def test_synintegration(filename, target_cell, source_type):
sim = Simulation('synintegration')
cell = SpinyStellate(SpinyStellate.prototype,
sim.model.path + '/SpinyStellate')
vm_table = cell.comp[cell.presyn].insertRecorder('Vm', 'Vm', sim.data)
# Create a common spike gen object
sp = moose.SpikeGen('spike', sim.model)
sp.threshold = 0.0
sp.edgeTriggered = 1
sptab = moose.Table('spike', sim.data)
sptab.stepMode = 3
sptab.connect('inputRequest', sp, 'state')
(comp_indices, syntype, gbar, tau1, tau2, Ek, ) = \
get_syninfo(filename, target_cell, source_type)
# Set up the synapses
for ii in range(len(comp_indices)):
print '%d\t%s\t%g\t%g\t%g\t%g' % (comp_indices[ii],
syntype[ii],
gbar[ii],
tau1[ii],
tau2[ii],
Ek[ii])
comp = cell.comp[comp_indices[ii]]
weight = 1.0
if syntype[ii] == 'nmda':
chan = moose.NMDAChan('nmda_from_%s' % (source_type), comp)
chan.MgConc = 1.5
weight = gbar[ii]
else:
chan = moose.SynChan('%s_from_%s' % (syntype[ii], source_type),
comp)
chan.Gbar = gbar[ii]
chan.tau1 = tau1[ii]
chan.tau2 = tau2[ii]
chan.Ek = Ek[ii]
comp.connect('channel', chan, 'channel')
sp.connect('event', chan, 'synapse')
count = chan.numSynapses
if source_type == 'TCR':
chan.delay[count-1] = 1e-3 # thalamocortical delay
else:
chan.delay[count-1] = 0.05e-3 # default delay
chan.weight[count-1] = weight
gktable = moose.Table('%s_%s_%s' % (cell.name, comp.name, chan.name), sim.data)
gktable.stepMode = 3
gktable.connect('inputRequest', chan, 'Gk')
pulsegen = moose.PulseGen('pulse', sim.model)
pulsegen.firstDelay = 3.0
pulsegen.firstLevel = 1.0
pulsegen.firstWidth = 1e-3
pulsegen.trigMode = moose.FREE_RUN
pulsegen.connect('outputSrc', sp, 'Vm')
ptable = moose.Table('pulse', sim.data)
ptable.stepMode = 3
ptable.connect('inputRequest', pulsegen, 'output')
sim.schedule(simdt=1e-6, plotdt=1e-6)
sim.run(10.0)
sim.save_data_h5(filename.replace('network_', 'synintegration_'))
def synintegration2(filename, target_cell):
raise NotImplementedError
syntab = None
netfile = h5.File(filename, 'r')
syntab = netfile['network/synapse'][:]
idx = np.char.startswith(syntab['dest'], target_cell)
syntab = syntab[idx]
sim = Simulation('synintegration')
cell = SpinyStellate(SpinyStellate.prototype,
sim.model.path + '/SpinyStellate')
vm_table = cell.comp[cell.presyn].insertRecorder('Vm', 'Vm', sim.data)
# Create a common spike gen object
sp = moose.SpikeGen('spike', sim.model)
sp.threshold = 0.0
sp.edgeTriggered = 1
sptab = moose.Table('spike', sim.data)
sptab.stepMode = 3
sptab.connect('inputRequest', sp, 'state')
for ii in range(len(syntab)):
source = syntab['source'][ii].partition('/')[0]
dest, compname = syntab['dest'][ii].split('/')
if source == dest:
print 'source = dest', source, filename
continue
comp_no = compname.split('_')[-1]
comp = cell[int(comp_no)]
weight = 1.0
if syntab['type'][ii] == 'nmda':
chan = moose.NMDAChan('nmda_from_%s' %
(source.split('_')[0]), comp)
chan.MgConc = 1.5
weight = syntab['Gbar'][ii]
else:
chan = moose.SynChan('%s_from_%s' %
(syntab['type'][ii], source.split('_')[0]),
comp)
chan.Gbar = syntab['Gbar'][ii]
chan.tau1 = syntab['tau1'][ii]
chan.tau2 = syntab['tau2'][ii]
chan.Ek = syntab['Ek'][ii]
comp.connect('channel', chan, 'channel')
sp.connect('event', chan, 'synapse')
count = chan.numSynapses
if source_type == 'TCR':
chan.delay[count-1] = 1e-3 # thalamocortical delay
else:
chan.delay[count-1] = 0.05e-3 # default delay
chan.weight[count-1] = weight
gktable = moose.Table('%s_%s_%s' % (cell.name, comp.name, chan.name), sim.data)
gktable.stepMode = 3
gktable.connect('inputRequest', chan, 'Gk')
def threecell_test():
sim = Simulation('threecell')
tcr_ix = netdata.celltype.index('TCR')
ss_ix = netdata.celltype.index('SpinyStellate')
basket_ix = netdata.celltype.index('DeepBasket')
ss = SpinyStellate(SpinyStellate.prototype,
sim.model.path + '/SpinyStellate')
tcr = TCR(TCR.prototype, sim.model.path + '/TCR')
basket = DeepBasket(DeepBasket.prototype, sim.model.path + '/DeepBasket')
cells = [ss, tcr, basket]
for postcell in cells:
for precell in cells:
if precell == postcell:
continue
for syntype in ['ampa', 'nmda', 'gaba']:
syn = make_synapse(precell, postcell, syntype)
if syn is not None:
tab = record_data(sim.data, 'gk_%s_%s' % (postcell.name, syn.name), syn, 'Gk')
record_data(sim.data, 'Vm_%s' % (postcell.name), postcell.comp[postcell.presyn], 'Vm')
pulsegen = moose.PulseGen('pulse', sim.model)
pulsegen.firstDelay = 3.0
pulsegen.firstLevel = 1e-9
pulsegen.firstWidth = 2e-3
pulsegen.trigMode = moose.FREE_RUN
pulsegen.connect('outputSrc', tcr.soma, 'injectMsg')
ptable = moose.Table('pulse', sim.data)
ptable.stepMode = 3
ptable.connect('inputRequest', pulsegen, 'output')
sim.schedule(simdt=25e-6, plotdt=25e-5)
for t in range(10):
start = datetime.now()
sim.run(1.0)
end = datetime.now()
delta = end - start
print 'Ran', t+1, '-th second in', delta.seconds + 1e-6 * delta.microseconds
sim.save_data_h5('threecells.h5')
