOut", dShell, "mmPump")
return pump
def test_diffshell():
lib = moose.Neutral('/library')
for tick in range(0, 7):
moose.setClock(tick, dt)
moose.setClock(8, 0.005) # set output clock
model = moose.Neutral('/model')
dend = moose.Compartment('/model/dend')
pulse = moose.PulseGen('/model/pulse')
data = moose.Neutral('/data')
vmtab = moose.Table('/data/dend_Vm')
gktab = moose.Table('/data/CaT_Gk')
iktab = moose.Table('/data/CaT_Ik')
dend.Cm = Cm
dend.Rm = Rm
dend.Em = Em
dend.initVm = Vm_0
dend.diameter = dend_diameter
dend.length = dend_length
pulse.delay[0] = 8.
pulse.width[0] = 500e-3
pulse.level[0] = inject
pulse.delay[1] = 1e9
chan = chan_proto.chan_proto('/library/CaL12', param_chan.Cal)
m = moose.connect(pulse, 'output', dend, 'injectMsg')
moose.connect(vmtab, 'requestOut', dend, 'getVm')
chan = addOneChan('CaL12', gbar, dend)
moose.connect(gktab, 'requestOut', chan, 'getGk')
moose.connect(iktab, 'requestOut', chan, 'getIk')
diftab = []
buftab = []
difs, difb = add_difshells_and_buffers(dend, difshell_no, difbuff_no)
if pumps:
pump = moose.MMPump('/model/dend/pump')
pump.Vmax = kcat
pump.Kd = km
moose.connect(pump, "PumpOut", difs[0], "mmPump")
if difs:
moose.connect(chan, "IkOut", difs[0], "influx")
moose.connect(difs[0], 'concentrationOut', chan, 'concen')
for i, dif in enumerate(difs):
res_dif = moose.Table('/data/' + difshell_name + str(i))
diftab.append(res_dif)
moose.connect(diftab[i], 'requestOut', dif, 'getC')
if (difbuff_no):
buftab.append([])
for j, buf in enumerate(difb[i]):
res_buf = moose.Table('/data/' + difshell_name + str(i) + '_' +
difbuff_name + str(j))
buftab[i].append(res_buf)
moose.connect(buftab[i][j], 'requestOut', buf, 'getBBound')
moose.reinit()
if not gbar:
for i, dif in enumerate(difs):
if i == 0:
dif.C = Ca_initial
else:
dif.C = 0
for j, dbuf in enumerate(difb[i]):
dbuf.bFree = dbuf.bTot
moose.start(t_stop)
t = np.linspace(0, t_stop, len(vmtab.vector))
fname = 'moose_results_difshell_no_' + str(
difshell_no) + '_difbuffer_no_' + str(difbuff_no) + '_pump_' + str(
pumps) + '_gbar_' + str(gbar) + '.txt'
header = 'time Vm Ik Gk'
number = 4 + difshell_no * (difbuff_no + 1)
res = np.zeros((len(t), number))
res[:, 0] = t
res[:, 1] = vmtab.vector
res[:, 2] = iktab.vector
res[:, 3] = gktab.vector
for i in range(difshell_no):
header += ' difshell_' + str(i)
res[:, 4 + i * (difbuff_no + 1)] = diftab[i].vector
if (difbuff_no):
for j, buf in enumerate(buftab[i]):
res[:, 4 + i * (difbuff_no + 1) + j + 1] = buf.vector
header += ' difshell_' + str(i) + '_difbuff_' + str(j)
np.savetxt(fname, res, header=header, comments='')
pulse.delay[0] = 8.
pulse.width[0] = 500e-3
pulse.level[0] = inject
pulse.delay[1] = 1e9
chan = chan_proto.chan_proto('/library/CaL12',param_chan.Cal)
m = moose.connect(pulse, 'output', dend, 'injectMsg')
moose.connect(vmtab, 'requestOut', dend, 'getVm')
chan = addOneChan('CaL12', gbar, dend)
moose.connect(gktab, 'requestOut', chan, 'getGk')
moose.connect(iktab, 'requestOut', chan, 'getIk')
diftab = []
buftab = []
difs, difb = add_difshells_and_buffers(dend,difshell_no,difbuff_no)
if pumps:
pump = moose.MMPump('/model/dend/pump')
pump.Vmax = kcat
pump.Kd = km
moose.connect(pump, "PumpOut", difs[0], "mmPump")
if difs:
moose.connect(chan, "IkOut", difs[0], "influx")
moose.connect(difs[0], 'concentrationOut', chan, 'concen')
for i, dif in enumerate(difs):
res_dif = moose.Table('/data/' + difshell_name + str(i))
diftab.append(res_dif)
moose.connect(diftab[i], 'requestOut', dif, 'getC')
if (difbuff_no):
buftab.append([])
for j, buf in enumerate(difb[i]):
res_buf = moose.Table(