def setup_synapse():
"""Create an intfire object and create two synapses on it."""
if4 = moose.IntFire('if4')
sf4 = moose.SimpleSynHandler('if4/sh')
sg1 = moose.SpikeGen('sg1')
sg2 = moose.SpikeGen('sg2')
sf4.synapse.num = 2 # set synapse count to 2
sf4.synapse[0].weight = 0.5
sf4.synapse[0].delay = 1e-3
sf4.synapse[1].weight = 2.0
sf4.synapse[1].delay = 2e-3
moose.connect(sg1, 'spikeOut', sf4.synapse[0], 'addSpike')
moose.connect(sg2, 'spikeOut', sf4.synapse[1], 'addSpike')
def make_synapse(path):
"""Create a synapse with two time constants."""
syn = moose.SynChan(path)
syn.tau1 = 5.0 # ms
syn.tau2 = 1.0 # ms
syn.Gbar = 1.0 # mS
syn.Ek = 0.0
synsh = moose.SimpleSynHandler(path + '/sh')
synsh.synapse.num = 1
# syn.bufferTime = 1.0 # ms
synsh.synapse.delay = 1.0
synsh.synapse.weight = 1.0
print(('Synapses:', len(synsh.synapse), 'w=', synsh.synapse[0].weight))
spikegen = moose.SpikeGen('%s/spike' % (syn.parent.path))
spikegen.edgeTriggered = False # Make it fire continuously when input is high
spikegen.refractT = 10.0 # With this setting it will fire at 1 s / 10 ms = 100 Hz
spikegen.threshold = 0.5
# This will send alternatind -1 and +1 to SpikeGen to make it fire
spike_stim = moose.PulseGen('%s/spike_stim' % (syn.parent.path))
spike_stim.delay[0] = 50.0
spike_stim.level[0] = 1.0
spike_stim.width[0] = 100.0
moose.connect(spike_stim, 'output', spikegen, 'Vm')
m = moose.connect(spikegen, 'spikeOut', synsh.synapse[0], 'addSpike')
return syn, spikegen
def create_population(container, netparams, name_soma):
netpath = container.path
proto=[]
neurXclass={}
locationlist=[]
#determine total number of neurons
size,numneurons,vol=count_neurons(netparams)
pop_percent=[]
for neurtype in netparams.pop_dict.keys():
if moose.exists(neurtype):
proto.append(moose.element(neurtype))
neurXclass[neurtype]=[]
pop_percent.append(netparams.pop_dict[neurtype].percent)
#create cumulative array of probabilities for selecting neuron type
choicearray=np.cumsum(pop_percent)
if choicearray[-1]<1.0:
log.info("Warning!!!! fractional populations sum to {}",choicearray[-1])
#array of random numbers that will be used to select neuron type
rannum = np.random.uniform(0,choicearray[-1],numneurons)
#Error check for last element in choicearray equal to 1.0
log.info("numneurons= {} {} choicarray={}", size, numneurons, choicearray)
log.debug("rannum={}", rannum)
for i,xloc in enumerate(np.linspace(netparams.grid[0]['xyzmin'], netparams.grid[0]['xyzmax'], size[0])):
for j,yloc in enumerate(np.linspace(netparams.grid[1]['xyzmin'], netparams.grid[1]['xyzmax'], size[1])):
for k,zloc in enumerate(np.linspace(netparams.grid[2]['xyzmin'], netparams.grid[2]['xyzmax'], size[2])):
#for each location in grid, assign neuron type, update soma location, add in spike generator
neurnumber=i*size[2]*size[1]+j*size[2]+k
neurtypenum=np.min(np.where(rannum[neurnumber]<choicearray))
log.debug("i,j,k {} {} {} neurnumber {} type {}", i,j,k, neurnumber, neurtypenum)
typename = proto[neurtypenum].name
tag = '{}_{}'.format(typename, neurnumber)
new_neuron=moose.copy(proto[neurtypenum],netpath, tag)
neurXclass[typename].append(container.path + '/' + tag)
comp=moose.element(new_neuron.path + '/'+name_soma)
comp.x=i*xloc
comp.y=j*yloc
comp.z=k*zloc
log.debug("x,y,z={},{},{} {}", comp.x, comp.y, comp.z, new_neuron.path)
locationlist.append([new_neuron.name,comp.x,comp.y,comp.z])
#spike generator - can this be done to the neuron prototype?
spikegen = moose.SpikeGen(comp.path + '/spikegen')
#should these be parameters in netparams?
spikegen.threshold = 0.0
spikegen.refractT=1e-3
m = moose.connect(comp, 'VmOut', spikegen, 'Vm')
#Create variability in neurons of network
for neurtype in netparams.chanvar.keys():
for chan,var in netparams.chanvar[neurtype].items():
#single multiplier for Gbar for all the channels compartments
if var>0:
log.debug('adding variability to {} soma {}, variance: {}', neurtype,chan, var)
GbarArray=abs(np.random.normal(1.0, var, len(neurXclass[neurtype])))
for ii,neurname in enumerate(neurXclass[neurtype]):
soma_chan_path=neurname+'/'+name_soma+'/'+chan
if moose.exists(soma_chan_path):
chancomp=moose.element(soma_chan_path)
chancomp.Gbar=chancomp.Gbar*GbarArray[ii]
#
return {'location': locationlist,
'pop':neurXclass}
def many_ematrix_to_one_element():
"""This is an example of event messages from multiple SpikeGen objects
into a synchan.
Create a SynChan element with 2 elements in synapse field.
Create 5 SpikeGen elements.
Connect alternet SpikeGen elements to synapse[0] and synapse[1]
... This is a minimal example. In real simulations the SpikeGens
will be embedded in compartments representing axon terminals and
the SynChans will be embedded in somatic/dendritic compartments.
"""
model = moose.Neutral('/model')
# data = moose.Neutral('/data')
synchan = moose.SynChan('/model/synchan')
synh = moose.SimpleSynHandler('/model/synchan/synh')
moose.connect(synh, 'activationOut', synchan, 'activation')
synh.synapse.num = 2
num_spikegen = 5
spikegens = [
moose.SpikeGen('/model/spikegen_%d' % (ii))
for ii in range(num_spikegen)
]
for ii in range(num_spikegen):
msg = moose.connect(spikegens[ii], 'spikeOut', synh.synapse[ii % 2],
'addSpike')
# synchan.synapse[ii].delay = ii * 1e-3
# synchan.synapse[ii].weight = (ii+1) * 0.1
for sg in spikegens:
print(sg.path, '-->', end=' ')
for m in sg.msgOut:
print(moose.element(m).adjacent[sg].path)
def make_spiny_compt():
comptLength = 100e-6
comptDia = 4e-6
numSpines = 5
compt = create_squid()
compt.inject = 0
compt.x0 = 0
compt.y0 = 0
compt.z0 = 0
compt.x = comptLength
compt.y = 0
compt.z = 0
compt.length = comptLength
compt.diameter = comptDia
synInput = moose.SpikeGen('/n/compt/synInput')
synInput.refractT = 47e-3
synInput.threshold = -1.0
synInput.edgeTriggered = 0
synInput.Vm(0)
cell = moose.element('/n')
for i in range(numSpines):
r = create_spine_with_receptor(compt, cell, i, i / float(numSpines))
r.synapse.num = 1
syn = moose.element(r.path + '/synapse')
moose.connect(synInput, 'spikeOut', syn, 'addSpike', 'single')
syn.weight = 0.2
syn.delay = i * 1.0e-4
def make_synapse(comp):
nmda, mgblock = make_NMDA(comp)
ampa = make_AMPA(comp)
spikegen = moose.SpikeGen('%s/spike' % (comp.path))
moose.connect(spikegen, 'spikeOut', ampa.synapse[0], 'addSpike')
moose.connect(spikegen, 'spikeOut', nmda.synapse[0], 'addSpike')
return {'ampa': ampa, 'nmda': nmda, 'mgblock': mgblock, 'spike': spikegen}
def makeSpinyCompt():
comptLength = 30e-6
comptDia = 6e-6
numSpines = 5
compt = createSquid()
compt.inject = 0
compt.x0 = 0
compt.y0 = 0
compt.z0 = 0
compt.x = comptLength
compt.y = 0
compt.z = 0
compt.length = comptLength
compt.diameter = comptDia
#kchan = moose.element( '/n/compt/K' )
#kchan.Gbar = 0.2e-3
synInput = moose.SpikeGen('/n/compt/synInput')
synInput.refractT = 47e-3
synInput.threshold = -1.0
synInput.edgeTriggered = 0
synInput.Vm(0)
cell = moose.element('/n')
for i in range(numSpines):
r = createSpineWithReceptor(compt, cell, i, i / float(numSpines))
r.synapse.num = 1
syn = moose.element(r.path + '/synapse')
moose.connect(synInput, 'spikeOut', syn, 'addSpike', 'Single')
syn.weight = 0.2 * i * (4 - i)
syn.delay = i * 1.0e-3
def testNMDAChan(simtime=1.0, simdt=1e-5, plotdt=1e-5):
context = moose.PyMooseBase.getContext()
container = moose.Neutral('test_NMDA')
soma_b = moose.Compartment('B', container)
soma_b.Rm = 5.3e9 # GM = 2e-5 S/cm^2
soma_b.Cm = 8.4823001646924426e-12 # CM = 0.9 uF/cm^2
soma_b.Em = -65e-3
soma_b.initVm = -65e-3
soma_b.Ra = 282942.12 # RA = 250 Ohm-cm
nmda = moose.NMDAChan('nmda', container)
nmda.tau2 = 5e-3
nmda.tau1 = 130e-3
nmda.Gbar = 1e-9
nmda.saturation = 1e10
nmda.connect('channel', soma_b, 'channel')
spikegen = moose.SpikeGen('spike', container)
spikegen.threshold = 0.5
spikegen.connect('event', nmda, 'synapse')
spikegen.refractT = 0.0
nmda.delay[0] = 1e-3
nmda.weight[0] = 1.0
pulsegen = moose.PulseGen('pulse', container)
pulsegen.setCount(3)
pulsegen.level[0] = 1.0
pulsegen.delay[0] = 10e-3
pulsegen.width[0] = 1e-3
pulsegen.level[1] = 1.0
pulsegen.delay[1] = 2e-3
pulsegen.width[1] = 1e-3
pulsegen.delay[2] = 1e9
pulsegen.connect('outputSrc', spikegen, 'Vm')
data = moose.Neutral('data')
vmB = moose.Table('Vm_B', data)
vmB.stepMode = 3
vmB.connect('inputRequest', soma_b, 'Vm')
pulse = moose.Table('pulse', data)
pulse.stepMode = 3
pulse.connect('inputRequest', pulsegen, 'output')
gNMDA = moose.Table('G', data)
gNMDA.stepMode = 3
gNMDA.connect('inputRequest', nmda, 'Gk')
context.setClock(0, simdt)
context.setClock(1, simdt)
context.setClock(2, simdt)
context.setClock(3, plotdt)
context.reset()
context.step(simtime)
# gNMDA.dumpFile('gNMDA.dat', False)
# vmA.dumpFile('Va.dat', False)
# vmB.dumpFile('Vb.dat', False)
ts = np.linspace(0, simtime, len(gNMDA))
pylab.plot(ts, pulse)
pylab.plot(ts, np.asarray(gNMDA) * 1e9, label='gNMDA')
pylab.show()
np.savetxt('../data/two_comp_nmda.plot', np.transpose(np.vstack((ts, vmB, gNMDA))))
def create_compartment(path):
comp = moose.Compartment(path)
comp.diameter = soma_dia
comp.Em = EREST_ACT + 10.613e-3
comp.initVm = EREST_ACT
sarea = np.pi * soma_dia * soma_dia
comp.Rm = 1/(0.3e-3 * 1e4 * sarea)
comp.Cm = 1e-6 * 1e4 * sarea
if moose.exists('/library/na'):
nachan = moose.element(moose.copy('/library/na', comp, 'na'))
else:
nachan = create_na_chan(comp.path)
nachan.Gbar = 120e-3 * sarea * 1e4
moose.showfield(nachan)
moose.connect(nachan, 'channel', comp, 'channel')
if moose.exists('/library/k'):
kchan = moose.element(moose.copy('/library/k', comp, 'k'))
else:
kchan = create_k_chan(comp.path)
kchan.Gbar = 36e-3 * sarea * 1e4
moose.connect(kchan, 'channel', comp, 'channel')
synchan = moose.SynChan(comp.path + '/synchan')
synchan.Gbar = 1e-8
synchan.tau1 = 2e-3
synchan.tau2 = 2e-3
synchan.Ek = 0.0
m = moose.connect(comp, 'channel', synchan, 'channel')
spikegen = moose.SpikeGen(comp.path + '/spikegen')
spikegen.threshold = 0.0
m = moose.connect(comp, 'VmOut', spikegen, 'Vm')
return comp
def createSynapseOnCompartment(compt):
FaradayConst = 96485.3415 # s A / mol
length = compt.length
dia = compt.diameter
gluR = moose.SynChan(compt.path + '/gluR')
gluR.tau1 = 4e-3
gluR.tau2 = 4e-3
gluR.Gbar = 1e-6
gluR.Ek = 10.0e-3
moose.connect(compt, 'channel', gluR, 'channel', 'Single')
gluSyn = moose.SimpleSynHandler(compt.path + '/gluR/sh')
moose.connect(gluSyn, 'activationOut', gluR, 'activation')
gluSyn.synapse.num = 1
# Ca comes in through this channel, at least for this example.
caPool = moose.CaConc(compt.path + '/ca')
caPool.CaBasal = 1e-4 # 0.1 micromolar
caPool.tau = 0.01
B = 1.0 / (FaradayConst * length * dia * dia * math.pi / 4)
B = B / 20.0 # scaling factor for Ca buffering
caPool.B = B
moose.connect(gluR, 'IkOut', caPool, 'current', 'Single')
# Provide a regular synaptic input.
synInput = moose.SpikeGen('/n/elec/compt/synInput')
synInput.refractT = 47e-3
synInput.threshold = -1.0
synInput.edgeTriggered = 0
synInput.Vm(0)
syn = moose.element(gluSyn.path + '/synapse')
moose.connect(synInput, 'spikeOut', syn, 'addSpike', 'Single')
syn.weight = 0.2
syn.delay = 1.0e-3
return gluR
def make_synapse(path):
"""Create a synapse with two time constants. Connect a spikegen to the
synapse. Create a pulsegen to drive the spikegen."""
syn = moose.SynChan(path)
syn.tau1 = 5.0 # ms
syn.tau2 = 1.0 # ms
syn.Gk = 1.0 # mS
syn.Ek = 0.0
syn.synapse.num = 1
# syn.bufferTime = 1.0 # ms
syn.synapse.delay = 1.0
syn.synapse.weight = 1.0
print 'Synapses:', len(syn.synapse), 'w=', syn.synapse[0].weight
spikegen = moose.SpikeGen('%s/spike' % (syn.parent.path))
spikegen.edgeTriggered = False # Make it fire continuously when input is high
spikegen.refractT = 10.0 # With this setting it will fire at 1 s / 10 ms = 100 Hz
spikegen.threshold = 0.5
# This will send alternatind -1 and +1 to SpikeGen to make it fire
spike_stim = moose.PulseGen('%s/spike_stim' % (syn.parent.path))
spike_stim.delay[0] = 1.0
spike_stim.level[0] = 1.0
spike_stim.width[0] = 100.0
moose.connect(spike_stim, 'output', spikegen, 'Vm')
# m = moose.connect(spikegen, 'spikeOut', syn.synapse.vec, 'addSpike', 'Sparse')
# m.setRandomConnectivity(1.0, 1)
m = moose.connect(spikegen, 'spikeOut', syn.synapse[0],
'addSpike') # this causes segfault
return syn, spikegen
def setup_model():
"""Setup a dummy model with a pulsegen and a spikegen detecting the
leading edges of the pulses. We record the pulse output as Uniform
data and leading edge time as Event data."""
simtime = 100.0
dt = 1e-3
model = moose.Neutral('/model')
pulse = moose.PulseGen('/model/pulse')
pulse.level[0] = 1.0
pulse.delay[0] = 10
pulse.width[0] = 20
t_lead = moose.SpikeGen('/model/t_lead')
t_lead.threshold = 0.5
moose.connect(pulse, 'output', t_lead, 'Vm')
nsdf = moose.NSDFWriter('/model/writer')
nsdf.filename = 'nsdf_demo.h5'
nsdf.mode = 2 #overwrite existing file
nsdf.flushLimit = 100
moose.connect(nsdf, 'requestOut', pulse, 'getOutputValue')
print 'event input', nsdf.eventInput, nsdf.eventInput.num
print nsdf
nsdf.eventInput.num = 1
ei = nsdf.eventInput[0]
print ei.path
moose.connect(t_lead, 'spikeOut', nsdf.eventInput[0], 'input')
tab = moose.Table('spiketab')
tab.threshold = t_lead.threshold
clock = moose.element('/clock')
for ii in range(32):
moose.setClock(ii, dt)
moose.connect(pulse, 'output', tab, 'spike')
print datetime.now().isoformat()
moose.reinit()
moose.start(simtime)
print datetime.now().isoformat()
np.savetxt('nsdf.txt', tab.vector)
###################################
# Set the environment attributes
###################################
nsdf.stringAttr['title'] = 'NSDF writing demo for moose'
nsdf.stringAttr[
'description'] = '''An example of writing data to NSDF file from MOOSE simulation. In
this simulation we generate square pules from a PulseGen object and
use a SpikeGen to detect the threshold crossing events of rising
edges. We store the pulsegen output as Uniform data and the threshold
crossing times as Event data. '''
nsdf.stringAttr['creator'] = getpass.getuser()
nsdf.stringVecAttr['software'] = ['python2.7', 'moose3']
nsdf.stringVecAttr['method'] = ['']
nsdf.stringAttr['rights'] = ''
nsdf.stringAttr['license'] = 'CC-BY-NC'
# Specify units. MOOSE is unit agnostic, so we explicitly set the
# unit attibutes on individual datasets
nsdf.stringAttr['/data/uniform/PulseGen/outputValue/tunit'] = 's'
nsdf.stringAttr['/data/uniform/PulseGen/outputValue/unit'] = 'A'
eventDataPath = '/data/event/SpikeGen/spikeOut/{}_{}_{}/unit'.format(
t_lead.vec.value, t_lead.getDataIndex(), t_lead.getFieldIndex())
nsdf.stringAttr[eventDataPath] = 's'
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 makeSynapse(self,
target,
classname='SynChan',
name='synapse',
threshold=0.0,
absRefract=1.5e-3,
Ek=0.0,
Gbar=None,
tau1=None,
tau2=None,
weight=1.0,
delay=0.0,
Pr=1.0):
"""Make a synaptic connection from this compartment to target
compartment and set the properties of the synaptic connection
as specified in the parametrs.
For NMDAChan, [Mg2+] has to be set separately. Also note that
the weight and delay vectors are not available until reset is
called. So these must be assigned afterwards.
"""
classobj = eval('moose.' + classname)
synapse = classobj(name, target)
synapse.Ek = float(Ek) # TODO set value according to original model
synapse.Gbar = float(
Gbar) # TODO set value according to original model
synapse.tau1 = float(tau1)
synapse.tau2 = float(tau2)
target.connect('channel', synapse, 'channel')
spikegen = None
spikegen = moose.SpikeGen('%s/spike' % (self.path))
spikegen.threshold = float(threshold)
spikegen.absRefract = float(absRefract)
self.connect('VmSrc', spikegen, 'Vm')
if not spikegen.connect('event', synapse, 'synapse'):
raise Exception('Error creating connection: %s->%s' %
(spikegen.path, synapse.path))
# This is too much of log info. Hence commenting out.
# else:
# config.LOGGER.debug('Connected %s->%s' % (spikegen.path, synapse.path))
# We had an awkward situation here: the weight and delay
# vectors were not updated until reset/setDelay/setWeight was
# called. So we had to use num_synapse (which should
# actually have been incremented by 1 due to the connection)
# instead of (num_synapse - 1).
# 2010-03-29 After making a mandatory call to updateNumSynapse()
# in getNumSynapses(), this is fixed.
num_synapses = synapse.numSynapses
synapse.delay[num_synapses - 1] = float(delay)
synapse.weight[num_synapses - 1] = float(weight)
if config.stochastic:
synapse.initPr[num_synapses - 1] = Pr
config.LOGGER.debug('Created synapse: %s of type %s' %
(synapse.path, synapse.className))
return synapse
def init_channel_lib():
"""Initialize the prototype channels in library"""
if not config.channel_lib:
config.LOGGER.debug('* Generating channel prototypes in /library')
for channel_name in config.channel_name_list:
channel_class = eval(channel_name)
channel = channel_class(channel_name, config.lib)
config.channel_lib[channel_name] = channel
config.LOGGER.debug('* Created %s' % (channel.path))
config.channel_lib['SpikeGen'] = moose.SpikeGen('spike', config.lib)
return config.channel_lib
def connect_spikegen():
"""Connect a SpikeGen object to an IntFire neuron such that spike
events in spikegen get transmitted to the synapse of the IntFire
neuron."""
if3 = moose.IntFire('if3')
sf3 = moose.SimpleSynHandler('if3/sh')
moose.connect(sf3, 'activationOut', if3, 'activation')
sf3.synapse.num = 1
sg = moose.SpikeGen('sg')
syn = moose.element(sf3.synapse)
moose.connect(sg, 'spikeOut', syn, 'addSpike')
def spiketables(neuron,param_cond):
spiketab=[]
for neur in neuron.keys():
soma=moose.element(neur+'/'+param_cond.NAME_SOMA)
spikegen=moose.SpikeGen(soma.path+'/spikegen')
spikegen.threshold=0.0
spikegen.refractT=1.0e-3
msg=moose.connect(soma,'VmOut',spikegen,'Vm')
spiketab.append(moose.Table('/data/spike_'+neur))
moose.connect(spikegen,'spikeOut',spiketab[-1],'spike')
return spiketab
def create_spikegen(name, type, refractory_period, rate=None, threshold=None):
''' Create spikegen which is used as pre synaptic trigger.
'''
if not moose.exists('/spikegens'):
spikelib = moose.Neutral('/spikegens')
if type.lower() in "random" and rate is not None:
spikegen = moose.RandSpike('/spikegens/' + name)
spikegen.rate = np.float(rate)
elif type.lower() in "linear" and threshold is not None:
spikegen = moose.SpikeGen('/spikegens/' + name)
spikegen.threshold = np.float(threshold)
spikegen.refractT = np.float(refractory_period)
return spikegen
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 createNetwork(self):
'''setting up of the cells and their connections'''
hopfield = moose.Neutral('/hopfield')
pg = moose.PulseGen('/hopfield/inPulGen')
pgTable = moose.Table('/hopfield/inPulGen/pgTable')
moose.connect(pgTable, 'requestOut', pg, 'getOutputValue')
pg.firstDelay = 10e-3
pg.firstWidth = 2e-03
pg.firstLevel = 3.0
pg.secondDelay = 1.0
for i in range(self.numNeurons):
cellPath = '/hopfield/cell_' + str(i)
cell = moose.IntFire(cellPath)
cell.setField('tau', 10e-3)
cell.setField('refractoryPeriod', 5e-3)
cell.setField('thresh', 0.99)
cell.synapse.num = self.numNeurons
#definite firing everytime ip is given
cell.synapse[i].weight = 1.00 #synapse i = input synapse
cell.synapse[i].delay = 0.0 #1e-3 #instantaneous
#VmVals = moose.Table(cellPath+'/Vm_cell_'+str(i))
#moose.connect(VmVals, 'requestOut', cell, 'getVm')
spikeVals = moose.Table(cellPath + '/spike_cell_' + str(i))
moose.connect(cell, 'spike', spikeVals, 'input')
inSpkGen = moose.SpikeGen(cellPath + '/inSpkGen')
inSpkGen.setField('edgeTriggered', True)
inSpkGen.setField('threshold', 2.0)
moose.connect(pg, 'output', inSpkGen, 'Vm')
#inTable = moose.Table(cellPath+'/inSpkGen/inTable')
#moose.connect(inTable, 'requestOut', inSpkGen, 'getHasFired')
moose.connect(inSpkGen, 'spikeOut', cell.synapse[i],
'addSpike') #self connection is the input
self.inSpike.append(inSpkGen)
#self.inTables.append(inTable)
#self.Vms.append(VmVals)
self.cells.append(cell)
self.allSpikes.append(spikeVals)
for ii in range(self.numNeurons):
for jj in range(self.numNeurons):
if ii == jj:
continue
self.cells[jj].synapse[ii].weight = 0
self.cells[jj].synapse[ii].delay = 20e-3
moose.connect(self.cells[ii], 'spike',
self.cells[jj].synapse[ii], 'addSpike')
def create_model():
"""Create two single compartmental neurons, neuron_A is the
presynaptic neuron and neuron_B is the postsynaptic neuron.
1. The presynaptic cell's Vm is monitored by a SpikeGen
object. Whenever the Vm crosses the threshold of the spikegen, it
sends out a spike event message.
2. This is event message is received by a SynHandler, which
passes the event as activation parameter to a SynChan object.
3. The SynChan, which is connected to the postsynaptic neuron
as a channel, updates its conductance based on the activation
parameter.
4. The change in conductance due to a spike may evoke an
action potential in the post synaptic neuron.
"""
model = moose.Neutral('/model')
nrn_a = create_1comp_neuron('/model/neuron_A')[0]
nrn_b = create_1comp_neuron('/model/neuron_B')[0]
#: SynChan for post synaptic neuron
synchan = moose.SynChan('/model/neuron_B/synchan')
synchan.Gbar = 1e-8
synchan.tau1 = 2e-3
synchan.tau2 = 2e-3
msg = moose.connect(nrn_b, 'channel', synchan, 'channel')
#: Create SynHandler to handle spike event input and set the
#: activation input of synchan
synhandler = moose.SimpleSynHandler('/model/neuron_B/synhandler')
synhandler.synapse.num = 1
synhandler.synapse[0].delay = 5e-3
moose.connect(synhandler, 'activationOut', synchan, 'activation')
#: SpikeGen detects when presynaptic Vm crosses threshold and
#: sends out a spike event
spikegen = moose.SpikeGen('/model/neuron_A/spikegen')
spikegen.threshold = 0.0
msg = moose.connect(nrn_a, 'VmOut', spikegen, 'Vm')
msg = moose.connect(spikegen, 'spikeOut', synhandler.synapse[0],
'addSpike')
return {
'presynaptic': nrn_a,
'postsynaptic': nrn_b,
'spikegen': spikegen,
'synchan': synchan,
'synhandler': synhandler
}
def loadModel(filename):
global soma_, cellSpikeTable_
neuromlR = NeuroML()
neuromlR.readNeuroMLFromFile(filename)
libcell = moose.Neuron('/library/CA1soma')
CA1Cellid = moose.copy(libcell,moose.Neutral('/cells'),'CA1')
CA1Cell = moose.Neuron(CA1Cellid)
spikeGen = moose.SpikeGen(CA1Cell.path+'/spikeGen')
spikeGen.threshold = -30e-3 # V
soma_ = moose.Compartment(CA1Cell.path+'/Seg0_soma_0_0')
soma_.inject = 0 # by default the cell has a current injection
moose.connect(soma_,'VmOut',spikeGen,'Vm')
table_path = moose.Neutral(CA1Cell.path+'/data').path
cellSpikeTable_ = moose.Table(table_path+'/spikesTable')
moose.connect(spikeGen,'spikeOut', cellSpikeTable_,'input')
def init_chanlib():
"""Return a dict of channel name, channel prototype pairs. If the
channel prototypes have not been initialized, this functions
initializes the same."""
global _channels
if _channels:
return _channels
if not moose.exists(config.modelSettings.libpath):
moose.Neutral(config.modelSettings.libpath)
_channels.update(nachans.initNaChannelPrototypes())
_channels.update(kchans.initKChannelPrototypes())
_channels.update(archan.initARChannelPrototypes())
_channels.update(cachans.initCaChannelPrototypes())
_channels.update(capool.initCaPoolPrototypes())
_channels['spike'] = moose.SpikeGen('{}/spike'.format(
config.modelSettings.libpath))
return _channels
def get_targets(cell_paths):
"""Get the cells post synaptic to cells listed in cell_paths."""
# print '###', cell_paths
target_sources_map = defaultdict(list)
for cp in cell_paths:
# print '###', cp
sg_list = moose.context.getWildcardList(cp + '/##[TYPE=SpikeGen]', True)
for sg in sg_list:
sg = moose.SpikeGen(sg)
for synId in sg.neighbours('event', 2):
print synId.path()
syn = moose.Neutral(synId)
if not(syn.className == 'SynChan' or syn.className == 'NMDAChan'):
continue
for comp in moose.Neutral(synId).neighbours('channel', 2):
# print '-->', comp.path()
target_sources_map[comp.path().rpartition('/')[0]].append(cp)
return target_sources_map
def __init__(self, *args):
moose.Compartment.__init__(self, *args)
self.spikegen = moose.SpikeGen('%s/spike' % (self.path))
self.spikegen.edgeTriggered = 1 # This ensures that spike is generated only on leading edge.
self.dynamics = moose.Func('%s/dynamics' % (self.path))
self.initVm = 0.0
self.Rm = 10e6
self.Ra = 1e4
self.Cm = 100e-9
self.Em = 0 #-65e-3
self.initVm = 0 #self.Em
# Note that the result is dependent on exact order of
# execution of SpikeGen and Func. If Func gets executed first
# SpikeGen will never cross threshold.
self.dynamics.expr = 'x >= y? z: x'
moose.connect(self, 'VmOut', self.dynamics, 'xIn')
moose.connect(self.dynamics, 'valueOut', self, 'setVm')
moose.connect(self, 'VmOut', self.spikegen, 'Vm')
def make_synapse(path):
"""Create a synapse with two time constants. Connect a spikegen to the
synapse. Create a pulsegen to drive the spikegen."""
syn = moose.SynChan(path)
syn.tau1 = 5.0 # ms
syn.tau2 = 1.0 # ms
syn.Gk = 1.0 # mS
syn.Ek = 0.0
## NOTE: This is old implementation.
#syn.synapse.num = 1
## syn.bufferTime = 1.0 # ms
#syn.synapse.delay = 1.0
#syn.synapse.weight = 1.0
#print 'Synapses:', len(syn.synapse), 'w=', syn.synapse[0].weight
# IN new implementation, there is SimpleSynHandler class which takes cares
# of multiple synapses. Class SynChan does not have any .synapse field.
synH = moose.SimpleSynHandler('%s/SynHandler' % path)
synH.synapse.num = 1
## syn.bufferTime = 1.0 # ms
synH.synapse.delay = 1.0
synH.synapse.weight = 1.0
synH.connect('activationOut', syn, 'activation')
print(('Synapses:', len(synH.synapse), 'w=', synH.synapse[0].weight))
spikegen = moose.SpikeGen('%s/spike' % (syn.parent.path))
spikegen.edgeTriggered = False # Make it fire continuously when input is high
spikegen.refractT = 10.0 # With this setting it will fire at 1 s / 10 ms = 100 Hz
spikegen.threshold = 0.5
# This will send alternatind -1 and +1 to SpikeGen to make it fire
spike_stim = moose.PulseGen('%s/spike_stim' % (syn.parent.path))
spike_stim.delay[0] = 1.0
spike_stim.level[0] = 1.0
spike_stim.width[0] = 100.0
moose.connect(spike_stim, 'output', spikegen, 'Vm')
m = moose.connect(spikegen, 'spikeOut', synH.synapse.vec, 'addSpike',
'Sparse')
m.setRandomConnectivity(1.0, 1)
m = moose.connect(spikegen, 'spikeOut', synH.synapse[0],
'addSpike') # this causes segfault
return syn, spikegen
def __init__(self,
path,
syn_shape,
Cm=1.0,
Em=0.0,
Rm=1.0,
Vr=0.0,
Vt=1.0,
refractT=0.0,
inject=0.0,
tau_e=0.001,
tau_i=0.001,
e_e=0.0,
e_i=-0.07):
moose.IntFire.__init__(self, path)
self.Cm = Cm
self.Em = Em
self.Rm = Rm
self.Vr = Vr
self.Vt = Vt
self.refractT = refractT
self.inject = inject
self.syn_shape = syn_shape
self.esyn = moose.SynChan("%s/excitatory" % path)
self.isyn = moose.SynChan("%s/inhibitory" % path)
for syn in self.esyn, self.isyn:
syn.tau2 = 1e-6 # instantaneous rise, for shape=='exp'
syn.Gbar = 1 * uS
self.connect("channel", syn, "channel")
syn.n_incoming_connections = 0
self.tau_e = tau_e
self.tau_i = tau_i
self.e_e = e_e
self.e_i = e_i
self.source = moose.SpikeGen("source", self)
self.source.thresh = 0.0
self.source.abs_refract = 2.0
self.connect("VmSrc", self.source, "Vm")
self.comp = self # for recorder mixin
def many_ematrix_to_one_element():
model = moose.Neutral('/model')
# data = moose.Neutral('/data')
synchan = moose.SynChan('/model/synchan')
synh = moose.SimpleSynHandler('/model/synchan/synh')
moose.connect(synh, 'activationOut', synchan, 'activation')
synh.synapse.num = 2
num_spikegen = 5
spikegens = [
moose.SpikeGen('/model/spikegen_%d' % (ii))
for ii in range(num_spikegen)
]
for ii in range(num_spikegen):
msg = moose.connect(spikegens[ii], 'spikeOut', synh.synapse[ii % 2],
'addSpike')
# synchan.synapse[ii].delay = ii * 1e-3
# synchan.synapse[ii].weight = (ii+1) * 0.1
for sg in spikegens:
print(sg.path, '-->', end=' ')
for m in sg.msgOut:
print(moose.element(m).adjacent[sg].path)
def setupmodel(modelpath, iaf_Rm, iaf_Cm, pulse_interval):
"""Create a LeakyIaF neuron under `modelpath` and a synaptic
channel (SynChan) in it. Create a spike generator stimulated by a
pulse generator to give input to the synapse.
"""
model_container = moose.Neutral(modelpath)
data_container = moose.Neutral(datapath)
iaf = moose.LIF('%s/iaf' % (modelpath))
iaf.Rm = iaf_Rm
iaf.Cm = iaf_Cm
iaf.initVm = -0.070
iaf.Em = -0.065
#iaf.Vreset = -0.070
iaf.thresh = -0.055
# iaf.refractoryPeriod = 0.005
syn = moose.SynChan('%s/syn' % (iaf.path))
synh = moose.SimpleSynHandler(syn.path + '/synh')
moose.connect(synh, 'activationOut', syn, 'activation')
synh.synapse.num = 1
synh.synapse[0].delay = 0.01
syn.Ek = 0.0
syn.Gbar = 1.0
moose.connect(syn, 'channel', iaf, 'channel')
moose.connect(iaf, 'VmOut', syn, 'Vm')
sg = moose.SpikeGen('%s/spike' % (modelpath))
sg.threshold = 0.1
moose.connect(sg, 'spikeOut', synh.synapse[0], 'addSpike')
pg = moose.PulseGen('%s/pulse' % (modelpath))
pg.delay[0] = pulse_interval
pg.width[0] = 1e-3
pg.level[0] = 0.5
moose.connect(pg, 'output', sg, 'Vm')
return {
'model': model_container,
'iaf': iaf,
'synchan': syn,
'spikegen': sg,
'pulsegen': pg
}
def setupTable(name,
obj,
qtyname,
tables_path=None,
threshold=None,
spikegen=None):
""" Sets up a table with 'name' which stores 'qtyname' field from 'obj'.
The table is created under tables_path if not None, else under obj.path . """
if tables_path is None:
tables_path = obj.path + "/data"
## in case tables_path does not exist, below wrapper will create it
tables_path_obj = moose.Neutral(tables_path)
qtyTable = moose.Table(tables_path_obj.path + "/" + name)
assert qtyTable, "%s not found" % qtyTable
## stepMode no longer supported, connect to 'input'/'spike' message dest to record Vm/spiktimes
# qtyTable.stepMode = TAB_BUF
if spikegen is None:
if threshold is None:
## below is wrong! reads qty twice every clock tick!
# moose.connect( obj, qtyname+'Out', qtyTable, "input")
## this is the correct method
moose.connect(qtyTable, "requestOut", obj, "get" + qtyname)
else:
## create new spikegen
spikegen = moose.SpikeGen(tables_path_obj.path + "/" + name +
"_spikegen")
## connect the compartment Vm to the spikegen
moose.connect(obj, "VmOut", spikegen, "Vm")
## spikegens for different synapse_types can have different thresholds
spikegen.threshold = threshold
spikegen.edgeTriggered = (
1 # This ensures that spike is generated only on leading edge.
)
else:
moose.connect(spikegen, "spikeOut", qtyTable,
"input") ## spikeGen gives spiketimes
return qtyTable
