def library1():
import moose.genesis
import moose.SBML
import moose.chemMerge
import moose.utils
import moose.network_utils
print('done')
p1 = moose.le()
a = moose.Pool('/a')
for i in range(10):
moose.Pool('/a/p%d' % i)
p2 = moose.le()
assert set(p2) - set(p1) == set(['/a'])
aa = moose.le(a)
assert len(aa) == 10
try:
moose.syncDataHandler('/a')
except NotImplementedError:
pass
try:
moose.showfield('/x')
except ValueError:
pass
moose.showfield('/a')
moose.showfields('/a')
def main():
"""
This example illustrates loading and running a reaction system that
spans two volumes, that is, is in different compartments. It uses a
kkit model file. You can tell if it is working if you see nice
relaxation oscillations.
"""
# the kkit reader doesn't know how to do multicompt solver setup.
solver = "ee"
mfile = '../Genesis_files/OSC_diff_vols.g'
runtime = 3000.0
simDt = 1.0
modelId = moose.loadModel( mfile, 'model', solver )
#moose.delete( '/model/kinetics/A/Stot' )
compt0 = moose.element( '/model/kinetics' )
compt1 = moose.element( '/model/compartment_1' )
assert( deq( compt0.volume, 2e-20 ) )
assert( deq( compt1.volume, 1e-20 ) )
dy = compt0.dy
compt1.y1 += dy
compt1.y0 = dy
assert( deq( compt1.volume, 1e-20 ) )
# We now have two cubes adjacent to each other. Compt0 has 2x vol.
# Compt1 touches it.
stoich0 = moose.Stoich( '/model/kinetics/stoich' )
stoich1 = moose.Stoich( '/model/compartment_1/stoich' )
ksolve0 = moose.Ksolve( '/model/kinetics/ksolve' )
ksolve1 = moose.Ksolve( '/model/compartment_1/ksolve' )
stoich0.compartment = compt0
stoich0.ksolve = ksolve0
stoich0.path = '/model/kinetics/##'
stoich1.compartment = compt1
stoich1.ksolve = ksolve1
stoich1.path = '/model/compartment_1/##'
#stoich0.buildXreacs( stoich1 )
print ksolve0.numLocalVoxels, ksolve0.numPools, stoich0.numAllPools
assert( ksolve0.numLocalVoxels == 1 )
assert( ksolve0.numPools == 7 )
assert( stoich0.numAllPools == 6 )
print len( stoich0.proxyPools[stoich1] ),
print len( stoich1.proxyPools[stoich0] )
assert( len( stoich0.proxyPools[stoich1] ) == 1 )
assert( len( stoich1.proxyPools[stoich0] ) == 1 )
print ksolve1.numLocalVoxels, ksolve1.numPools, stoich1.numAllPools
assert( ksolve1.numLocalVoxels == 1 )
assert( ksolve1.numPools == 6 )
assert( stoich1.numAllPools == 5 )
stoich0.buildXreacs( stoich1 )
print moose.element( '/model/kinetics/endo' )
print moose.element( '/model/compartment_1/exo' )
moose.le( '/model/compartment_1' )
moose.reinit()
moose.start( runtime )
# Display all plots.
for x in moose.wildcardFind( '/model/#graphs/conc#/#' ):
t = numpy.arange( 0, x.vector.size, 1 ) * simDt
pylab.plot( t, x.vector, label=x.name )
pylab.legend()
pylab.show()
def testChemAlone():
nid = makeChemInCubeMesh()
moose.le( '/n' )
makeChemPlots()
moose.setClock( 5, 1e-2 )
moose.setClock( 6, 1e-2 )
moose.setClock( 7, 1.0 )
moose.setClock( 8, 1.0 )
moose.setClock( 9, 1.0 )
moose.useClock( 5, '/n/##', 'init' )
moose.useClock( 6, '/n/##', 'process' )
#moose.useClock( 7, '/graphs/#', 'process' )
moose.useClock( 8, '/graphs/#', 'process' )
moose.reinit()
moose.start( 100 )
dumpPlots( 'chem.plot' )
# Make ksolver and rerun.
ksolve = moose.GslStoich( '/n/solver' )
ksolve.path = '/n/##'
ksolve.method = 'rk5'
moose.useClock( 5, '/n/solver', 'process' )
moose.setClock( 5, 1 )
moose.setClock( 6, 1 )
moose.reinit()
moose.start( 100 )
dumpPlots( 'kchem.plot' )
def main():
simtime = 1
simdt = 0.25e-5
plotdt = 0.25e-3
for i in range(10):
moose.setClock(i, simdt)
moose.setClock(8, plotdt)
model = moose.Neutral('/model')
comp = create_1comp_neuron('/model/neuron')
sh, preSyns = createRandomSynapse(comp, "excitatory", 0, 10)
sh2, preSyns2 = createRandomSynapse(comp, "inhibitory", -80, 2)
moose.le("/model/neuron")
# stim = create_pulse("/model/stimulus", 20e-3, 40e-3, 1e-9, comp)
data = moose.Neutral('/data')
preTables = []
for i, preSyn in enumerate(preSyns):
print(i)
print(preSyn)
preTables.append(create_spike_table("/data/pre" + str(i), preSyn))
moose.reinit()
moose.start(simtime)
plot_spike_tables(preTables)
# current_tab = create_table("/data/current", stim, "getOutputValue")
vm_tab = create_table("/data/Vm", comp, "getVm")
moose.reinit()
moose.start(simtime)
#ts = np.linspace(0, simtime, len(vm_tab.vector))
plot_table(vm_tab) #, current_tab
def main():
global params
fig = plt.figure(figsize=(6, 10), facecolor='white')
library = moose.Neutral('/library')
for ii in range(len(sys.argv)):
if sys.argv[ii][:2] == '--':
argName = sys.argv[ii][2:]
if argName in params:
params[argName] = float(sys.argv[ii + 1])
if argName == 'sequence':
params[argName] = sys.argv[ii + 1] # Leave it as a str.
moose.seed(int(params['seed']))
'''
'''
makePassiveSoma('cell', params['dendLength'], params['dendDiameter'])
moose.le('/library')
panelBCsingleCompt(fig)
moose.le('/library')
moose.delete('/library/soma')
params['dendLength'] = 60e-6
makePassiveSoma('cell', params['dendLength'], params['dendDiameter'])
panelEFspatialSeq(fig)
plt.tight_layout()
plt.show()
def test_elec_alone():
eeDt = 2e-6
hSolveDt = 2e-5
runTime = 0.02
make_spiny_compt()
make_elec_plots()
head2 = moose.element( '/n/head2' )
moose.setClock( 0, 2e-6 )
moose.setClock( 1, 2e-6 )
moose.setClock( 2, 2e-6 )
moose.setClock( 8, 0.1e-3 )
moose.useClock( 0, '/n/##[ISA=Compartment]', 'init' )
moose.useClock( 1, '/n/##[ISA=Compartment]', 'process' )
moose.useClock( 2, '/n/##[ISA=ChanBase],/n/##[ISA=SynBase],/n/##[ISA=CaConc],/n/##[ISA=SpikeGen]','process')
moose.useClock( 8, '/graphs/elec/#', 'process' )
moose.reinit()
moose.start( runTime )
dump_plots( 'instab.png' )
# make Hsolver and rerun
hsolve = moose.HSolve( '/n/hsolve' )
moose.useClock( 1, '/n/hsolve', 'process' )
hsolve.dt = 20e-6
hsolve.target = '/n/compt'
moose.le( '/n' )
for dt in ( 20e-6, 50e-6, 100e-6 ):
print(('running at dt =', dt))
moose.setClock( 0, dt )
moose.setClock( 1, dt )
moose.setClock( 2, dt )
hsolve.dt = dt
moose.reinit()
moose.start( runTime )
dump_plots( 'h_instab' + str( dt ) + '.png' )
def main():
library = moose.Neutral('/library')
#makePassiveSoma( 'cell', params['dendL'], params['dendDia'] )
makeDendProto()
makeChemProto()
rdes = rd.rdesigneur(
turnOffElec=True,
chemPlotDt=0.1,
diffusionLength=params['diffusionL'],
#cellProto=[['cell','soma']],
cellProto=[['elec', 'dend']],
chemProto=[['hydra', 'hydra']],
chemDistrib=[['hydra', '#soma#,#dend#', 'install', '1']],
plotList=[
['soma', '1', 'dend/A', 'n', '# of A'],
['soma', '1', 'dend/B', 'n', '# of B'],
],
# moogList = [['soma', '1', 'dend/A', 'n', 'num of A (number)']]
)
moose.le('/library')
moose.le('/library/hydra')
#moose.showfield( '/library/soma/soma' )
rdes.buildModel()
#moose.element('/model/chem/dend/B').vec[50].nInit=15.5
A = moose.element('/model/chem/dend/A')
B = moose.element('/model/chem/dend/B')
C = moose.element('/model/chem/dend/C')
A.diffConst = 1e-13
B.diffConst = 50 * 1e-12
C.diffConst = 0.8 * 1e-12
avec = moose.vec('/model/chem/dend/A').n
savec = avec.size
randper = np.random.uniform(1, 2, savec)
#for i in range(0,savec-1,1):
#moose.element('/model/chem/dend/A').vec[i].nInit = randper[i]
moose.element('/model/chem/dend/A').vec[50].nInit = 100
moose.element('/model/chem/dend/B').vec[50].nInit = 100
moose.element('/model/chem/dend/C').vec.nInit = 0
storeAvec = []
storeBvec = []
storeCvec = []
moose.reinit()
for i in range(1, 4000, 10):
moose.start(10)
avec = moose.vec('/model/chem/dend/A').n
bvec = moose.vec('/model/chem/dend/B').n
cvec = moose.vec('/model/chem/dend/C').n
storeAvec.append(avec)
storeBvec.append(bvec)
storeCvec.append(cvec)
trialNum = '1'
fileName = 'mechano.xml'
writeXML(storeAvec, trialNum, fileName)
return storeAvec, storeBvec, storeCvec
def test_elec_alone():
eeDt = 2e-6
hSolveDt = 2e-5
runTime = 0.02
make_spiny_compt()
make_elec_plots()
head2 = moose.element( '/n/head2' )
moose.setClock( 0, 2e-6 )
moose.setClock( 1, 2e-6 )
moose.setClock( 2, 2e-6 )
moose.setClock( 8, 0.1e-3 )
moose.useClock( 0, '/n/##[ISA=Compartment]', 'init' )
moose.useClock( 1, '/n/##[ISA=Compartment]', 'process' )
moose.useClock( 2, '/n/##[ISA=ChanBase],/n/##[ISA=SynBase],/n/##[ISA=CaConc],/n/##[ISA=SpikeGen]','process')
moose.useClock( 8, '/graphs/elec/#', 'process' )
moose.reinit()
moose.start( runTime )
dump_plots( 'instab.plot' )
print "||||", len(moose.wildcardFind('/##[ISA=HHChannel]'))
# make Hsolver and rerun
hsolve = moose.HSolve( '/n/hsolve' )
moose.useClock( 1, '/n/hsolve', 'process' )
hsolve.dt = 20e-6
hsolve.target = '/n/compt'
moose.le( '/n' )
for dt in ( 20e-6, 50e-6, 100e-6 ):
print 'running at dt =', dt
moose.setClock( 0, dt )
moose.setClock( 1, dt )
moose.setClock( 2, dt )
hsolve.dt = dt
moose.reinit()
moose.start( runTime )
dump_plots( 'h_instab' + str( dt ) + '.plot' )
def main():
"""
This example illustrates loading and running a reaction system that
spans two volumes, that is, is in different compartments. It uses a
kkit model file. You can tell if it is working if you see nice
relaxation oscillations.
"""
# the kkit reader doesn't know how to do multicompt solver setup.
solver = "ee"
mfile = '../Genesis_files/OSC_diff_vols.g'
runtime = 3000.0
simDt = 1.0
modelId = moose.loadModel(mfile, 'model', solver)
#moose.delete( '/model/kinetics/A/Stot' )
compt0 = moose.element('/model/kinetics')
compt1 = moose.element('/model/compartment_1')
assert (deq(compt0.volume, 2e-20))
assert (deq(compt1.volume, 1e-20))
dy = compt0.dy
compt1.y1 += dy
compt1.y0 = dy
assert (deq(compt1.volume, 1e-20))
# We now have two cubes adjacent to each other. Compt0 has 2x vol.
# Compt1 touches it.
stoich0 = moose.Stoich('/model/kinetics/stoich')
stoich1 = moose.Stoich('/model/compartment_1/stoich')
ksolve0 = moose.Ksolve('/model/kinetics/ksolve')
ksolve1 = moose.Ksolve('/model/compartment_1/ksolve')
stoich0.compartment = compt0
stoich0.ksolve = ksolve0
stoich0.path = '/model/kinetics/##'
stoich1.compartment = compt1
stoich1.ksolve = ksolve1
stoich1.path = '/model/compartment_1/##'
#stoich0.buildXreacs( stoich1 )
print ksolve0.numLocalVoxels, ksolve0.numPools, stoich0.numAllPools
assert (ksolve0.numLocalVoxels == 1)
assert (ksolve0.numPools == 7)
assert (stoich0.numAllPools == 6)
print len(stoich0.proxyPools[stoich1]),
print len(stoich1.proxyPools[stoich0])
assert (len(stoich0.proxyPools[stoich1]) == 1)
assert (len(stoich1.proxyPools[stoich0]) == 1)
print ksolve1.numLocalVoxels, ksolve1.numPools, stoich1.numAllPools
assert (ksolve1.numLocalVoxels == 1)
assert (ksolve1.numPools == 6)
assert (stoich1.numAllPools == 5)
stoich0.buildXreacs(stoich1)
print moose.element('/model/kinetics/endo')
print moose.element('/model/compartment_1/exo')
moose.le('/model/compartment_1')
moose.reinit()
moose.start(runtime)
# Display all plots.
for x in moose.wildcardFind('/model/#graphs/conc#/#'):
t = numpy.arange(0, x.vector.size, 1) * simDt
pylab.plot(t, x.vector, label=x.name)
pylab.legend()
pylab.show()
def scanDistDtGrid():
seqList, seqScore = makeSequence( numSpine )
#moose.setClock(18, 0.02 )
#print "DT = ", moose.element( '/model/graphs/plot0').dt
seqDtRange = ( 0.5, 1.0, 1.5, 2.0, 3.0, 4.0, 6.0 ) # Interval between stimuli, in sec
drange = ( 5, 10, 15, 20, 25, 30 ) # Distance covered, in diffLen.
if displayMoogli:
seqDtRange = ( moogliDt, )
drange = ( moogliDistance, )
# seqDtRange = ( 0.5, 1.0, 1.5, 2.0, 3.0, 4.0, 6.0 ) # Interval between stimuli, in sec
# drange = ( 5, 10, 15, 20, 25, 30 )
allSimOutput = []
ampl = moose.vec( '/model/chem/dend/ampl' )
print("ampl: ", len(ampl))
ampl.nInit = params['stimAmplitude']
blanks = params['blankVoxelsAtEnd']
preStim = params['preStimTime']
postStim = params['postStimTime']
diffusionLength = params['diffusionLength']
for seqDt in seqDtRange:
temp2 = []
temp3 = []
for d in drange:
# compt = moose.Compartment( '/model/chem/soma')
# compt.diameter = params['dendDiameter']/8
dend = moose.element( '/model/chem/dend')
# print("dend diameter: ", dend.diameter)
moose.le( '/model/chem/dend' )
phase = moose.vec( '/model/chem/dend/phase' )
ampl = moose.vec( '/model/chem/dend/ampl' )
# Old version. Assumes we activate density * d compartments.
#ampl.nInit = float(v)/float(d)
ampl.nInit = params['stimAmplitude']
Z = moose.vec( '/model/chem/dend/Z' )
stride = int(d) / numSpine
Z.nInit = 0
phase.nInit = 10000.0
temp = []
slopes = []
for seq in seqList:
print '.',
sys.stdout.flush()
for j in range( numSpine ):
k = (blanks + j * stride)
Z[ k ].nInit = 1
phase[ k ].nInit = preStim + seq[j] * seqDt
temp.append( runTrial( diffusionLength, seqDt, d, blanks, preStim, postStim ))
#print temp
simOut = np.array( temp )
temp3.append( simOut )
print seqDt, d #temp[-1], temp[-2],
allSimOutput.append( temp3 )
return allSimOutput, seqDtRange, drange
def makeModel():
if len( sys.argv ) == 1:
useGsolve = True
else:
useGsolve = ( sys.argv[1] == 'True' )
# create container for model
model = moose.Neutral( 'model' )
compartment = moose.CubeMesh( '/model/compartment' )
compartment.volume = 1e-22
# the mesh is created automatically by the compartment
moose.le( '/model/compartment' )
mesh = moose.element( '/model/compartment/mesh' )
# create molecules and reactions
a = moose.Pool( '/model/compartment/a' )
b = moose.Pool( '/model/compartment/b' )
# create functions of time
f1 = moose.Function( '/model/compartment/f1' )
f2 = moose.Function( '/model/compartment/f2' )
# connect them up for reactions
moose.connect( f1, 'valueOut', a, 'setConc' )
moose.connect( f2, 'valueOut', b, 'increment' )
# Assign parameters
a.concInit = 0
b.concInit = 1
#f1.numVars = 1
#f2.numVars = 1
f1.expr = '1 + sin(t)'
f2.expr = '10 * cos(t)'
# Create the output tables
graphs = moose.Neutral( '/model/graphs' )
outputA = moose.Table2 ( '/model/graphs/nA' )
outputB = moose.Table2 ( '/model/graphs/nB' )
# connect up the tables
moose.connect( outputA, 'requestOut', a, 'getN' );
moose.connect( outputB, 'requestOut', b, 'getN' );
# Set up the solvers
if useGsolve:
gsolve = moose.Gsolve( '/model/compartment/gsolve' )
gsolve.useClockedUpdate = True
else:
gsolve = moose.Ksolve( '/model/compartment/gsolve' )
stoich = moose.Stoich( '/model/compartment/stoich' )
stoich.compartment = compartment
stoich.ksolve = gsolve
stoich.path = '/model/compartment/##'
'''
'''
# We need a finer timestep than the default 0.1 seconds,
# in order to get numerical accuracy.
for i in range (10, 19 ):
moose.setClock( i, 0.1 ) # for computational objects
def makeModel():
if len(sys.argv) == 1:
useGsolve = True
else:
useGsolve = (sys.argv[1] == 'True')
# create container for model
model = moose.Neutral('model')
compartment = moose.CubeMesh('/model/compartment')
compartment.volume = 1e-22
# the mesh is created automatically by the compartment
moose.le('/model/compartment')
mesh = moose.element('/model/compartment/mesh')
# create molecules and reactions
a = moose.Pool('/model/compartment/a')
b = moose.Pool('/model/compartment/b')
# create functions of time
f1 = moose.Function('/model/compartment/f1')
f2 = moose.Function('/model/compartment/f2')
# connect them up for reactions
moose.connect(f1, 'valueOut', a, 'setConc')
moose.connect(f2, 'valueOut', b, 'increment')
# Assign parameters
a.concInit = 0
b.concInit = 1
#f1.numVars = 1
#f2.numVars = 1
f1.expr = '1 + sin(t)'
f2.expr = '10 * cos(t)'
# Create the output tables
graphs = moose.Neutral('/model/graphs')
outputA = moose.Table2('/model/graphs/nA')
outputB = moose.Table2('/model/graphs/nB')
# connect up the tables
moose.connect(outputA, 'requestOut', a, 'getN')
moose.connect(outputB, 'requestOut', b, 'getN')
# Set up the solvers
if useGsolve:
gsolve = moose.Gsolve('/model/compartment/gsolve')
gsolve.useClockedUpdate = True
else:
gsolve = moose.Ksolve('/model/compartment/gsolve')
stoich = moose.Stoich('/model/compartment/stoich')
stoich.compartment = compartment
stoich.ksolve = gsolve
stoich.path = '/model/compartment/##'
'''
'''
# We need a finer timestep than the default 0.1 seconds,
# in order to get numerical accuracy.
for i in range(10, 19):
moose.setClock(i, 0.1) # for computational objects
def main():
library = moose.Neutral('/library')
makePassiveSoma('cell', params['dendL'], params['dendDia'])
makeChemProto()
rdes = rd.rdesigneur(
turnOffElec=True,
chemPlotDt=0.1,
diffusionLength=params['diffusionL'],
cellProto=[['cell', 'soma']],
chemProto=[['hydra', 'hydra']],
chemDistrib=[['hydra', 'soma', 'install', '1']],
plotList=[['soma', '1', 'dend/A', 'n', '# of A'],
['soma', '1', 'dend/B', 'n', '# of B']],
# moogList = [['soma', '1', 'dend/A', 'n', 'num of A (number)']]
)
moose.le('/library')
moose.le('/library/hydra')
moose.showfield('/library/soma/soma')
rdes.buildModel()
#moose.element('/model/chem/dend/B').vec[50].nInit=15.5
A = moose.vec('/model/chem/dend/A')
#B = moose.vec('/model/chem/dend/B')
# A.concInit=1
# B.concInit=10
moose.element('/model/chem/dend/B').vec[50].nInit = 100
#moose.element('/model/chem/dend/B').vec[25].nInit=0
#A.nInit=1
#B.nInit=15
#Adot = moose.element('/model/chem/dend/A/Adot')
#Bdot = moose.element('/model/chem/dend/B/Bdot')
#print "\n\n\t\t Before Run", Adot, Bdot, A.nInit, B.nInit, A.n, B.n, A.concInit, B.concInit
moose.reinit()
moose.start(500)
#print "\n\n\t\t After Run", A.nInit, B.nInit, A.n, B.n, A.concInit, B.concInit
# rdes.display()
# rdes.displayMoogli( 1, 400, 0.001 )
avec = moose.vec('/model/chem/dend/A').n
bvec = moose.vec('/model/chem/dend/B').n
#tab = moose.element( '/model/graphs/plot0')
#dt = tab.dt
#tvec=[]
#tvec.append( tab.vector )
# xplot = []
# xplot.append( avec )
## t = np.arange( 0, len( tvec[0] ), 1.0 ) * dt
plt.plot(avec)
#print bvec, len(bvec), bvec
return bvec, avec
def setup_clocks(simdt, plotdt):
print 'Setting up clocks: simdt', simdt, 'plotdt', plotdt
moose.setClock(INITCLOCK, simdt)
moose.setClock(ELECCLOCK, simdt)
moose.setClock(CHANCLOCK, simdt)
moose.setClock(POOLCLOCK, simdt)
moose.setClock(LOOKUPCLOCK, simdt)
moose.setClock(STIMCLOCK, simdt)
moose.setClock(PLOTCLOCK, plotdt)
moose.le('/clock')
def setup_clocks(simdt, plotdt):
print("Setting up clocks: simdt", simdt, "plotdt", plotdt)
moose.setClock(INITCLOCK, simdt)
moose.setClock(ELECCLOCK, simdt)
moose.setClock(CHANCLOCK, simdt)
moose.setClock(POOLCLOCK, simdt)
moose.setClock(LOOKUPCLOCK, simdt)
moose.setClock(STIMCLOCK, simdt)
moose.setClock(PLOTCLOCK, plotdt)
moose.le("/clock")
def test_le():
# see issue BhallaLab/moose-core#423
x = moose.le('/')
assert len(x) > 5, x
try:
moose.le('/abrakadabra')
except ValueError:
pass
else:
raise RuntimeError("This should have raised ValueError")
def main():
library = moose.Neutral('/library')
#makePassiveSoma( 'cell', params['dendL'], params['dendDia'] )
makeDendProto()
makeChemProto()
rdes = rd.rdesigneur(
turnOffElec=True,
chemPlotDt=0.1,
diffusionLength=params['diffusionL'],
#cellProto=[['cell','soma']],
cellProto=[['elec', 'dend']],
chemProto=[['hydra', 'hydra']],
chemDistrib=[['hydra', '#soma#,#dend#', 'install', '1']],
plotList=[['soma', '1', 'dend/A', 'n', '# of A'],
['soma', '1', 'dend/B', 'n', '# of B']],
# moogList = [['soma', '1', 'dend/A', 'n', 'num of A (number)']]
)
moose.le('/library')
moose.le('/library/hydra')
#moose.showfield( '/library/soma/soma' )
rdes.buildModel()
#moose.element('/model/chem/dend/B').vec[50].nInit=15.5
A = moose.element('/model/chem/dend/A')
B = moose.element('/model/chem/dend/B')
C = moose.element('/model/chem/dend/C')
A.diffConst = 1e-13
B.diffConst = 0
C.diffConst = 0
B.motorConst = 1e-06
C.motorConst = -1e-06
# A.concInit=1
# B.concInit=10
avec = moose.vec('/model/chem/dend/A').n
savec = avec.size
for i in range(0, savec - 1, 1):
moose.element('/model/chem/dend/A').vec[i].nInit = np.random.uniform(
0, 1)
print moose.element('/model/chem/dend/A').vec[i].nInit
print 'simulation start'
moose.reinit()
#moose.start(2)
for t in range(0, 4000, 500):
moose.start(500)
print 'in loop', t
avec = moose.vec('/model/chem/dend/A').n
plt.plot(avec)
avec = moose.vec('/model/chem/dend/A').n
bvec = moose.vec('/model/chem/dend/B').n
cvec = moose.vec('/model/chem/dend/C').n
#plt.plot(bvec)
return bvec, avec, cvec
def _setup_network(self):
"""Sets up the network (_init_network is enough)"""
self.network = moose.LIF( 'network', self.N );
moose.le( '/network' )
self.network.vec.Em = self.el
self.network.vec.thresh = self.vt
self.network.vec.refractoryPeriod = self.refrT
self.network.vec.Rm = self.Rm
self.network.vec.vReset = self.vr
self.network.vec.Cm = self.Cm
self.network.vec.inject = self.Iinject
def _setup_network(self):
"""Sets up the network (_init_network is enough)"""
self.network = moose.LIF('network', self.N)
moose.le('/network')
self.network.vec.Em = self.el
self.network.vec.thresh = self.vt
self.network.vec.refractoryPeriod = self.refrT
self.network.vec.Rm = self.Rm
self.network.vec.vReset = self.vr
self.network.vec.Cm = self.Cm
self.network.vec.inject = self.Iinject
def main():
library = moose.Neutral('/library')
#makePassiveSoma( 'cell', params['dendL'], params['dendDia'] )
makeDendProto()
makeChemProto()
rdes = rd.rdesigneur(
turnOffElec=True,
chemPlotDt=0.1,
diffusionLength=params['diffusionL'],
#cellProto=[['cell','soma']],
cellProto=[['elec', 'dend']],
chemProto=[['hydra', 'hydra']],
chemDistrib=[['hydra', '#soma#,#dend#', 'install', '1']],
plotList=[['soma', '1', 'dend/A', 'n', '# of A'],
['soma', '1', 'dend/B', 'n', '# of B']],
# moogList = [['soma', '1', 'dend/A', 'n', 'num of A (number)']]
)
moose.le('/library')
moose.le('/library/hydra')
#moose.showfield( '/library/soma/soma' )
rdes.buildModel()
#moose.element('/model/chem/dend/B').vec[50].nInit=15.5
A = moose.element('/model/chem/dend/A')
B = moose.element('/model/chem/dend/B')
A.diffConst = 1e-13
B.diffConst = 1e-12
moose.element('/model/chem/dend/A').vec[25].nInit = 0.1
moose.element('/model/chem/dend/B').vec[25].nInit = 0.1
moose.element('/model/chem/dend/A').vec[30].nInit = 0.1
moose.element('/model/chem/dend/B').vec[30].nInit = 0.1
moose.element('/model/chem/dend/A').vec[45].nInit = 0.1
moose.element('/model/chem/dend/B').vec[45].nInit = 0.1
storeAvec = []
storeBvec = []
for i in range(50):
moose.element('/model/chem/dend/space').vec[i].nInit = moose.element(
'/model/chem/dend/mesh').vec[i].Coordinates[0]
print moose.element('/model/chem/dend/space').vec[i].nInit
moose.reinit()
for i in range(1, 5000, 10):
moose.start(10)
avec = moose.vec('/model/chem/dend/A').n
bvec = moose.vec('/model/chem/dend/B').n
storeAvec.append(avec)
storeBvec.append(bvec)
bvec = moose.vec('/model/chem/dend/B').n
avec = moose.vec('/model/chem/dend/A').n
svec = moose.vec('/model/chem/dend/space').n
return svec, bvec, avec, storeAvec, storeBvec
def main():
# Schedule the whole lot
moose.setClock( 4, 0.1 ) # for the computational objects
moose.setClock( 5, 0.1 ) # clock for the solver
moose.setClock( 8, 1.0 ) # for the plots
# The wildcard uses # for single level, and ## for recursive.
#compartment = makeModel()
moose.loadModel( '../Genesis_files/M1719.cspace', '/model', 'ee' )
compartment = moose.element( 'model/kinetics' )
compartment.name = 'compartment'
ksolve = moose.Ksolve( '/model/compartment/ksolve' )
stoich = moose.Stoich( '/model/compartment/stoich' )
stoich.compartment = compartment
stoich.ksolve = ksolve
#ksolve.stoich = stoich
stoich.path = "/model/compartment/##"
state = moose.SteadyState( '/model/compartment/state' )
moose.useClock( 5, '/model/compartment/ksolve', 'process' )
moose.useClock( 8, '/model/graphs/#', 'process' )
moose.reinit()
state.stoich = stoich
#state.showMatrices()
state.convergenceCriterion = 1e-7
moose.le( '/model/graphs' )
a = moose.element( '/model/compartment/a' )
b = moose.element( '/model/compartment/b' )
c = moose.element( '/model/compartment/c' )
for i in range( 0, 100 ):
getState( ksolve, state )
moose.start( 100.0 ) # Run the model for 100 seconds.
b = moose.element( '/model/compartment/b' )
c = moose.element( '/model/compartment/c' )
# move most molecules over to b
b.conc = b.conc + c.conc * 0.95
c.conc = c.conc * 0.05
moose.start( 100.0 ) # Run the model for 100 seconds.
# move most molecules back to a
c.conc = c.conc + b.conc * 0.95
b.conc = b.conc * 0.05
moose.start( 100.0 ) # Run the model for 100 seconds.
# Iterate through all plots, dump their contents to data.plot.
displayPlots()
quit()
def main():
"""
Demonstrates how one can visualise morphology of a neuron using the MOOSE.
"""
app = QtGui.QApplication(sys.argv)
filename = 'barrionuevo_cell1zr.CNG.swc'
moose.Neutral('/library')
moose.Neutral('/model')
cell = moose.loadModel(filename, '/model/testSwc')
for i in range(8):
moose.setClock(i, simdt)
hsolve = moose.HSolve('/model/testSwc/hsolve')
hsolve.dt = simdt
hsolve.target = '/model/testSwc/soma'
moose.le(cell)
moose.reinit()
# Now we set up the display
compts = moose.wildcardFind("/model/testSwc/#[ISA=CompartmentBase]")
compts[0].inject = inject
ecomptPath = [x.path for x in compts]
morphology = moogli.extensions.moose.read(path="/model/testSwc",
vertices=15)
viewer = moogli.Viewer("Viewer")
viewer.attach_shapes(morphology.shapes.values())
view = moogli.View("main-view")
viewer.attach_view(view)
# morphology = moogli.read_morphology_from_moose(name = "", path = "/model/testSwc")
# morphology.create_group( "group_all", ecomptPath, -0.08, 0.02, \
# [0.0, 0.5, 1.0, 1.0], [1.0, 0.0, 0.0, 0.9] )
# viewer = moogli.DynamicMorphologyViewerWidget(morphology)
def callback(morphology, viewer):
moose.start(frameRunTime)
Vm = [moose.element(x).Vm for x in compts]
morphology.set_color("group_all", Vm)
currTime = moose.element('/clock').currentTime
#print currTime, compts[0].Vm
if (currTime < runtime):
return True
return False
#viewer.set_callback( callback, idletime = 0 )
#viewer.showMaximized()
viewer.show()
app.exec_()
def _setup_network(self):
"""Sets up the network (_init_network is enough)"""
self.network = moose.LIF("network", self.N)
moose.le("/network")
self.network.vec.Em = self.el
self.network.vec.thresh = self.vt
self.network.vec.refractoryPeriod = self.refrT
self.network.vec.Rm = self.Rm
self.network.vec.vReset = self.vr
self.network.vec.Cm = self.Cm
if not noiseInj:
self.network.vec.inject = self.Iinject
else:
## inject a constant + noisy current
## values are set in self.simulate()
self.noiseTables = moose.StimulusTable("noiseTables", self.N)
moose.connect(self.noiseTables, "output", self.network, "setInject", "OneToOne")
def main():
# The wildcard uses # for single level, and ## for recursive.
#compartment = makeModel()
moose.loadModel('../Genesis_files/M1719.cspace', '/model', 'ee')
compartment = moose.element('model/kinetics')
compartment.name = 'compartment'
ksolve = moose.Ksolve('/model/compartment/ksolve')
stoich = moose.Stoich('/model/compartment/stoich')
stoich.compartment = compartment
stoich.ksolve = ksolve
#ksolve.stoich = stoich
stoich.path = "/model/compartment/##"
state = moose.SteadyState('/model/compartment/state')
moose.reinit()
state.stoich = stoich
#state.showMatrices()
state.convergenceCriterion = 1e-7
moose.le('/model/graphs')
a = moose.element('/model/compartment/a')
b = moose.element('/model/compartment/b')
c = moose.element('/model/compartment/c')
for i in range(0, 100):
getState(ksolve, state)
moose.start(100.0) # Run the model for 100 seconds.
b = moose.element('/model/compartment/b')
c = moose.element('/model/compartment/c')
# move most molecules over to b
b.conc = b.conc + c.conc * 0.95
c.conc = c.conc * 0.05
moose.start(100.0) # Run the model for 100 seconds.
# move most molecules back to a
c.conc = c.conc + b.conc * 0.95
b.conc = b.conc * 0.05
moose.start(100.0) # Run the model for 100 seconds.
# Iterate through all plots, dump their contents to data.plot.
displayPlots()
quit()
def main():
"""
Demonstrates how one can visualise morphology of a neuron using the MOOSE.
"""
app = QtGui.QApplication(sys.argv)
filename = 'barrionuevo_cell1zr.CNG.swc'
moose.Neutral( '/library' )
moose.Neutral( '/model' )
cell = moose.loadModel( filename, '/model/testSwc' )
for i in range( 8 ):
moose.setClock( i, simdt )
hsolve = moose.HSolve( '/model/testSwc/hsolve' )
hsolve.dt = simdt
hsolve.target = '/model/testSwc/soma'
moose.le( cell )
moose.reinit()
# Now we set up the display
compts = moose.wildcardFind( "/model/testSwc/#[ISA=CompartmentBase]" )
compts[0].inject = inject
ecomptPath = [x.path for x in compts]
morphology = moogli.extensions.moose.read(path="/model/testSwc", vertices=15)
viewer = moogli.Viewer("Viewer")
viewer.attach_shapes( morphology.shapes.values() )
view = moogli.View("main-view")
viewer.attach_view( view )
# morphology = moogli.read_morphology_from_moose(name = "", path = "/model/testSwc")
# morphology.create_group( "group_all", ecomptPath, -0.08, 0.02, \
# [0.0, 0.5, 1.0, 1.0], [1.0, 0.0, 0.0, 0.9] )
# viewer = moogli.DynamicMorphologyViewerWidget(morphology)
def callback( morphology, viewer ):
moose.start( frameRunTime )
Vm = [moose.element( x ).Vm for x in compts]
morphology.set_color( "group_all", Vm )
currTime = moose.element( '/clock' ).currentTime
#print currTime, compts[0].Vm
if ( currTime < runtime ):
return True
return False
#viewer.set_callback( callback, idletime = 0 )
#viewer.showMaximized()
viewer.show()
app.exec_()
def _setup_network(self):
"""Sets up the network (_init_network is enough)"""
self.network = moose.LIF( 'network', self.N );
moose.le( '/network' )
self.network.vec.Em = self.el
self.network.vec.thresh = self.vt
self.network.vec.refractoryPeriod = self.refrT
self.network.vec.Rm = self.Rm
self.network.vec.vReset = self.vr
self.network.vec.Cm = self.Cm
if not noiseInj:
self.network.vec.inject = self.Iinject
else:
## inject a constant + noisy current
## values are set in self.simulate()
self.noiseTables = moose.StimulusTable('noiseTables',self.N)
moose.connect( self.noiseTables, 'output', \
self.network, 'setInject', 'OneToOne')
def addSpineProto( self, name, RM, RA, CM, \
shaftLen = 1.e-6 , shaftDia = 0.2e-6, \
headLen = 0.5e-6, headDia = 0.5e-6, \
synList = ( ['glu', 0.0, 2e-3, 9e-3, 200.0, False],
['NMDA', 0.0, 20e-3, 20e-3, 40.0, True] ),
chanList = ( ['LCa', 40.0, True ], ),
caTau = 13.333e-3
):
if not moose.exists('/library'):
library = moose.Neutral('/library')
spine = moose.Neutral('/library/spine')
shaft = self._buildCompt(spine, 'shaft', shaftLen, shaftDia, 0.0, RM,
RA, CM)
head = self._buildCompt(spine, 'head', headLen, headDia, shaftLen, RM,
RA, CM)
moose.connect(shaft, 'raxial', head, 'axial')
if caTau > 0.0:
conc = moose.CaConc(head.path + '/Ca_conc')
conc.tau = caTau
# B = 1/(ion_charge * Faraday * volume)
vol = head.length * head.diameter * head.diameter * PI / 4.0
conc.B = 1.0 / (2.0 * FaradayConst * vol)
conc.Ca_base = 0.0
for i in synList:
syn = self._buildSyn(i[0], head, i[1], i[2], i[3], i[4], CM)
if i[5] and caTau > 0.0:
moose.connect(syn, 'IkOut', conc, 'current')
for i in chanList:
if (moose.exists('/library/' + i[0])):
chan = moose.copy('/library/' + i[0], head)
chan.Gbar = i[1] * head.Cm / CM
print "CHAN = ", chan, chan.tick
moose.connect(head, 'channel', chan, 'channel')
if i[2] and caTau > 0.0:
moose.connect(chan, 'IkOut', conc, 'current')
else:
print "Warning: addSpineProto: channel '", i[0], \
"' not found on /library."
moose.le('/library')
self._transformNMDAR('/library/spine')
return spine
def test_vec():
a = moose.Pool('/p111', 100)
v = moose.vec(a)
# le can cause segfault in some cases.
moose.le(v)
assert len(v) == 100, len(v)
assert v == v.vec
assert v[0] == v.vec[0], (v[0], v.vec[0])
x = [random.random() for i in range(100)]
v.conc = x
assert sum(v.conc) == sum(x)
assert np.allclose(v.conc, x), (v.conc, x)
# assign bool to double.
y = [float(x < 5) for x in range(100)]
v.concInit = y
assert (v.concInit[:5] == 1.0).all(), v.concInit[:5]
assert (v.concInit[5:] == 0.0).all(), v.concInit[5:]
def addSpineProto( self, name = 'spine', \
RM = 1.0, RA = 1.0, CM = 0.01, \
shaftLen = 1.e-6 , shaftDia = 0.2e-6, \
headLen = 0.5e-6, headDia = 0.5e-6, \
synList = ( ['glu', 0.0, 2e-3, 9e-3, 200.0, False],
['NMDA', 0.0, 20e-3, 20e-3, 40.0, True] ),
chanList = ( ['LCa', 40.0, True ], ),
caTau = 13.333e-3
):
if not moose.exists( '/library' ):
library = moose.Neutral( '/library' )
spine = moose.Neutral( '/library/spine' )
shaft = self._buildCompt( spine, 'shaft', shaftLen, shaftDia, 0.0, RM, RA, CM )
head = self._buildCompt( spine, 'head', headLen, headDia, shaftLen, RM, RA, CM )
moose.connect( shaft, 'raxial', head, 'axial' )
if caTau > 0.0:
conc = moose.CaConc( head.path + '/Ca_conc' )
conc.tau = caTau
# B = 1/(ion_charge * Faraday * volume)
vol = head.length * head.diameter * head.diameter * PI / 4.0
conc.B = 1.0 / ( 2.0 * FaradayConst * vol )
conc.Ca_base = 0.0
for i in synList:
syn = self._buildSyn( i[0], head, i[1], i[2], i[3], i[4], CM )
if i[5] and caTau > 0.0:
moose.connect( syn, 'IkOut', conc, 'current' )
for i in chanList:
if ( moose.exists( '/library/' + i[0] ) ):
chan = moose.copy( '/library/' + i[0], head )
chan.Gbar = i[1] * head.Cm / CM
#print "CHAN = ", chan, chan.tick
moose.connect( head, 'channel', chan, 'channel' )
if i[2] and caTau > 0.0:
moose.connect( chan, 'IkOut', conc, 'current' )
else:
print "Warning: addSpineProto: channel '", i[0], \
"' not found on /library."
moose.le( '/library' )
self._transformNMDAR( '/library/spine' )
return spine
def main():
neuron = moose.Neutral("/neuron")
inputs = moose.Neutral("/inputs")
outputs = moose.Neutral("/outputs")
soma = create_spherical_compartment("/neuron/soma",25e-6,20e-6,2.8,4.0,0.03)
dend = create_spherical_compartment("/neuron/dendrite",25e-6,20e-6,2.8,4.0,0.03)
#cell = moose.loadModel(fileName, cellPath)moose.connect(soma)
pulse = create_pulse("/inputs/somaPulse",50e-3,100e-3,1e-9,soma)
vmtable = create_table('outputs/somaVmTable',soma,"getVm")
print(soma.tick)
print(soma.dt)
#moose.reinit()
#moose.start(900e-3)
#moose.showfields(vmtable)
#moose.showmsg(soma)
#moose.showmsg(pulse)
#moose.showmsg(vmtable)
plot_table(vmtable)
pyplot.show()
pNeuron = load_genesis_file("layer2.p", "/pNeuron")
swcNeuron = load_neuron_file("538ser3sl5-cell1-2-a.CNG.swc", "/swcNeuron", 0.678, 2.0, 0.0295)
moose.le(neuron)
moose.le(pNeuron)
moose.le(swcNeuron)
def main():
app = QtGui.QApplication(sys.argv)
filename = 'barrionuevo_cell1zr.CNG.swc'
moose.Neutral('/library')
moose.Neutral('/model')
cell = moose.loadModel(filename, '/model/testSwc')
for i in range(8):
moose.setClock(i, simdt)
hsolve = moose.HSolve('/model/testSwc/hsolve')
hsolve.dt = simdt
hsolve.target = '/model/testSwc/soma'
moose.le(cell)
moose.reinit()
# Now we set up the display
compts = moose.wildcardFind("/model/testSwc/#[ISA=CompartmentBase]")
compts[0].inject = inject
ecomptPath = map(lambda x: x.path, compts)
morphology = moogli.read_morphology_from_moose(name="",
path="/model/testSwc")
morphology.create_group( "group_all", ecomptPath, -0.08, 0.02, \
[0.0, 0.5, 1.0, 1.0], [1.0, 0.0, 0.0, 0.9] )
viewer = moogli.DynamicMorphologyViewerWidget(morphology)
def callback(morphology, viewer):
moose.start(frameRunTime)
Vm = map(lambda x: moose.element(x).Vm, compts)
morphology.set_color("group_all", Vm)
currTime = moose.element('/clock').currentTime
#print currTime, compts[0].Vm
if (currTime < runtime):
return True
return False
viewer.set_callback(callback, idletime=0)
viewer.showMaximized()
viewer.show()
app.exec_()
def attachStimulus2( fname ):
ampar = moose.wildcardFind( '/model/elec/#/glu' )
nmdar = moose.wildcardFind( '/model/elec/#/NMDA' )
numSyn = len( ampar )
assert( numSyn == len( nmdar ) );
moose.le( '/model' )
moose.RandSpike( '/model/elec/spike', len( ampar ) )
spikes = moose.vec( '/model/elec/spike' )
spikes.rate = params['meanSpikeRate']
spikes.refractT = params['refractoryPeriod']
amparSynWeight = params['amparSynapseWeight']
nmdarSynWeight = params['nmdarSynapseWeight']
for i in range( numSyn ):
sh = moose.element( ampar[i].path + '/sh' )
sh.numSynapses = 1
sh.synapse[0].weight = amparSynWeight
moose.connect( spikes[i], 'spikeOut', sh.synapse[0], 'addSpike' )
sh = moose.element( nmdar[i].path + '/sh' )
sh.numSynapses = 1
sh.synapse[0].weight = nmdarSynWeight
moose.connect( spikes[i], 'spikeOut', sh.synapse[0], 'addSpike' )
def createCell(self, name):
model_container = moose.Neutral('/model')
data_container = moose.Neutral('/data')
moose.le(model_container)
moose.le(data_container)
for ch in model_container.children:
moose.delete(ch)
for ch in data_container.children:
moose.delete(ch)
params = setup_current_step_model(model_container,
data_container,
name,
[[0, 0, 0],
[1e9, 0, 0]])
# moose.le(model_container)
# moose.le(data_container)
print '11111'
print model_container.path, data_container.path
params['modelRoot'] = model_container.path
params['dataRoot'] = data_container.path
print 'here'
return params
def main():
app = QtGui.QApplication(sys.argv)
filename = 'barrionuevo_cell1zr.CNG.swc'
moose.Neutral( '/library' )
moose.Neutral( '/model' )
cell = moose.loadModel( filename, '/model/testSwc' )
for i in range( 8 ):
moose.setClock( i, simdt )
hsolve = moose.HSolve( '/model/testSwc/hsolve' )
hsolve.dt = simdt
hsolve.target = '/model/testSwc/soma'
moose.le( cell )
moose.reinit()
# Now we set up the display
compts = moose.wildcardFind( "/model/testSwc/#[ISA=CompartmentBase]" )
compts[0].inject = inject
ecomptPath = map( lambda x : x.path, compts )
morphology = moogli.read_morphology_from_moose(name = "", path = "/model/testSwc")
morphology.create_group( "group_all", ecomptPath, -0.08, 0.02, \
[0.0, 0.5, 1.0, 1.0], [1.0, 0.0, 0.0, 0.9] )
viewer = moogli.DynamicMorphologyViewerWidget(morphology)
def callback( morphology, viewer ):
moose.start( frameRunTime )
Vm = map( lambda x: moose.element( x ).Vm, compts )
morphology.set_color( "group_all", Vm )
currTime = moose.element( '/clock' ).currentTime
#print currTime, compts[0].Vm
if ( currTime < runtime ):
return True
return False
viewer.set_callback( callback, idletime = 0 )
viewer.showMaximized()
viewer.show()
app.exec_()
def dummy():
print "Starting Dummy"
makePassiveSoma('cell', 0.5e-6, params['dendDiameter'])
moose.reinit()
moose.seed(int(params['seed']))
rdes = rd.rdesigneur(
useGssa=False,
turnOffElec=True,
chemPlotDt=0.02,
diffusionLength=params['diffusionLength'],
spineProto=[['makePassiveSpine()', 'spine']],
spineDistrib=[['spine', '#', '0.4e-6', '1e-7', '1.4', '0']],
cellProto=[['cell', 'soma']],
chemProto=[[params['chemModel'], 'chem']],
chemDistrib=[['chem', 'soma', 'install', '1']],
#moogList = [ ['soma', '1', '.', 'Vm', 'Vm', -0.1, 0.05], ]
)
rdes.buildModel()
moose.le('/library')
moose.delete('/library/soma')
moose.delete('/library/chem')
moose.le('/')
moose.delete('/model')
print "Finsihed dummy "
def load():
rdes = rd.rdesigneur(
elecDt=50e-6,
chemDt=0.002,
diffDt=0.002,
chemPlotDt=0.02,
useGssa=False,
# cellProto syntax: ['ballAndStick', 'name', somaDia, somaLength, dendDia, dendLength, numDendSegments ]
cellProto=[['ballAndStick', 'soma', 12e-6, 12e-6, 4e-6, 100e-6, 1]],
chemProto=[['../chem/CaMKII_MAPK_7.g', 'chem']],
spineProto=[['makeActiveSpine()', 'spine']],
chanProto=[['make_Na()', 'Na'], ['make_K_DR()', 'K_DR'],
['make_K_A()', 'K_A'], ['make_glu()', 'glu'],
['make_Ca()', 'Ca'], ['make_Ca_conc()', 'Ca_conc']],
passiveDistrib=[['soma', 'CM', '0.01', 'Em', '-0.06']],
spineDistrib=[['spine', '#dend#', '100e-6', '1e-6']],
chemDistrib=[['chem', '#', 'install', '1']],
chanDistrib=[['Na', 'soma', 'Gbar', '300'],
['K_DR', 'soma', 'Gbar', '250'],
['K_A', 'soma', 'Gbar', '200'],
['glu', 'dend#', 'Gbar', '20'],
['Ca_conc', 'soma', 'tau', '0.0333'],
['Ca', 'soma', 'Gbar', '40']],
adaptorList=[['psd/tot_phospho_R', 'n', 'glu', 'modulation', 1.0, 0.3],
['Ca_conc', 'Ca', 'psd/Ca', 'conc', 0.00008, 3]],
# Syn wt is 0.2, specified in 2nd argument
stimList=[['head#', '0.2', 'glu', 'periodicsyn', '0']],
)
moose.seed(1234567)
rdes.buildModel()
print "asdfasdfasf", moose.le('/')
#moose.element( '/model/chem/dend/ksolve' ).numThreads = 4
#moose.showfield( '/model/chem/dend/ksolve' )
#moose.element( '/model/chem/dend/ksolve' ).method = "rk4"
moose.delete('/model/stims/stim0')
inputElm = moose.element('/model/elec/head0/glu/sh/synapse/synInput_rs')
inputElm.name = 'synInput'
moose.connect(inputElm, 'spikeOut', '/model/elec/head0/glu/sh/synapse',
'addSpike')
#moose.showmsg( '/model/elec/head0/glu/sh/synapse/synInput_rs' )
import presettle_CaMKII_MAPK7_init
moose.reinit()
return rdes.model
def test_children():
a1 = moose.Neutral('/a')
a2 = moose.Neutral('/a/b')
a3 = moose.Neutral('/a/b/c1')
moose.Neutral('/a/b/c2')
assert len(a1.children) == 1
assert len(a2.children) == 2
moose.le(a1)
moose.le(a2)
moose.le(a3)
moose.setCwe(a3)
s = moose.getCwe()
assert s == a3, (s, a3)
a11 = a1.children[0]
ax = moose.element(a1)
ax1 = ax.children[0]
assert ax == a1
assert ax1 == a11
assert a11[0].isA['Neutral'], a11.isA
assert ax1[0].isA['Neutral'], a11.isA
print("test_children is done")
def make_network():
size = 1024
dt = 0.2
runsteps = 50
delayMin = 0
delayMax = 4
weightMax = 1
Vmax = 1.0
thresh = 0.4
refractoryPeriod = 0.4
tau = 0.5
connectionProbability = 0.01
random.seed( 123 )
nprand.seed( 456 )
t0 = time.time()
network = moose.IntFire( 'network', size );
syns = moose.SimpleSynHandler( '/network/syns', size );
moose.connect( syns, 'activationOut', network, 'activation', 'OneToOne' )
moose.le( '/network' )
syns.vec.numSynapses = [1] * size
sv = moose.vec( '/network/syns/synapse' )
print(('before connect t = ', time.time() - t0))
mid = moose.connect( network, 'spikeOut', sv, 'addSpike', 'Sparse')
print(('after connect t = ', time.time() - t0))
#print mid.destFields
m2 = moose.element( mid )
m2.setRandomConnectivity( connectionProbability, 5489 )
print(('after setting connectivity, t = ', time.time() - t0))
#network.vec.Vm = [(Vmax*random.random()) for r in range(size)]
network.vec.Vm = nprand.rand( size ) * Vmax
network.vec.thresh = thresh
network.vec.refractoryPeriod = refractoryPeriod
network.vec.tau = tau
numSynVec = syns.vec.numSynapses
print(('Middle of setup, t = ', time.time() - t0))
numTotSyn = sum( numSynVec )
print((numSynVec.size, ', tot = ', numTotSyn, ', numSynVec = ', numSynVec))
for item in syns.vec:
sh = moose.element( item )
sh.synapse.delay = delayMin + (delayMax - delayMin ) * nprand.rand( len( sh.synapse ) )
#sh.synapse.delay = [ (delayMin + random.random() * (delayMax - delayMin ) for r in range( len( sh.synapse ) ) ]
sh.synapse.weight = nprand.rand( len( sh.synapse ) ) * weightMax
print(('after setup, t = ', time.time() - t0))
numStats = 100
stats = moose.SpikeStats( '/stats', numStats )
stats.vec.windowLength = 1 # timesteps to put together.
plots = moose.Table( '/plot', numStats )
convergence = size / numStats
for i in range( numStats ):
for j in range( size/numStats ):
k = i * convergence + j
moose.connect( network.vec[k], 'spikeOut', stats.vec[i], 'addSpike' )
moose.connect( plots, 'requestOut', stats, 'getMean', 'OneToOne' )
#moose.useClock( 0, '/network/syns,/network', 'process' )
moose.useClock( 0, '/network/syns', 'process' )
moose.useClock( 1, '/network', 'process' )
moose.useClock( 2, '/stats', 'process' )
moose.useClock( 3, '/plot', 'process' )
moose.setClock( 0, dt )
moose.setClock( 1, dt )
moose.setClock( 2, dt )
moose.setClock( 3, dt )
moose.setClock( 9, dt )
t1 = time.time()
moose.reinit()
print(('reinit time t = ', time.time() - t1))
network.vec.Vm = nprand.rand( size ) * Vmax
print(('setting Vm , t = ', time.time() - t1))
t1 = time.time()
print('starting')
moose.start(runsteps * dt)
print(('runtime, t = ', time.time() - t1))
print((network.vec.Vm[99:103], network.vec.Vm[900:903]))
t = [i * dt for i in range( plots.vec[0].vector.size )]
i = 0
for p in plots.vec:
pylab.plot( t, p.vector, label=str( i) )
i += 1
pylab.xlabel( "Time (s)" )
pylab.ylabel( "Vm (mV)" )
pylab.legend()
pylab.show()
def readMorphML(self,cell,params={},lengthUnits="micrometer"):
"""
returns cellDict = { cellname: (segDict, cableDict) } # note: single cell only
where segDict = { segid1 : [ segname,(proximalx,proximaly,proximalz),
(distalx,distaly,distalz),diameter,length,[potential_syn1, ... ] ] , ... }
segname is "<name>_<segid>" because 1) guarantees uniqueness,
& 2) later scripts obtain segid from the compartment's name!
and cableDict = { cablegroupname : [campartment1name, compartment2name, ... ], ... }.
params is dict which can contain, combineSegments and/or createPotentialSynapses,
both boolean.
"""
if lengthUnits in ['micrometer','micron']:
self.length_factor = 1e-6
else:
self.length_factor = 1.0
cellname = cell.attrib["name"]
moose.Neutral('/library') # creates /library in MOOSE tree; elif present, wraps
_logger.info("Loading cell %s into /library ." % cellname)
#~ moosecell = moose.Cell('/library/'+cellname)
#using moose Neuron class - in previous version 'Cell' class Chaitanya
moosecell = moose.Neuron('/library/'+cellname)
self.cellDictBySegmentId[cellname] = [moosecell,{}]
self.cellDictByCableId[cellname] = [moosecell,{}]
self.segDict = {}
if 'combineSegments' in params:
self.combineSegments = params['combineSegments']
else:
self.combineSegments = False
if 'createPotentialSynapses' in params:
self.createPotentialSynapses = params['createPotentialSynapses']
else:
self.createPotentialSynapses = False
_logger.info("readMorphML using combineSegments = %s" % self.combineSegments)
###############################################
#### load cablegroups into a dictionary
self.cablegroupsDict = {}
self.cablegroupsInhomoparamsDict = {}
## Two ways of specifying cablegroups in neuroml 1.x
## <cablegroup>s with list of <cable>s
cablegroups = cell.findall(".//{"+self.mml+"}cablegroup")
for cablegroup in cablegroups:
cablegroupname = cablegroup.attrib['name']
self.cablegroupsDict[cablegroupname] = []
self.cablegroupsInhomoparamsDict[cablegroupname] = []
for cable in cablegroup.findall(".//{"+self.mml+"}cable"):
cableid = cable.attrib['id']
self.cablegroupsDict[cablegroupname].append(cableid)
# parse inhomogenous_params
for inhomogeneous_param in cablegroup.findall(".//{"+self.mml+"}inhomogeneous_param"):
metric = inhomogeneous_param.find(".//{"+self.mml+"}metric")
if metric.text == 'Path Length from root':
inhomoparamname = inhomogeneous_param.attrib['name']
inhomoparamvar = inhomogeneous_param.attrib['variable']
self.cablegroupsInhomoparamsDict[cablegroupname].append(\
(inhomoparamname,inhomoparamvar))
else:
_logger.warning('Only "Path Length from root" metric is '
' supported currently, ignoring %s ' % metric.text
)
## <cable>s with list of <meta:group>s
cables = cell.findall(".//{"+self.mml+"}cable")
for cable in cables:
cableid = cable.attrib['id']
cablegroups = cable.findall(".//{"+self.meta+"}group")
for cablegroup in cablegroups:
cablegroupname = cablegroup.text
if cablegroupname in self.cablegroupsDict:
self.cablegroupsDict[cablegroupname].append(cableid)
else:
self.cablegroupsDict[cablegroupname] = [cableid]
###################################################
## load all mechanisms in this cell into /library for later copying
## set which compartments have integrate_and_fire mechanism
self.intFireCableIds = {} # dict with keys as Compartments/cableIds which are IntFire
# with mechanismnames as values
for mechanism in cell.findall(".//{"+self.bio+"}mechanism"):
mechanismname = mechanism.attrib["name"]
passive = False
if "passive_conductance" in mechanism.attrib:
if mechanism.attrib['passive_conductance'] in ["true",'True','TRUE']:
passive = True
if not passive:
## if channel does not exist in library load it from xml file
if not moose.exists("/library/"+mechanismname):
_logger.info("Loading mechanism %s into library." % mechanismname)
cmlR = ChannelML(self.nml_params)
model_filename = mechanismname+'.xml'
model_path = neuroml_utils.find_first_file(model_filename,self.model_dir)
if model_path is not None:
cmlR.readChannelMLFromFile(model_path)
else:
raise IOError(
'For mechanism {0}: files {1} not found under {2}.'.format(
mechanismname, model_filename, self.model_dir)
)
## set those compartments to be LIF for which
## any integrate_and_fire parameter is set
if not moose.exists( "/library/"+mechanismname):
_logger.warn("Mechanism doesn't exist: %s " % mechanismname)
moose.le( '/library' )
moosemech = moose.element("/library/"+mechanismname)
if moose.exists(moosemech.path+"/integrate_and_fire"):
mooseIaF = moose.element(moosemech.path+"/integrate_and_fire") # Mstring
if mooseIaF.value in ['true','True','TRUE']:
mech_params = mechanism.findall(".//{"+self.bio+"}parameter")
for parameter in mech_params:
parametername = parameter.attrib['name']
## check for the integrate_and_fire parameters
if parametername in ['threshold', 't_refrac', 'v_reset','g_refrac']:
for group in parameter.findall(".//{"+self.bio+"}group"):
cablegroupname = group.text
if cablegroupname == 'all':
self.intFireCableIds = {'all':mechanismname}
break
else:
for cableid in self.cablegroupsDict[cablegroupname]:
## only one intfire mechanism is allowed in a cable
## the last one parsed will override others
self.intFireCableIds[cableid] = mechanismname
if 'all' in self.intFireCableIds:
break
############################################################
#### load morphology and connections between compartments
## Many neurons exported from NEURON have multiple segments in a section
## If self.combineSegments = True,
## then combine those segments into one Compartment / section
## for combining, assume segments of a compartment/section are in increasing order
## and assume all segments of a compartment/section have the same cableid
## findall() returns elements in document order:
running_cableid = ''
running_segid = ''
running_comp = None
running_diameter = 0.0
running_dia_nums = 0
segments = cell.findall(".//{"+self.mml+"}segment")
segmentstotal = len(segments)
for segnum,segment in enumerate(segments):
segmentname = segment.attrib['name']
## cable is an optional attribute. WARNING: Here I assume it is always present.
cableid = segment.attrib['cable']
segmentid = segment.attrib['id']
## if old cableid still running AND self.combineSegments == True,
## then don't start a new compartment, skip to next segment
if cableid == running_cableid and self.combineSegments:
self.cellDictBySegmentId[cellname][1][segmentid] = running_comp
proximal = segment.find('./{'+self.mml+'}proximal')
if proximal is not None:
running_diameter += float(proximal.attrib["diameter"]) * self.length_factor
running_dia_nums += 1
distal = segment.find('./{'+self.mml+'}distal')
if distal is not None:
running_diameter += float(distal.attrib["diameter"]) * self.length_factor
running_dia_nums += 1
## if (self.combineSegments and new cableid starts) or if not self.combineSegments,
## then start a new compartment
else:
## Create a new compartment
## the moose "hsolve" method assumes compartments to be
## asymmetric compartments and symmetrizes them
## but that is not what we want when translating
## from Neuron which has only symcompartments -- so be careful!
## Check if integrate_and_fire mechanism is present,
## if so use LIF instead of Compartment
moosecompname = segmentname+'_'+segmentid # just segmentname is NOT unique
# eg: mitral bbmit exported from NEURON
moosecomppath = moosecell.path+'/'+moosecompname
mechanismname = None
if 'all' in self.intFireCableIds:
mechanismname = self.intFireCableIds['all']
if cableid in self.intFireCableIds:
mechanismname = self.intFireCableIds[cableid]
if mechanismname is not None: # this cableid is an intfire
# create LIF (subclass of Compartment) and set to default values
moosecomp = moose.LIF(moosecomppath)
mname = '/library/' + mechanismname
moosechannel = moose.element(mname) if moose.exists(mname) else moose.Neutral(mname)
# Mstring values are 'string'; make sure to convert them to
# float else it will seg-fault with python3+
moosechannelval = moose.Mstring(moosechannel.path+'/vReset')
moosecomp.vReset = float(moosechannelval.value)
moosechannelval = moose.Mstring(moosechannel.path+'/thresh')
moosecomp.thresh = float( moosechannelval.value )
moosechannelval = moose.Mstring(moosechannel.path+'/refracT')
moosecomp.refractoryPeriod = eval(moosechannelval.value)
## refracG is currently not supported by moose.LIF
## when you implement it, check if refracG or g_refrac
## is a conductance density or a conductance, I think the former
#moosechannelval = moose.Mstring(moosechannel.path+'/refracG')
else:
moosecomp = moose.Compartment(moosecomppath)
self.cellDictBySegmentId[cellname][1][segmentid] = moosecomp
## cables are grouped and mechanism densities are set for cablegroups later.
## hence I will need to refer to segment according to which cable it belongs to.
## if combineSegments is False, there can be multiple segments per cable,
## so make array of compartments for cellDictByCableId[cellname][1][cableid]
if cableid in self.cellDictByCableId[cellname][1]:
self.cellDictByCableId[cellname][1][cableid].append(moosecomp)
else:
self.cellDictByCableId[cellname][1][cableid] = [moosecomp]
running_cableid = cableid
running_segid = segmentid
running_comp = moosecomp
running_diameter = 0.0
running_dia_nums = 0
if 'parent' in segment.attrib:
parentid = segment.attrib['parent'] # I assume the parent is created before the child
# so that I can immediately connect the child.
parent = self.cellDictBySegmentId[cellname][1][parentid]
## It is always assumed that axial of parent is connected to raxial of moosesegment
## THIS IS WHAT GENESIS readcell() DOES!!! UNLIKE NEURON!
## THIS IS IRRESPECTIVE OF WHETHER PROXIMAL x,y,z OF PARENT = PROXIMAL x,y,z OF CHILD.
## THIS IS ALSO IRRESPECTIVE OF fraction_along_parent SPECIFIED IN CABLE!
## THUS THERE WILL BE NUMERICAL DIFFERENCES BETWEEN MOOSE/GENESIS and NEURON.
## moosesegment sends Ra and Vm to parent, parent sends only Vm
## actually for symmetric compartment, both parent and moosesegment require each other's Ra/2,
## but axial and raxial just serve to distinguish ends.
moose.connect(parent,'axial',moosecomp,'raxial')
else:
parent = None
proximal = segment.find('./{'+self.mml+'}proximal')
if proximal is None: # If proximal tag is not present,
# then parent attribute MUST be present in the segment tag!
## if proximal is not present, then
## by default the distal end of the parent is the proximal end of the child
moosecomp.x0 = parent.x
moosecomp.y0 = parent.y
moosecomp.z0 = parent.z
else:
moosecomp.x0 = float(proximal.attrib["x"])*self.length_factor
moosecomp.y0 = float(proximal.attrib["y"])*self.length_factor
moosecomp.z0 = float(proximal.attrib["z"])*self.length_factor
running_diameter += float(proximal.attrib["diameter"]) * self.length_factor
running_dia_nums += 1
distal = segment.find('./{'+self.mml+'}distal')
if distal is not None:
running_diameter += float(distal.attrib["diameter"]) * self.length_factor
running_dia_nums += 1
## finished creating new compartment
## Update the end position, diameter and length, and segDict of this comp/cable/section
## with each segment that is part of this cable (assumes contiguous segments in xml).
## This ensures that we don't have to do any 'closing ceremonies',
## if a new cable is encoutered in next iteration.
if distal is not None:
running_comp.x = float(distal.attrib["x"])*self.length_factor
running_comp.y = float(distal.attrib["y"])*self.length_factor
running_comp.z = float(distal.attrib["z"])*self.length_factor
## Set the compartment diameter as the average diameter of all the segments in this section
running_comp.diameter = running_diameter / float(running_dia_nums)
## Set the compartment length
running_comp.length = math.sqrt((running_comp.x-running_comp.x0)**2+\
(running_comp.y-running_comp.y0)**2+(running_comp.z-running_comp.z0)**2)
## NeuroML specs say that if (x0,y0,z0)=(x,y,z), then round compartment e.g. soma.
## In Moose set length = dia to give same surface area as sphere of dia.
if running_comp.length == 0.0:
running_comp.length = running_comp.diameter
## Set the segDict
## the empty list at the end below will get populated
## with the potential synapses on this segment, in function set_compartment_param(..)
self.segDict[running_segid] = [running_comp.name,\
(running_comp.x0,running_comp.y0,running_comp.z0),\
(running_comp.x,running_comp.y,running_comp.z),\
running_comp.diameter,running_comp.length,[]]
if neuroml_utils.neuroml_debug:
_logger.info('Set up compartment/section %s' % running_comp.name)
###############################################
#### load biophysics into the compartments
biophysics = cell.find(".//{"+self.neuroml+"}biophysics")
if biophysics is not None:
## see pg 219 (sec 13.2) of Book of Genesis for Physiological Units
if biophysics.attrib["units"] == 'Physiological Units':
CMfactor = 1e-2 # F/m^2 from microF/cm^2
Cfactor = 1e-6 # F from microF
RAfactor = 1e1 # Ohm*m from KOhm*cm
RMfactor = 1e-1 # Ohm*m^2 from KOhm*cm^2
Rfactor = 1e-3 # Ohm from KOhm
Efactor = 1e-3 # V from mV
Gfactor = 1e1 # S/m^2 from mS/cm^2
Ifactor = 1e-6 # A from microA
Tfactor = 1e-3 # s from ms
else:
CMfactor = 1.0
Cfactor = 1.0
RAfactor = 1.0
RMfactor = 1.0
Rfactor = 1.0
Efactor = 1.0
Gfactor = 1.0
Ifactor = 1.0
Tfactor = 1.0
spec_capacitance = cell.find(".//{"+self.bio+"}spec_capacitance")
for parameter in spec_capacitance.findall(".//{"+self.bio+"}parameter"):
self.set_group_compartment_param(cell, cellname, parameter,\
'CM', float(parameter.attrib["value"])*CMfactor, self.bio)
spec_axial_resitance = cell.find(".//{"+self.bio+"}spec_axial_resistance")
for parameter in spec_axial_resitance.findall(".//{"+self.bio+"}parameter"):
self.set_group_compartment_param(cell, cellname, parameter,\
'RA', float(parameter.attrib["value"])*RAfactor, self.bio)
init_memb_potential = cell.find(".//{"+self.bio+"}init_memb_potential")
for parameter in init_memb_potential.findall(".//{"+self.bio+"}parameter"):
self.set_group_compartment_param(cell, cellname, parameter,\
'initVm', float(parameter.attrib["value"])*Efactor, self.bio)
chan_distrib = [] # the list for moose to parse inhomogeneous params (filled below)
for mechanism in cell.findall(".//{"+self.bio+"}mechanism"):
mechanismname = mechanism.attrib["name"]
passive = False
if "passive_conductance" in mechanism.attrib:
if mechanism.attrib['passive_conductance'] in ["true",'True','TRUE']:
passive = True
_logger.info("Loading mechanism %s " % mechanismname)
## ONLY creates channel if at least one parameter (like gmax) is specified in the xml
## Neuroml does not allow you to specify all default values.
## However, granule cell example in neuroconstruct has Ca ion pool without
## a parameter, applying default values to all compartments!
mech_params = mechanism.findall(".//{"+self.bio+"}parameter")
## if no params, apply all default values to all compartments
if len(mech_params) == 0:
for compartment_list in self.cellDictByCableId[cellname][1].values():
for compartment in compartment_list:
self.set_compartment_param(compartment,None,'default',mechanismname)
## if params are present, apply params to specified cable/compartment groups
for parameter in mech_params:
parametername = parameter.attrib['name']
if passive:
if parametername in ['gmax']:
self.set_group_compartment_param(cell, cellname, parameter,\
'RM', RMfactor*1.0/float(parameter.attrib["value"]), self.bio)
elif parametername in ['e','erev']:
self.set_group_compartment_param(cell, cellname, parameter,\
'Em', Efactor*float(parameter.attrib["value"]), self.bio)
elif parametername in ['inject']:
self.set_group_compartment_param(cell, cellname, parameter,\
'inject', Ifactor*float(parameter.attrib["value"]), self.bio)
else:
_logger.warning(["Yo programmer of MorphML! You didn't"
, " implement parameter %s " % parametername
, " in mechanism %s " % mechanismname
]
)
else:
if parametername in ['gmax']:
gmaxval = float(eval(parameter.attrib["value"],{"__builtins__":None},{}))
self.set_group_compartment_param(cell, cellname, parameter,\
'Gbar', Gfactor*gmaxval, self.bio, mechanismname)
elif parametername in ['e','erev']:
self.set_group_compartment_param(cell, cellname, parameter,\
'Ek', Efactor*float(parameter.attrib["value"]), self.bio, mechanismname)
elif parametername in ['depth']: # has to be type Ion Concentration!
self.set_group_compartment_param(cell, cellname, parameter,\
'thick', self.length_factor*float(parameter.attrib["value"]),\
self.bio, mechanismname)
elif parametername in ['v_reset']:
self.set_group_compartment_param(cell, cellname, parameter,\
'v_reset', Efactor*float(parameter.attrib["value"]),\
self.bio, mechanismname)
elif parametername in ['threshold']:
self.set_group_compartment_param(cell, cellname, parameter,\
'threshold', Efactor*float(parameter.attrib["value"]),\
self.bio, mechanismname)
elif parametername in ['t_refrac']:
self.set_group_compartment_param(cell, cellname, parameter,\
't_refrac', Tfactor*float(parameter.attrib["value"]),\
self.bio, mechanismname)
else:
_logger.warning(["Yo programmer of MorphML import! You didn't"
, " implement parameter %s " % parametername
, " in mechanism %s " % mechanismname ]
)
## variable parameters:
## varying with:
## p, g, L, len, dia
## p: path distance from soma, measured along dendrite, in metres.
## g: geometrical distance from soma, in metres.
## L: electrotonic distance (# of lambdas) from soma, along dend. No units.
## len: length of compartment, in metres.
## dia: for diameter of compartment, in metres.
var_params = mechanism.findall(".//{"+self.bio+"}variable_parameter")
if len(var_params) > 0:
## if variable params are present
## and use MOOSE to apply the variable formula
for parameter in var_params:
parametername = parameter.attrib['name']
cablegroupstr4moose = ""
## the neuroml spec says there should be a single group in a variable_parameter
## of course user can always have multiple variable_parameter tags,
## if user wants multiple groups conforming to neuroml specs.
group = parameter.find(".//{"+self.bio+"}group")
cablegroupname = group.text
if cablegroupname == 'all':
cablegroupstr4moose = "#"
else:
for cableid in self.cablegroupsDict[cablegroupname]:
for compartment in self.cellDictByCableId[cellname][1][cableid]:
cablegroupstr4moose += "#"+compartment.name+"#,"
if cablegroupstr4moose[-1] == ',':
cablegroupstr4moose = cablegroupstr4moose[:-1] # remove last comma
inhomo_value = parameter.find(".//{"+self.bio+"}inhomogeneous_value")
inhomo_value_name = inhomo_value.attrib['param_name']
inhomo_value_value = inhomo_value.attrib['value']
if parametername == 'gmax':
inhomo_eqn = '('+inhomo_value_value+')*'+str(Gfactor)
# careful about physiol vs SI units
else:
inhomo_eqn = inhomo_value_value
_logger.warning('Physiol. vs SI units translation not'
' implemented for parameter '+parametername+
'in channel '+mechanismname)+'. Use SI units'
'or ask for implementation.'
chan_distrib.extend((mechanismname,cablegroupstr4moose,parametername,inhomo_eqn,""))
# use extend, not append, moose wants it this way
## get mooose to parse the variable parameter gmax channel distributions
#pu.info("Some channel parameters distributed as per "+str(chan_distrib))
moosecell.channelDistribution = chan_distrib
#### Connect the Ca pools and channels
#### Am connecting these at the very end so that all channels and pools have been created
#### Note: this function is in moose.utils not moose.neuroml.utils !
for compartment_list in self.cellDictByCableId[cellname][1].values():
moose_utils.connect_CaConc(compartment_list,\
self.temperature+neuroml_utils.ZeroCKelvin) # temperature should be in Kelvin for Nernst
##########################################################
#### load connectivity / synapses into the compartments
connectivity = cell.find(".//{"+self.neuroml+"}connectivity")
if connectivity is not None:
for potential_syn_loc in cell.findall(".//{"+self.nml+"}potential_syn_loc"):
if 'synapse_direction' in potential_syn_loc.attrib:
if potential_syn_loc.attrib['synapse_direction'] in ['post','preAndOrPost']:
self.set_group_compartment_param(cell, cellname, potential_syn_loc,\
'synapse_type', potential_syn_loc.attrib['synapse_type'],\
self.nml, mechanismname='synapse')
if potential_syn_loc.attrib['synapse_direction'] in ['pre','preAndOrPost']:
self.set_group_compartment_param(cell, cellname, potential_syn_loc,\
'spikegen_type', potential_syn_loc.attrib['synapse_type'],\
self.nml, mechanismname='spikegen')
##########################################################
#### annotate each compartment with the cablegroups it belongs to
self.cableDict = {}
for cablegroupname in self.cablegroupsDict:
comp_list = []
for cableid in self.cablegroupsDict[cablegroupname]:
for compartment in self.cellDictByCableId[cellname][1][cableid]:
cableStringPath = compartment.path+'/cable_groups'
cableString = moose.Mstring(cableStringPath)
if cableString.value == '':
cableString.value += cablegroupname
else:
cableString.value += ',' + cablegroupname
comp_list.append(compartment.name)
self.cableDict[cablegroupname] = comp_list
_logger.info("Finished loading into library, cell: %s " % cellname)
return {cellname:(self.segDict,self.cableDict)}
## Leaky integrate and fire neuron
Vrest = -65e-3 # V # resting potential
Vt_base = -45e-3 # V # threshold
Vreset = -55e-3 # V # in current steps, Vreset is same as pedestal
R = 1e8 # Ohm
tau = 10e-3 # s
refrT = 2e-3 # s
# ###########################################
# Initialize neuron group
# ###########################################
## two neurons: index 0 will be presynaptic, 1 will be postsynaptic
network = moose.LIF('network', 2)
moose.le('/network')
network.vec.Em = Vrest
network.vec.thresh = Vt_base
network.vec.refractoryPeriod = refrT
network.vec.Rm = R
network.vec.vReset = Vreset
network.vec.Cm = tau / R
network.vec.inject = 0.
network.vec.initVm = Vrest
#############################################
# Ca Plasticity parameters: synapses (not for ExcInhNetBase)
#############################################
### Cortical slice values -- Table Suppl 2 in Graupner & Brunel 2012
### Also used in Higgins et al 2014
def main():
"""
Simulate current injection into various Integrate and Fire neurons.
All integrate and fire (IF) neurons are subclasses of compartment,
so they have all the fields of a passive compartment. Multicompartmental neurons can be created.
Even ion channels and synaptic channels can be added to them, say for sub-threshold behaviour.
The key addition is that they have a reset mechanism when the membrane potential Vm crosses a threshold.
On each reset, a spikeOut message is generated, and the membrane potential is reset to Vreset.
The threshold may be the spike generation threshold as for LIF and AdThreshIF,
or it may be the peak of the spike as for QIF, ExIF, AdExIF, and IzhIF.
The adaptive IFs have an extra adapting variable apart from membrane potential Vm.
Details of the IFs are given below.
The fields of the MOOSE objects are named exactly as the parameters in the equations below.
LIF: Leaky Integrate and Fire:
Rm*Cm * dVm/dt = -(Vm-Em) + Rm*I
QIF: Quadratic LIF:
Rm*Cm * dVm/dt = a0*(Vm-Em)*(Vm-vCritical) + Rm*I
ExIF: Exponential leaky integrate and fire:
Rm*Cm * dVm/dt = -(Vm-Em) + deltaThresh * exp((Vm-thresh)/deltaThresh) + Rm*I
AdExIF: Adaptive Exponential LIF:
Rm*Cm * dVm/dt = -(Vm-Em) + deltaThresh * exp((Vm-thresh)/deltaThresh) + Rm*I - w,
tau_w * dw/dt = a0*(Vm-Em) - w,
At each spike, w -> w + b0 "
AdThreshIF: Adaptive threshold LIF:
Rm*Cm * dVm/dt = -(Vm-Em) + Rm*I,
tauThresh * d threshAdaptive / dt = a0*(Vm-Em) - threshAdaptive,
At each spike, threshAdaptive is increased by threshJump
the spiking threshold adapts as thresh + threshAdaptive
IzhIF: Izhikevich:
d Vm /dt = a0 * Vm^2 + b0 * Vm + c0 - u + I/Cm,
d u / dt = a * ( b * Vm - u ),
At each spike, u -> u + d,
By default, a0 = 0.04e6/V/s, b0 = 5e3/s, c0 = 140 V/s are set to SI units,
so use SI consistently, or change a0, b0, c0 also if you wish to use other units.
Rm from Compartment is not used here, vReset is same as c in the usual formalism.
At rest, u0 = b V0, and V0 = ( -(-b0-b) +/- sqrt((b0-b)^2 - 4*a0*c0)) / (2*a0).
On the command-line, in moose-examples/snippets directory, run ``python IntegrateFireZoo.py``.
The script will ask you which neuron you want to simulate and you can choose and run what you want.
Play with the parameters of the IF neurons in the source code.
"""
neuronChoices = {'LIF':moose.LIF, 'QIF':moose.QIF, 'ExIF':moose.ExIF, 'AdExIF':moose.AdExIF,
'AdThreshIF':moose.AdThreshIF, 'IzhIF':moose.IzhIF}
#### CHOOSE ONE OF THE NEURON KEYS AS choiceKey FROM BELOW DICTIONARY ####
#choiceKey = 'LIF'
#### No need, am inputting it from the user on the terminal
choiceKeys = list(neuronChoices.keys()) # keys() does not retain the order in dict defn above!
choiceIndex = eval(str(input('Choose a number corresponding to your desired neuron: '+str([(i,key) for (i,key) in enumerate(choiceKeys)])+' -- ')))
choiceKey = choiceKeys[choiceIndex]
neuronChoice = neuronChoices[choiceKey]
# ###########################################
# Initialize neuron group
# ###########################################
# neuron instantiation
network = neuronChoice( 'network' ); # choose neuron type above
moose.le( '/network' )
network.vec.Em = Vrest
network.vec.thresh = Vt_base
network.vec.refractoryPeriod = refrT
network.vec.Rm = R
network.vec.vReset = Vreset
network.vec.Cm = tau/R
network.vec.initVm = Vrest
# neuron specific parameters and current injected I
if choiceKey == 'LIF':
network.vec.inject = 5e-10 # Amp # injected current I
if choiceKey == 'QIF':
network.vec.a0 = a0
network.vec.vCritical = vCritical
network.vec.inject = 5e-10 # Amp # injected current I
elif choiceKey == 'ExIF':
network.vec.deltaThresh = deltaThresh
network.vec.vPeak = vPeak # reset at vPeak, not at thresh
network.vec.inject = 5e-9 # Amp # injected current I
elif choiceKey == 'AdExIF':
network.vec.deltaThresh = deltaThresh
network.vec.vPeak = vPeak # reset at vPeak, not at thresh
network.vec.a0 = a0AdEx
network.vec.b0 = b0
network.vec.tauW = tauW
network.vec.inject = 5e-9 # Amp # injected current I
elif choiceKey == 'AdThreshIF':
network.vec.a0 = a0AdTh
network.vec.threshJump = threshJump
network.vec.tauThresh = tauThresh
network.vec.inject = 1e-9 # Amp # injected current I
elif choiceKey == 'IzhIF':
network.vec.a = a
network.vec.b = b
network.vec.d = d
network.vec.uInit = uRest # Just sets the initial value of u
network.vec.vPeak = vPeak # reset at vPeak, not at thresh
network.vec.inject = 5e-9 # Amp # injected current I
print(("Injecting current =",network.vec[0].inject,"in",choiceKey,"neuron."))
# ###########################################
# Setting up table
# ###########################################
Vm = moose.Table( '/plotVm' )
moose.connect( network, 'VmOut', Vm, 'input', 'OneToOne')
spikes = moose.Table( '/plotSpikes' )
moose.connect( network, 'spikeOut', spikes, 'input', 'OneToOne')
# ###########################################
# Simulate the current injection
# ###########################################
dt = 5e-6 # s
runtime = 0.02 # s
# moose simulation
moose.useClock( 1, '/network', 'process' )
moose.useClock( 2, '/plotSpikes', 'process' )
moose.useClock( 3, '/plotVm', 'process' )
moose.setClock( 0, dt )
moose.setClock( 1, dt )
moose.setClock( 2, dt )
moose.setClock( 3, dt )
moose.setClock( 9, dt )
moose.reinit()
moose.start(runtime)
# ###########################################
# Plot the simulated Vm-s and STDP curve
# ###########################################
# Voltage plots
Vmseries = Vm.vector
numsteps = len(Vmseries)
if choiceKey not in ['ExIF','AdExIF','IzhIF']:
# insert spikes so that Vm reset at thresh doesn't look weird
# for ExIF, etc. reset is at vPeak, so not weird.
for t in spikes.vector:
Vmseries[int(t/dt)-1] = 30e-3 # V
timeseries = np.arange(0.,1000*numsteps*dt-1e-10,dt*1000)
plt.figure(facecolor='w')
plt.plot(timeseries,Vmseries*1000,color='r') # neuron's Vm
plt.xlabel('time (ms)')
plt.ylabel('Vm (mV)')
plt.title(choiceKey+"neuron, current="+str(network.vec[0].inject)+"A")
plt.show()
def main():
"""
Simulate a pseudo-STDP protocol and plot the STDP kernel
that emerges from Ca plasticity of Graupner and Brunel 2012.
Author: Aditya Gilra, NCBS, Bangalore, October, 2014.
"""
# ###########################################
# Neuron models
# ###########################################
## Leaky integrate and fire neuron
Vrest = -65e-3 # V # resting potential
Vt_base = -45e-3 # V # threshold
Vreset = -55e-3 # V # in current steps, Vreset is same as pedestal
R = 1e8 # Ohm
tau = 10e-3 # s
refrT = 2e-3 # s
# ###########################################
# Initialize neuron group
# ###########################################
## two neurons: index 0 will be presynaptic, 1 will be postsynaptic
network = moose.LIF( 'network', 2 );
moose.le( '/network' )
network.vec.Em = Vrest
network.vec.thresh = Vt_base
network.vec.refractoryPeriod = refrT
network.vec.Rm = R
network.vec.vReset = Vreset
network.vec.Cm = tau/R
network.vec.inject = 0.
network.vec.initVm = Vrest
#############################################
# Ca Plasticity parameters: synapses (not for ExcInhNetBase)
#############################################
### Cortical slice values -- Table Suppl 2 in Graupner & Brunel 2012
### Also used in Higgins et al 2014
#tauCa = 22.6936e-3 # s # Ca decay time scale
#tauSyn = 346.3615 # s # synaptic plasticity time scale
### in vitro values in Higgins et al 2014, faster plasticity
#CaPre = 0.56175 # mM
#CaPost = 1.2964 # mM
### in vivo values in Higgins et al 2014, slower plasticity
##CaPre = 0.33705 # mM
##CaPost = 0.74378 # mM
#delayD = 4.6098e-3 # s # CaPre is added to Ca after this delay
## proxy for rise-time of NMDA
#thetaD = 1.0 # mM # depression threshold for Ca
#thetaP = 1.3 # mM # potentiation threshold for Ca
#gammaD = 331.909 # factor for depression term
#gammaP = 725.085 # factor for potentiation term
#J = 5e-3 # V # delta function synapse, adds to Vm
#weight = 0.43 # initial synaptic weight
## gammaP/(gammaP+gammaD) = eq weight w/o noise
## see eqn (22), noiseSD also appears
## but doesn't work here,
## weights away from 0.4 - 0.5 screw up the STDP rule!!
#bistable = True # if bistable is True, use bistable potential for weights
#noisy = False # use noisy weight updates given by noiseSD
#noiseSD = 3.3501 # if noisy, use noiseSD (3.3501 from Higgins et al 2014)
########################################
## DP STDP curve (Fig 2C) values -- Table Suppl 1 in Graupner & Brunel 2012
tauCa = 20e-3 # s # Ca decay time scale
tauSyn = 150.0 # s # synaptic plasticity time scale
CaPre = 1.0 # arb
CaPost = 2.0 # arb
delayD = 13.7e-3 # s # CaPre is added to Ca after this delay
# proxy for rise-time of NMDA
thetaD = 1.0 # mM # depression threshold for Ca
thetaP = 1.3 # mM # potentiation threshold for Ca
gammaD = 200.0 # factor for depression term
gammaP = 321.808 # factor for potentiation term
J = 5e-3 # V # delta function synapse, adds to Vm
weight = 0.5 # initial synaptic weight
# gammaP/(gammaP+gammaD) = eq weight w/o noise
# see eqn (22), noiseSD also appears
# but doesn't work here,
# weights away from 0.4 - 0.5 screw up the STDP rule!!
bistable = True # if bistable is True, use bistable potential for weights
noisy = False # use noisy weight updates given by noiseSD
noiseSD = 2.8284 # if noisy, use noiseSD (3.3501 in Higgins et al 2014)
##########################################
syn = moose.GraupnerBrunel2012CaPlasticitySynHandler( '/network/syn' )
syn.numSynapses = 1 # 1 synapse
# many pre-synaptic inputs can connect to a synapse
# synapse onto postsynaptic neuron
moose.connect( syn, 'activationOut', network.vec[1], 'activation' )
# synapse from presynaptic neuron
moose.connect( network.vec[0],'spikeOut', syn.synapse[0], 'addSpike')
# post-synaptic spikes also needed for STDP
moose.connect( network.vec[1], 'spikeOut', syn, 'addPostSpike')
syn.synapse[0].delay = 0.0
syn.synapse[0].weight = weight
syn.CaInit = 0.0
syn.tauCa = tauCa
syn.tauSyn = tauSyn
syn.CaPre = CaPre
syn.CaPost = CaPost
syn.delayD = delayD
syn.thetaD = thetaD
syn.thetaP = thetaP
syn.gammaD = gammaD
syn.gammaP = gammaP
syn.weightScale = J # weight ~1, weightScale ~ J
# weight*weightScale is activation,
# i.e. delta-fn added to postsynaptic Vm
syn.weightMax = 1.0 # bounds on the weight
syn.weightMin = 0.
syn.noisy = noisy
syn.noiseSD = noiseSD
syn.bistable = bistable
# ###########################################
# Setting up tables
# ###########################################
Vms = moose.Table( '/plotVms', 2 )
moose.connect( network, 'VmOut', Vms, 'input', 'OneToOne')
spikes = moose.Table( '/plotSpikes', 2 )
moose.connect( network, 'spikeOut', spikes, 'input', 'OneToOne')
CaTable = moose.Table( '/plotCa', 1 )
moose.connect( CaTable, 'requestOut', syn, 'getCa')
WtTable = moose.Table( '/plotWeight', 1 )
moose.connect( WtTable, 'requestOut', syn.synapse[0], 'getWeight')
# ###########################################
# Simulate the STDP curve with spaced pre-post spike pairs
# ###########################################
dt = 1e-3 # s
# moose simulation
moose.useClock( 0, '/network/syn', 'process' )
moose.useClock( 1, '/network', 'process' )
moose.useClock( 2, '/plotSpikes', 'process' )
moose.useClock( 3, '/plotVms', 'process' )
moose.useClock( 3, '/plotCa', 'process' )
moose.useClock( 3, '/plotWeight', 'process' )
moose.setClock( 0, dt )
moose.setClock( 1, dt )
moose.setClock( 2, dt )
moose.setClock( 3, dt )
moose.setClock( 9, dt )
moose.reinit()
# function to make the aPlus and aMinus settle to equilibrium values
settletime = 100e-3 # s
def reset_settle():
""" Call this between every pre-post pair
to reset the neurons and make them settle to rest.
"""
syn.synapse[0].weight = weight
syn.Ca = 0.0
moose.start(settletime)
# Ca gets a jump at pre-spike+delayD
# So this event can occur during settletime
# So set Ca and weight once more after settletime
syn.synapse[0].weight = weight
syn.Ca = 0.0
# function to inject a sharp current pulse to make neuron spike
# immediately at a given time step
def make_neuron_spike(nrnidx,I=1e-7,duration=1e-3):
""" Inject a brief current pulse to
make a neuron spike
"""
network.vec[nrnidx].inject = I
moose.start(duration)
network.vec[nrnidx].inject = 0.
dwlist_neg = []
ddt = 2e-3 # s
# since CaPlasticitySynHandler is event based
# multiple pairs are needed for Ca to be registered above threshold
# Values from Fig 2, last line of legend
numpairs = 60 # number of spike parts per deltat
t_between_pairs = 1.0 # time between each spike pair
t_extent = 100e-3 # s # STDP kernel extent,
# t_extent > t_between_pairs/2 inverts pre-post pairing!
# dt = tpost - tpre
# negative dt corresponds to post before pre
print('-----------------------------------------------')
for deltat in arange(t_extent,0.0,-ddt):
reset_settle()
for i in range(numpairs):
# post neuron spike
make_neuron_spike(1)
moose.start(deltat)
# pre neuron spike after deltat
make_neuron_spike(0)
moose.start(t_between_pairs) # weight changes after pre-spike+delayD
# must run for at least delayD after pre-spike
dw = ( syn.synapse[0].weight - weight ) / weight
print(('post before pre, dt = %1.3f s, dw/w = %1.3f'%(-deltat,dw)))
dwlist_neg.append(dw)
print('-----------------------------------------------')
# positive dt corresponds to pre before post
dwlist_pos = []
for deltat in arange(ddt,t_extent+ddt,ddt):
reset_settle()
for i in range(numpairs):
# pre neuron spike
make_neuron_spike(0)
moose.start(deltat)
# post neuron spike after deltat
make_neuron_spike(1)
moose.start(t_between_pairs)
dw = ( syn.synapse[0].weight - weight ) / weight
print(('pre before post, dt = %1.3f s, dw/w = %1.3f'%(deltat,dw)))
dwlist_pos.append(dw)
print('-----------------------------------------------')
print(('Each of the above pre-post pairs was repeated',\
numpairs,'times, with',t_between_pairs,'s between pairs.'))
print()
print('Due to event based updates, Ca decays suddenly at events:')
print('pre-spike, pre-spike + delayD, and post-spike;')
print('apart from the usual CaPre and CaPost jumps at')
print('pre-spike + delayD and post-spike respectively.')
print('Because of the event based update, multiple pre-post pairs are used.')
print()
print('If you reduce the t_between_pairs,')
print(' you\'ll see potentiation for the LTD part without using any triplet rule!')
print()
print("If you turn on noise, the weights fluctuate too much,")
print(" not sure if there's a bug in my noise implementation.")
print('-----------------------------------------------')
# ###########################################
# Plot the simulated Vm-s and STDP curve
# ###########################################
# insert spikes so that Vm reset doesn't look weird
Vmseries0 = Vms.vec[0].vector
numsteps = len(Vmseries0)
for t in spikes.vec[0].vector:
Vmseries0[int(t/dt)-1] = 30e-3 # V
Vmseries1 = Vms.vec[1].vector
for t in spikes.vec[1].vector:
Vmseries1[int(t/dt)-1] = 30e-3 # V
timeseries = linspace(0.,1000*numsteps*dt,numsteps)
# Voltage plots
figure(facecolor='w')
plot(timeseries,Vmseries0,color='r') # pre neuron's vm
plot(timeseries,Vmseries1,color='b') # post neuron's vm
xlabel('time (ms)')
ylabel('Vm (V)')
title("pre (r) and post (b) neurons' Vm")
# Ca plots for the synapse
figure(facecolor='w')
plot(timeseries,CaTable.vector[:len(timeseries)],color='r')
plot((timeseries[0],timeseries[-1]),(thetaP,thetaP),color='k',\
linestyle='dashed',label='pot thresh')
plot((timeseries[0],timeseries[-1]),(thetaD,thetaD),color='b',\
linestyle='dashed',label='dep thresh')
legend()
xlabel('time (ms)')
ylabel('Ca (arb)')
title("Ca conc in the synapse")
# Weight plots for the synapse
figure(facecolor='w')
plot(timeseries,WtTable.vector[:len(timeseries)],color='r')
xlabel('time (ms)')
ylabel('Efficacy')
title("Efficacy of the synapse")
# STDP curve
fig = figure(facecolor='w')
ax = fig.add_subplot(111)
ax.plot(arange(-t_extent,0,ddt)*1000,array(dwlist_neg),'.-r')
ax.plot(arange(ddt,(t_extent+ddt),ddt)*1000,array(dwlist_pos),'.-b')
xmin,xmax = ax.get_xlim()
ymin,ymax = ax.get_ylim()
ax.set_xticks([xmin,0,xmax])
ax.set_yticks([ymin,0,ymax])
ax.plot((0,0),(ymin,ymax),linestyle='dashed',color='k')
ax.plot((xmin,xmax),(0,0),linestyle='dashed',color='k')
ax.set_xlabel('$t_{post}-t_{pre}$ (ms)')
ax.set_ylabel('$\Delta w / w$')
fig.tight_layout()
#fig.subplots_adjust(hspace=0.3,wspace=0.5) # use after tight_layout()
show()
def loadFile(filename, target, solver="gsl", merge=True):
"""Try to load a model from specified `filename` under the element
`target`.
if `merge` is True, the contents are just loaded at target. If
false, everything is deleted from the parent of target unless the
parent is root.
Returns
-------
a dict containing at least these three entries:
modeltype: type of the loaded model.
subtype: subtype of the loaded model, None if no specific subtype
modelroot: root element of the model, None if could not be located - as is the case with Python scripts
"""
num = 1
newTarget = target
while moose.exists(newTarget):
newTarget = target + "-" + str(num)
num = num + 1
target = newTarget
istext = True
with open(filename, "rb") as infile:
istext = mtypes.istextfile(infile)
if not istext:
print("Cannot handle any binary formats yet")
return None
parent, child = posixpath.split(target)
p = moose.Neutral(parent)
if not merge and p.path != "/":
for ch in p.children:
moose.delete(ch)
try:
modeltype = mtypes.getType(filename)
subtype = mtypes.getSubtype(filename, modeltype)
except KeyError:
raise FileLoadError("Do not know how to handle this filetype: %s" % (filename))
pwe = moose.getCwe()
# self.statusBar.showMessage('Loading model, please wait')
# app = QtGui.qApp
# app.setOverrideCursor(QtGui.QCursor(Qt.Qt.BusyCursor)) #shows a hourglass - or a busy/working arrow
if modeltype == "genesis":
if subtype == "kkit" or subtype == "prototype":
model, modelpath = loadGenCsp(target, filename, solver)
if moose.exists(moose.element(modelpath).path):
moose.Annotator(moose.element(modelpath).path + "/info").modeltype = "kkit"
else:
print(" path doesn't exists")
moose.le(modelpath)
else:
print("Only kkit and prototype files can be loaded.")
elif modeltype == "cspace":
model, modelpath = loadGenCsp(target, filename)
if moose.exists(modelpath):
moose.Annotator((moose.element(modelpath).path + "/info")).modeltype = "cspace"
addSolver(modelpath, "gsl")
elif modeltype == "xml":
if subtype == "neuroml":
popdict, projdict = neuroml.loadNeuroML_L123(filename)
# Circus to get the container of populations from loaded neuroml
for popinfo in list(popdict.values()):
for cell in list(popinfo[1].values()):
solver = moose.HSolve(cell.path + "/hsolve")
solver.target = cell.path
# model = cell.parent
# break
# break
# Moving model to a new location under the model name
# model name is the filename without extension
model = moose.Neutral("/" + splitext(basename(filename))[0])
element = moose.Neutral(model.path + "/model")
if moose.exists("/cells"):
moose.move("/cells", element.path)
if moose.exists("/elec"):
moose.move("/elec", model.path)
if moose.exists("/library"):
moose.move("/library", model.path)
# moose.move("cells/", cell.path)
elif subtype == "sbml":
if target != "/":
if moose.exists(target):
moose.delete(target)
model = mooseReadSBML(filename, target)
if moose.exists(moose.element(model).path):
moose.Annotator(moose.element(model).path + "/info").modeltype = "sbml"
addSolver(target, "gsl")
else:
raise FileLoadError("Do not know how to handle this filetype: %s" % (filename))
moose.setCwe(
pwe
) # The MOOSE loadModel changes the current working element to newly loaded model. We revert that behaviour
# TODO: check with Aditya how to specify the target for
# neuroml reader
# app.restoreOverrideCursor()
return {"modeltype": modeltype, "subtype": subtype, "model": model}
def test_mgblock():
model = moose.Neutral('/model')
data = moose.Neutral('/data')
soma = moose.Compartment('/model/soma')
soma.Em = -60e-3
soma.Rm = 1e7
soma.Cm = 1e-9
###################################################
# This is where we create the synapse with MgBlock
#--------------------------------------------------
nmda = moose.SynChan('/model/soma/nmda')
nmda.Gbar = 1e-9
mgblock = moose.MgBlock('/model/soma/mgblock')
mgblock.CMg = 2.0
mgblock.KMg_A = 1/0.33
mgblock.KMg_B = 1/60.0
# The synHandler manages the synapses and their learning rules if any.
synHandler = moose.SimpleSynHandler( '/model/soma/nmda/handler' )
synHandler.synapse.num = 1
moose.connect( synHandler, 'activationOut', nmda, 'activation' )
# MgBlock sits between original channel nmda and the
# compartment. The origChannel receives the channel message from
# the nmda SynChan.
moose.connect(soma, 'VmOut', nmda, 'Vm' )
moose.connect(nmda, 'channelOut', mgblock, 'origChannel')
moose.connect(mgblock, 'channel', soma, 'channel')
# This is for comparing with MgBlock
nmda_noMg = moose.copy(nmda, soma, 'nmda_noMg')
moose.connect( nmda_noMg, 'channel', soma, 'channel')
moose.le( nmda_noMg )
#########################################
# The rest is for experiment setup
spikegen = moose.SpikeGen('/model/spike')
pulse = moose.PulseGen('/model/input')
pulse.delay[0] = 10e-3
pulse.level[0] = 1.0
pulse.width[0] = 50e-3
moose.connect(pulse, 'output', spikegen, 'Vm')
moose.le( synHandler )
#syn = moose.element(synHandler.path + '/synapse' )
syn = synHandler.synapse[0]
syn.delay = simdt * 2
syn.weight = 10
moose.connect(spikegen, 'spikeOut', synHandler.synapse[0], 'addSpike')
moose.le( nmda_noMg )
noMgSyn = moose.element(nmda_noMg.path + '/handler/synapse' )
noMgSyn.delay = 0.01
noMgSyn.weight = 1
moose.connect(spikegen, 'spikeOut', noMgSyn, 'addSpike')
moose.showfields( syn )
moose.showfields( noMgSyn )
Gnmda = moose.Table('/data/Gnmda')
moose.connect(Gnmda, 'requestOut', mgblock, 'getGk')
Gnmda_noMg = moose.Table('/data/Gnmda_noMg')
moose.connect(Gnmda_noMg, 'requestOut', nmda_noMg, 'getGk')
Vm = moose.Table('/data/Vm')
moose.connect(Vm, 'requestOut', soma, 'getVm')
for i in range( 10 ):
moose.setClock( i, simdt )
moose.setClock( Gnmda.tick, plotdt )
print((spikegen.dt, Gnmda.dt))
moose.reinit()
moose.start( simtime )
t = pylab.linspace(0, simtime*1e3, len(Vm.vector))
pylab.plot(t, (Vm.vector + 0.06) * 1000, label='Vm (mV)')
pylab.plot(t, Gnmda.vector * 1e9, label='Gnmda (nS)')
pylab.plot(t, Gnmda_noMg.vector * 1e9, label='Gnmda no Mg (nS)')
pylab.legend()
#data = pylab.vstack((t, Gnmda.vector, Gnmda_noMg.vector)).transpose()
#pylab.savetxt('mgblock.dat', data)
pylab.show()
def make_network():
size = 1024
timestep = 0.2
runtime = 100.0
delayMin = timestep
delayMax = 4
weightMax = 0.02
Vmax = 1.0
thresh = 0.2
tau = 1 # Range of tau
tau0 = 0.5 # minimum tau
refr = 0.3
refr0 = 0.2
connectionProbability = 0.1
random.seed( 123 )
nprand.seed( 456 )
t0 = time.time()
clock = moose.element( '/clock' )
network = moose.IntFire( 'network', size, 1 );
network.vec.bufferTime = [delayMax * 2] * size
moose.le( '/network' )
network.vec.numSynapses = [1] * size
# Interesting. This fails because we haven't yet allocated
# the synapses. I guess it is fair to avoid instances of objects that
# don't have allocations.
#synapse = moose.element( '/network/synapse' )
sv = moose.vec( '/network/synapse' )
print('before connect t = ', time.time() - t0)
mid = moose.connect( network, 'spikeOut', sv, 'addSpike', 'Sparse')
print('after connect t = ', time.time() - t0)
#print mid.destFields
m2 = moose.element( mid )
m2.setRandomConnectivity( connectionProbability, 5489 )
print('after setting connectivity, t = ', time.time() - t0)
network.vec.Vm = [(Vmax*random.random()) for r in range(size)]
network.vec.thresh = thresh
network.vec.refractoryPeriod = [( refr0 + refr * random.random()) for r in range( size) ]
network.vec.tau = [(tau0 + tau*random.random()) for r in range(size)]
numSynVec = network.vec.numSynapses
print('Middle of setup, t = ', time.time() - t0)
numTotSyn = sum( numSynVec )
for item in network.vec:
neuron = moose.element( item )
neuron.synapse.delay = [ (delayMin + random.random() * delayMax) for r in range( len( neuron.synapse ) ) ]
neuron.synapse.weight = nprand.rand( len( neuron.synapse ) ) * weightMax
print('after setup, t = ', time.time() - t0, ", numTotSyn = ", numTotSyn)
"""
netvec = network.vec
for i in range( size ):
synvec = netvec[i].synapse.vec
synvec.weight = [ (random.random() * weightMax) for r in range( synvec.len )]
synvec.delay = [ (delayMin + random.random() * delayMax) for r in range( synvec.len )]
"""
#moose.useClock( 9, '/postmaster', 'process' )
moose.useClock( 0, '/network', 'process' )
moose.setClock( 0, timestep )
moose.setClock( 9, timestep )
t1 = time.time()
moose.reinit()
print('reinit time t = ', time.time() - t1)
network.vec.Vm = [(Vmax*random.random()) for r in range(size)]
print('setting Vm , t = ', time.time() - t1)
t1 = time.time()
print('starting')
moose.start(runtime)
print('runtime, t = ', time.time() - t1)
print('Vm100:103', network.vec.Vm[100:103])
print('Vm900:903', network.vec.Vm[900:903])
print('weights 100:', network.vec[100].synapse.delay[0:5])
print('weights 900:', network.vec[900].synapse.delay[0:5])
def main():
'''
On the command-line, in moose-examples/snippets directory, run ``python IntegrateFireZoo.py``.
The script will ask you which neuron you want to simulate and you can choose and run what you want.
Play with the parameters of the IF neurons in the source code.
'''
neuronChoices = {'LIF':moose.LIF, 'QIF':moose.QIF, 'ExIF':moose.ExIF, 'AdExIF':moose.AdExIF,
'AdThreshIF':moose.AdThreshIF, 'IzhIF':moose.IzhIF}
#### CHOOSE ONE OF THE NEURON KEYS AS choiceKey FROM BELOW DICTIONARY ####
#choiceKey = 'LIF'
#### No need, am inputting it from the user on the terminal
choiceKeys = list(neuronChoices.keys()) # keys() does not retain the order in dict defn above!
choiceIndex = eval(input('Choose a number corresponding to your desired neuron: '+ \
str([(i,key) for (i,key) in enumerate(choiceKeys)])+' -- '))
choiceKey = choiceKeys[choiceIndex]
neuronChoice = neuronChoices[choiceKey]
# ###########################################
# Initialize neuron group
# ###########################################
# neuron instantiation
network = neuronChoice( 'network' ); # choose neuron type above
moose.le( '/network' )
network.vec.Em = Vrest
network.vec.thresh = Vt_base
network.vec.refractoryPeriod = refrT
network.vec.Rm = R
network.vec.vReset = Vreset
network.vec.Cm = tau/R
network.vec.initVm = Vrest
# neuron specific parameters and current injected I
if choiceKey == 'LIF':
network.vec.inject = 5e-10 # Amp # injected current I
if choiceKey == 'QIF':
network.vec.a0 = a0
network.vec.vCritical = vCritical
network.vec.inject = 5e-10 # Amp # injected current I
elif choiceKey == 'ExIF':
network.vec.deltaThresh = deltaThresh
network.vec.vPeak = vPeak # reset at vPeak, not at thresh
network.vec.inject = 5e-9 # Amp # injected current I
elif choiceKey == 'AdExIF':
network.vec.deltaThresh = deltaThresh
network.vec.vPeak = vPeak # reset at vPeak, not at thresh
network.vec.a0 = a0AdEx
network.vec.b0 = b0
network.vec.tauW = tauW
network.vec.inject = 5e-9 # Amp # injected current I
elif choiceKey == 'AdThreshIF':
network.vec.a0 = a0AdTh
network.vec.threshJump = threshJump
network.vec.tauThresh = tauThresh
network.vec.inject = 1e-9 # Amp # injected current I
elif choiceKey == 'IzhIF':
network.vec.a = a
network.vec.b = b
network.vec.d = d
network.vec.uInit = uRest # Just sets the initial value of u
network.vec.vPeak = vPeak # reset at vPeak, not at thresh
network.vec.inject = 5e-9 # Amp # injected current I
print(("Injecting current =",network.vec[0].inject,"in",choiceKey,"neuron."))
# ###########################################
# Setting up table
# ###########################################
Vm = moose.Table( '/plotVm' )
moose.connect( network, 'VmOut', Vm, 'input', 'OneToOne')
spikes = moose.Table( '/plotSpikes' )
moose.connect( network, 'spikeOut', spikes, 'input', 'OneToOne')
# ###########################################
# Simulate the current injection
# ###########################################
dt = 5e-6 # s
runtime = 0.02 # s
# moose simulation
moose.useClock( 1, '/network', 'process' )
moose.useClock( 2, '/plotSpikes', 'process' )
moose.useClock( 3, '/plotVm', 'process' )
moose.setClock( 0, dt )
moose.setClock( 1, dt )
moose.setClock( 2, dt )
moose.setClock( 3, dt )
moose.setClock( 9, dt )
moose.reinit()
moose.start(runtime)
# ###########################################
# Plot the simulated Vm-s and STDP curve
# ###########################################
# Voltage plots
Vmseries = Vm.vector
numsteps = len(Vmseries)
if choiceKey not in ['ExIF','AdExIF','IzhIF']:
# insert spikes so that Vm reset at thresh doesn't look weird
# for ExIF, etc. reset is at vPeak, so not weird.
for t in spikes.vector:
Vmseries[int(t/dt)-1] = 30e-3 # V
timeseries = np.arange(0.,1000*numsteps*dt-1e-10,dt*1000)
plt.figure(facecolor='w')
plt.plot(timeseries,Vmseries*1000,color='r') # neuron's Vm
plt.xlabel('time (ms)')
plt.ylabel('Vm (mV)')
plt.title(choiceKey+"neuron, current="+str(network.vec[0].inject)+"A")
plt.show()
## Leaky integrate and fire neuron
Vrest = -65e-3 # V # resting potential
Vt_base = -45e-3 # V # threshold
Vreset = -55e-3 # V # in current steps, Vreset is same as pedestal
R = 1e8 # Ohm
tau = 10e-3 # s
refrT = 2e-3 # s
# ###########################################
# Initialize neuron group
# ###########################################
## two neurons: index 0 will be presynaptic, 1 will be postsynaptic
network = moose.LIF("network", 2)
moose.le("/network")
network.vec.Em = Vrest
network.vec.thresh = Vt_base
network.vec.refractoryPeriod = refrT
network.vec.Rm = R
network.vec.vReset = Vreset
network.vec.Cm = tau / R
network.vec.inject = 0.0
network.vec.initVm = Vrest
#############################################
# Ca Plasticity parameters: synapses (not for ExcInhNetBase)
#############################################
### Cortical slice values -- Table Suppl 2 in Graupner & Brunel 2012
### Also used in Higgins et al 2014
def test_mgblock():
"""
Demonstrates the use of MgBlock.
Creates an NMDA channel with MgBlock and another without.
Connects them up to the compartment on one hand, and to a
SynHandler on the other, so as to receive synaptic input.
Delivers two pulses to each receptor, with a small delay in between.
Plots out the conductance change at each receptor and the reslting
membrane potential rise at the compartment.
Note that these NMDA channels do NOT separate out the contributions
due to calcium and other ions. To do this correctly one should use
the GHK object.
"""
model = moose.Neutral('/model')
data = moose.Neutral('/data')
soma = moose.Compartment('/model/soma')
soma.Em = -60e-3
soma.Rm = 1e7
soma.Cm = 1e-9
###################################################
# This is where we create the synapse with MgBlock
#--------------------------------------------------
nmda = moose.SynChan('/model/soma/nmda')
nmda.Gbar = 1e-9
mgblock = moose.MgBlock('/model/soma/mgblock')
mgblock.CMg = 2.0
mgblock.KMg_A = 1/0.33
mgblock.KMg_B = 1/60.0
# The synHandler manages the synapses and their learning rules if any.
synHandler = moose.SimpleSynHandler( '/model/soma/nmda/handler' )
synHandler.synapse.num = 1
moose.connect( synHandler, 'activationOut', nmda, 'activation' )
# MgBlock sits between original channel nmda and the
# compartment. The origChannel receives the channel message from
# the nmda SynChan.
moose.connect(soma, 'VmOut', nmda, 'Vm' )
moose.connect(nmda, 'channelOut', mgblock, 'origChannel')
moose.connect(mgblock, 'channel', soma, 'channel')
# This is for comparing with MgBlock
nmda_noMg = moose.copy(nmda, soma, 'nmda_noMg')
moose.connect( nmda_noMg, 'channel', soma, 'channel')
moose.le( nmda_noMg )
#########################################
# The rest is for experiment setup
spikegen = moose.SpikeGen('/model/spike')
pulse = moose.PulseGen('/model/input')
pulse.delay[0] = 10e-3
pulse.level[0] = 1.0
pulse.width[0] = 50e-3
moose.connect(pulse, 'output', spikegen, 'Vm')
moose.le( synHandler )
#syn = moose.element(synHandler.path + '/synapse' )
syn = synHandler.synapse[0]
syn.delay = simdt * 2
syn.weight = 10
moose.connect(spikegen, 'spikeOut', synHandler.synapse[0], 'addSpike')
moose.le( nmda_noMg )
noMgSyn = moose.element(nmda_noMg.path + '/handler/synapse' )
noMgSyn.delay = 0.01
noMgSyn.weight = 1
moose.connect(spikegen, 'spikeOut', noMgSyn, 'addSpike')
moose.showfields( syn )
moose.showfields( noMgSyn )
Gnmda = moose.Table('/data/Gnmda')
moose.connect(Gnmda, 'requestOut', mgblock, 'getGk')
Gnmda_noMg = moose.Table('/data/Gnmda_noMg')
moose.connect(Gnmda_noMg, 'requestOut', nmda_noMg, 'getGk')
Vm = moose.Table('/data/Vm')
moose.connect(Vm, 'requestOut', soma, 'getVm')
for i in range( 10 ):
moose.setClock( i, simdt )
moose.setClock( Gnmda.tick, plotdt )
print spikegen.dt, Gnmda.dt
moose.reinit()
moose.start( simtime )
t = pylab.linspace(0, simtime*1e3, len(Vm.vector))
pylab.plot(t, (Vm.vector + 0.06) * 1000, label='Vm (mV)')
pylab.plot(t, Gnmda.vector * 1e9, label='Gnmda (nS)')
pylab.plot(t, Gnmda_noMg.vector * 1e9, label='Gnmda no Mg (nS)')
pylab.legend()
#data = pylab.vstack((t, Gnmda.vector, Gnmda_noMg.vector)).transpose()
#pylab.savetxt('mgblock.dat', data)
pylab.show()
CaRGbar = 0.07
CaLGbar = 0.51
CaNGbar = 1.76
KSKGbar = 4.28006e-02
KBKGbar = 5.08559e-03
ChP = 'Srikanth2015/ChannelProtos_Sri2015_base'
sm_diam = 100e-6
sm_len = 100e-6
Ca_tau = 0.2 / 7 #Not sure about this
Ca_B = np.pi * sm_diam * 1e16 / 2 / F #Not sure about this
try:
# [moose.delete(x) for x in ['/model', '/library']]
for ff in moose.le('library'):
if ff != '/library[0]/KBK_chan':
moose.delete(ff)
[moose.delete(x) for x in ['/model']]
except:
pass
rdes = rd.rdesigneur(
# cellProto = [['somaProto', 'soma', 12.76e-6, 0.01e-6]],
cellProto=[['somaProto', 'soma', sm_diam, sm_len]],
chanProto=[
[ChP + '.Na_SChan()', 'Na_Schan'],
[ChP + '.KDR_SChan()', 'KDR_Schan'],
[ChP + '.KA_SChan()', 'KA_Schan'],
[ChP + '.KM_Chan()', 'KM_chan'],
[ChP + '.h_Chan()', 'h_chan'],
def main():
cm = ChannelML( {'temperature': 32 })
cm.readChannelMLFromFile( 'CA1_migliore_reference/hd.xml' )
cm.readChannelMLFromFile( 'CA1_migliore_reference/kap.xml' )
cm.readChannelMLFromFile( 'CA1_migliore_reference/kad.xml' )
cm.readChannelMLFromFile( 'CA1_migliore_reference/kdr.xml' )
cm.readChannelMLFromFile( 'CA1_migliore_reference/na3.xml' )
cm.readChannelMLFromFile( 'CA1_migliore_reference/nax.xml' )
if ( len( sys.argv ) < 2 ):
print("Usage: ", sys.argv[0], " filename")
return
# filename = "./Bhavika_swcplusnmlfiles/preliminarily corrected nmlfiles/ascoli+buzsaki/valid/" + sys.argv[1]
filename = sys.argv[1]
moose.Neutral( '/model' )
# Load in the swc file.
cell = moose.loadModel( filename, '/model/ca1' )
for i in moose.wildcardFind( '/library/##' ):
i.tick = -1
chanDistrib = [ \
"EM", "#", "-58e-3", \
"initVm", "#", "-65e-3", \
"RM", "#", "2.8", \
"CM", "#", "0.01", \
"RA", "#", "1.5", \
"RA", "#axon#", "0.5", \
"hd", "#dend#,#apical#", "5e-2*(1+(r*3e4))", \
"kdr", "#", "100", \
"na3", "#soma#,#dend#,#apical#", "250", \
"nax", "#axon#", "1250", \
"kap", "#axon#,#soma#", "300", \
"kap", "#dend#,#apical#", "150*(1+sign(100-r*1e6)) * (1+(r*1e4))", \
"kad", "#dend#,#apical#", "150*(1+sign(r*1e6-100))*(1+r*1e4)", \
]
moose.showfields( cell[0] )
cell[0].channelDistribution = chanDistrib
cell[0].parseChanDistrib()
for i in range( 8 ):
moose.setClock( i, simdt )
hsolve = moose.HSolve( '/model/ca1/hsolve' )
hsolve.dt = simdt
hsolve.target = '/model/ca1/soma'
'''
'''
moose.reinit()
makePlot( cell[0] )
# Now we set up the display
moose.le( '/model/ca1/soma' )
soma = moose.element( '/model/ca1/soma' )
kap = moose.element( '/model/ca1/soma/kap' )
graphs = moose.Neutral( '/graphs' )
vtab = moose.Table( '/graphs/vtab' )
moose.connect( vtab, 'requestOut', soma, 'getVm' )
kaptab = moose.Table( '/graphs/kaptab' )
moose.connect( kaptab, 'requestOut', kap, 'getGk' )
compts = moose.wildcardFind( "/model/ca1/#[ISA=CompartmentBase]" )
'''
for i in compts:
if moose.exists( i.path + '/Na' ):
print i.path, moose.element( i.path + '/Na' ).Gbar, \
moose.element( i.path + '/K_DR' ).Gbar, \
i.Rm, i.Ra, i.Cm
'''
'''
Na = moose.wildcardFind( '/model/ca1/#/Na#' )
print Na
Na2 = []
for i in compts:
if ( moose.exists( i.path + '/NaF2' ) ):
Na2.append( moose.element( i.path + '/NaF2' ) )
if ( moose.exists( i.path + '/NaPF_SS' ) ):
Na2.append( moose.element( i.path + '/NaPF_SS' ) )
ecomptPath = map( lambda x : x.path, compts )
print "Na placed in ", len( Na ), len( Na2 ), " out of ", len( compts ), " compts."
'''
compts[0].inject = inject
ecomptPath = [x.path for x in compts]
# Graphics stuff here.
app = QtGui.QApplication(sys.argv)
morphology = moogli.read_morphology_from_moose(name = "", path = "/model/ca1")
morphology.create_group( "group_all", ecomptPath, -0.08, 0.02, \
[0.0, 0.0, 1.0, 1.0], [1.0, 0.0, 0.0, 0.1] )
viewer = moogli.DynamicMorphologyViewerWidget(morphology)
def callback( morphology, viewer ):
moose.start( frameRunTime )
Vm = [moose.element( x ).Vm for x in compts]
morphology.set_color( "group_all", Vm )
currTime = moose.element( '/clock' ).currentTime
#print currTime, compts[0].Vm
if ( currTime < runtime ):
return True
return False
viewer.set_callback( callback, idletime = 0 )
viewer.showMaximized()
viewer.show()
app.exec_()
t = numpy.arange( 0, runtime, vtab.dt )
fig = plt.figure()
p1 = fig.add_subplot(311)
p2 = fig.add_subplot(312)
p2.plot( t, vtab.vector, label = 'Vm Soma' )
p2.legend()
p3 = fig.add_subplot(313)
p3.plot( t, kaptab.vector, label = 'kap Soma' )
p3.legend()
plt.show()
def makeModel():
# create container for model
model = moose.Neutral( 'model' )
compartment = moose.CubeMesh( '/model/compartment' )
compartment.volume = 1e-15
# the mesh is created automatically by the compartment
moose.le( '/model/compartment' )
mesh = moose.element( '/model/compartment/mesh' )
# create molecules and reactions
a = moose.Pool( '/model/compartment/a' )
b = moose.Pool( '/model/compartment/b' )
c = moose.Pool( '/model/compartment/c' )
enz1 = moose.Enz( '/model/compartment/b/enz1' )
enz2 = moose.Enz( '/model/compartment/c/enz2' )
cplx1 = moose.Pool( '/model/compartment/b/enz1/cplx' )
cplx2 = moose.Pool( '/model/compartment/c/enz2/cplx' )
reac = moose.Reac( '/model/compartment/reac' )
# connect them up for reactions
moose.connect( enz1, 'sub', a, 'reac' )
moose.connect( enz1, 'prd', b, 'reac' )
moose.connect( enz1, 'enz', b, 'reac' )
moose.connect( enz1, 'cplx', cplx1, 'reac' )
moose.connect( enz2, 'sub', b, 'reac' )
moose.connect( enz2, 'prd', a, 'reac' )
moose.connect( enz2, 'enz', c, 'reac' )
moose.connect( enz2, 'cplx', cplx2, 'reac' )
moose.connect( reac, 'sub', a, 'reac' )
moose.connect( reac, 'prd', b, 'reac' )
# connect them up to the compartment for volumes
#for x in ( a, b, c, cplx1, cplx2 ):
# moose.connect( x, 'mesh', mesh, 'mesh' )
# Assign parameters
a.concInit = 1
b.concInit = 0
c.concInit = 0.01
enz1.kcat = 0.4
enz1.Km = 4
enz2.kcat = 0.6
enz2.Km = 0.01
reac.Kf = 0.001
reac.Kb = 0.01
# Create the output tables
graphs = moose.Neutral( '/model/graphs' )
outputA = moose.Table2 ( '/model/graphs/concA' )
outputB = moose.Table2 ( '/model/graphs/concB' )
# connect up the tables
moose.connect( outputA, 'requestOut', a, 'getConc' );
moose.connect( outputB, 'requestOut', b, 'getConc' );
# We need a finer timestep than the default 0.1 seconds,
# in order to get numerical accuracy.
for i in range (11, 15 ):
moose.setClock( i, 0.001 ) # for computational objects
def loadFile(filename, target, solver="gsl", merge=True):
"""Try to load a model from specified `filename` under the element
`target`.
if `merge` is True, the contents are just loaded at target. If
false, everything is deleted from the parent of target unless the
parent is root.
Returns
-------
a dict containing at least these three entries:
modeltype: type of the loaded model.
subtype: subtype of the loaded model, None if no specific subtype
modelroot: root element of the model, None if could not be located - as is the case with Python scripts
"""
num = 1
newTarget = target
while moose.exists(newTarget):
newTarget = target + "-" + str(num)
num = num + 1
target = newTarget
istext = True
with open(filename, 'rb') as infile:
istext = mtypes.istextfile(infile)
if not istext:
print 'Cannot handle any binary formats yet'
return None
parent, child = posixpath.split(target)
p = moose.Neutral(parent)
if not merge and p.path != '/':
for ch in p.children:
moose.delete(ch)
try:
modeltype = mtypes.getType(filename)
subtype = mtypes.getSubtype(filename, modeltype)
except KeyError:
raise FileLoadError('Do not know how to handle this filetype: %s' %
(filename))
pwe = moose.getCwe()
#self.statusBar.showMessage('Loading model, please wait')
# app = QtGui.qApp
# app.setOverrideCursor(QtGui.QCursor(Qt.Qt.BusyCursor)) #shows a hourglass - or a busy/working arrow
if modeltype == 'genesis':
if subtype == 'kkit' or subtype == 'prototype':
model, modelpath = loadGenCsp(target, filename, solver)
if moose.exists(moose.element(modelpath).path):
moose.Annotator(moose.element(modelpath).path +
'/info').modeltype = "kkit"
else:
print " path doesn't exists"
moose.le(modelpath)
else:
print 'Only kkit and prototype files can be loaded.'
elif modeltype == 'cspace':
model, modelpath = loadGenCsp(target, filename)
if moose.exists(modelpath):
moose.Annotator(
(moose.element(modelpath).path + '/info')).modeltype = "cspace"
addSolver(modelpath, 'gsl')
elif modeltype == 'xml':
if subtype == 'neuroml':
popdict, projdict = neuroml.loadNeuroML_L123(filename)
# Circus to get the container of populations from loaded neuroml
for popinfo in popdict.values():
for cell in popinfo[1].values():
solver = moose.HSolve(cell.path + "/hsolve")
solver.target = cell.path
# model = cell.parent
# break
# break
# Moving model to a new location under the model name
# model name is the filename without extension
model = moose.Neutral("/" + splitext(basename(filename))[0])
element = moose.Neutral(model.path + "/model")
if (moose.exists("/cells")): moose.move("/cells", element.path)
if (moose.exists("/elec")): moose.move("/elec", model.path)
if (moose.exists("/library")): moose.move("/library", model.path)
# moose.move("cells/", cell.path)
elif subtype == 'sbml':
if target != '/':
if moose.exists(target):
moose.delete(target)
model = mooseReadSBML(filename, target)
if moose.exists(moose.element(model).path):
moose.Annotator(moose.element(model).path +
'/info').modeltype = "sbml"
addSolver(target, 'gsl')
else:
raise FileLoadError('Do not know how to handle this filetype: %s' %
(filename))
moose.setCwe(
pwe
) # The MOOSE loadModel changes the current working element to newly loaded model. We revert that behaviour
# TODO: check with Aditya how to specify the target for
# neuroml reader
# app.restoreOverrideCursor()
return {'modeltype': modeltype, 'subtype': subtype, 'model': model}
def makeNeuroMeshModel():
diffLength = 10e-6 # Aim for 2 soma compartments.
elec = loadElec()
loadChem( diffLength )
neuroCompt = moose.element( '/model/chem/dend' )
neuroCompt.diffLength = diffLength
neuroCompt.cellPortion( elec, '/model/elec/#' )
for x in moose.wildcardFind( '/model/chem/##[ISA=PoolBase]' ):
if (x.diffConst > 0):
x.diffConst = 1e-11
for x in moose.wildcardFind( '/model/chem/##/Ca' ):
x.diffConst = 1e-10
# Put in dend solvers
ns = neuroCompt.numSegments
ndc = neuroCompt.numDiffCompts
print 'ns = ', ns, ', ndc = ', ndc
assert( neuroCompt.numDiffCompts == neuroCompt.mesh.num )
assert( ns == 36 ) #
assert( ndc == 278 ) #
nmksolve = moose.Ksolve( '/model/chem/dend/ksolve' )
nmdsolve = moose.Dsolve( '/model/chem/dend/dsolve' )
nmstoich = moose.Stoich( '/model/chem/dend/stoich' )
nmstoich.compartment = neuroCompt
nmstoich.ksolve = nmksolve
nmstoich.dsolve = nmdsolve
nmstoich.path = "/model/chem/dend/##"
print 'done setting path, numPools = ', nmdsolve.numPools
assert( nmdsolve.numPools == 1 )
assert( nmdsolve.numAllVoxels == ndc )
assert( nmstoich.numAllPools == 1 )
# oddly, numLocalFields does not work.
ca = moose.element( '/model/chem/dend/DEND/Ca' )
assert( ca.numData == ndc )
# Put in spine solvers. Note that these get info from the neuroCompt
spineCompt = moose.element( '/model/chem/spine' )
sdc = spineCompt.mesh.num
print 'sdc = ', sdc
assert( sdc == 13 )
smksolve = moose.Ksolve( '/model/chem/spine/ksolve' )
smdsolve = moose.Dsolve( '/model/chem/spine/dsolve' )
smstoich = moose.Stoich( '/model/chem/spine/stoich' )
smstoich.compartment = spineCompt
smstoich.ksolve = smksolve
smstoich.dsolve = smdsolve
smstoich.path = "/model/chem/spine/##"
print 'spine num Pools = ', smstoich.numAllPools
assert( smstoich.numAllPools == 3 )
assert( smdsolve.numPools == 3 )
assert( smdsolve.numAllVoxels == sdc )
# Put in PSD solvers. Note that these get info from the neuroCompt
psdCompt = moose.element( '/model/chem/psd' )
pdc = psdCompt.mesh.num
assert( pdc == 13 )
pmksolve = moose.Ksolve( '/model/chem/psd/ksolve' )
pmdsolve = moose.Dsolve( '/model/chem/psd/dsolve' )
pmstoich = moose.Stoich( '/model/chem/psd/stoich' )
pmstoich.compartment = psdCompt
pmstoich.ksolve = pmksolve
pmstoich.dsolve = pmdsolve
pmstoich.path = "/model/chem/psd/##"
assert( pmstoich.numAllPools == 3 )
assert( pmdsolve.numPools == 3 )
assert( pmdsolve.numAllVoxels == pdc )
foo = moose.element( '/model/chem/psd/Ca' )
print 'PSD: numfoo = ', foo.numData
print 'PSD: numAllVoxels = ', pmksolve.numAllVoxels
# Put in junctions between the diffusion solvers
nmdsolve.buildNeuroMeshJunctions( smdsolve, pmdsolve )
"""
CaNpsd = moose.vec( '/model/chem/psdMesh/PSD/PP1_PSD/CaN' )
print 'numCaN in PSD = ', CaNpsd.nInit, ', vol = ', CaNpsd.volume
CaNspine = moose.vec( '/model/chem/spine/SPINE/CaN_BULK/CaN' )
print 'numCaN in spine = ', CaNspine.nInit, ', vol = ', CaNspine.volume
"""
##################################################################
# set up adaptors
aCa = moose.Adaptor( '/model/chem/spine/adaptCa', sdc )
adaptCa = moose.vec( '/model/chem/spine/adaptCa' )
chemCa = moose.vec( '/model/chem/spine/Ca' )
#print 'aCa = ', aCa, ' foo = ', foo, "len( ChemCa ) = ", len( chemCa ), ", numData = ", chemCa.numData, "len( adaptCa ) = ", len( adaptCa )
assert( len( adaptCa ) == sdc )
assert( len( chemCa ) == sdc )
for i in range( sdc ):
elecCa = moose.element( '/model/elec/spine_head_14_' + str(i+1) + '/NMDA_Ca_conc' )
#print elecCa
moose.connect( elecCa, 'concOut', adaptCa[i], 'input', 'Single' )
moose.connect( adaptCa, 'output', chemCa, 'setConc', 'OneToOne' )
adaptCa.inputOffset = 0.0 #
adaptCa.outputOffset = 0.00008 # 80 nM offset in chem.
adaptCa.scale = 1e-4 # 520 to 0.0052 mM
#print adaptCa.outputOffset
moose.le( '/model/chem/dend/DEND' )
compts = neuroCompt.elecComptList
begin = neuroCompt.startVoxelInCompt
end = neuroCompt.endVoxelInCompt
aCa = moose.Adaptor( '/model/chem/dend/DEND/adaptCa', len( compts))
adaptCa = moose.vec( '/model/chem/dend/DEND/adaptCa' )
chemCa = moose.vec( '/model/chem/dend/DEND/Ca' )
#print 'aCa = ', aCa, ' foo = ', foo, "len( ChemCa ) = ", len( chemCa ), ", numData = ", chemCa.numData, "len( adaptCa ) = ", len( adaptCa )
assert( len( chemCa ) == ndc )
for i in zip( compts, adaptCa, begin, end ):
name = i[0].path + '/Ca_conc'
if ( moose.exists( name ) ):
elecCa = moose.element( name )
#print i[2], i[3], ' ', elecCa
#print i[1]
moose.connect( elecCa, 'concOut', i[1], 'input', 'Single' )
for j in range( i[2], i[3] ):
moose.connect( i[1], 'output', chemCa[j], 'setConc', 'Single' )
adaptCa.inputOffset = 0.0 #
adaptCa.outputOffset = 0.00008 # 80 nM offset in chem.
adaptCa.scale = 20e-6 # 10 arb units to 2 uM.
def makeNeuroMeshModel():
diffLength = 10e-6 # Aim for 2 soma compartments.
elec = loadElec()
loadChem(diffLength)
neuroCompt = moose.element('/model/chem/dend')
neuroCompt.diffLength = diffLength
neuroCompt.cellPortion(elec, '/model/elec/#')
for x in moose.wildcardFind('/model/chem/##[ISA=PoolBase]'):
if (x.diffConst > 0):
x.diffConst = 1e-11
for x in moose.wildcardFind('/model/chem/##/Ca'):
x.diffConst = 1e-10
# Put in dend solvers
ns = neuroCompt.numSegments
ndc = neuroCompt.numDiffCompts
print 'ns = ', ns, ', ndc = ', ndc
assert (neuroCompt.numDiffCompts == neuroCompt.mesh.num)
assert (ns == 36) #
assert (ndc == 278) #
nmksolve = moose.Ksolve('/model/chem/dend/ksolve')
nmdsolve = moose.Dsolve('/model/chem/dend/dsolve')
nmstoich = moose.Stoich('/model/chem/dend/stoich')
nmstoich.compartment = neuroCompt
nmstoich.ksolve = nmksolve
nmstoich.dsolve = nmdsolve
nmstoich.path = "/model/chem/dend/##"
print 'done setting path, numPools = ', nmdsolve.numPools
assert (nmdsolve.numPools == 1)
assert (nmdsolve.numAllVoxels == ndc)
assert (nmstoich.numAllPools == 1)
# oddly, numLocalFields does not work.
ca = moose.element('/model/chem/dend/DEND/Ca')
assert (ca.numData == ndc)
# Put in spine solvers. Note that these get info from the neuroCompt
spineCompt = moose.element('/model/chem/spine')
sdc = spineCompt.mesh.num
print 'sdc = ', sdc
assert (sdc == 13)
smksolve = moose.Ksolve('/model/chem/spine/ksolve')
smdsolve = moose.Dsolve('/model/chem/spine/dsolve')
smstoich = moose.Stoich('/model/chem/spine/stoich')
smstoich.compartment = spineCompt
smstoich.ksolve = smksolve
smstoich.dsolve = smdsolve
smstoich.path = "/model/chem/spine/##"
print 'spine num Pools = ', smstoich.numAllPools, smdsolve.numPools
assert (smstoich.numAllPools == 35)
assert (smdsolve.numPools == 30)
assert (smdsolve.numAllVoxels == sdc)
# Put in PSD solvers. Note that these get info from the neuroCompt
psdCompt = moose.element('/model/chem/psd')
pdc = psdCompt.mesh.num
assert (pdc == 13)
pmksolve = moose.Ksolve('/model/chem/psd/ksolve')
pmdsolve = moose.Dsolve('/model/chem/psd/dsolve')
pmstoich = moose.Stoich('/model/chem/psd/stoich')
pmstoich.compartment = psdCompt
pmstoich.ksolve = pmksolve
pmstoich.dsolve = pmdsolve
pmstoich.path = "/model/chem/psd/##"
print 'psd num Pools = ', pmstoich.numAllPools, pmdsolve.numPools
assert (pmstoich.numAllPools == 55)
assert (pmdsolve.numPools == 48)
assert (pmdsolve.numAllVoxels == pdc)
foo = moose.element('/model/chem/psd/Ca')
print 'PSD: numfoo = ', foo.numData
print 'PSD: numAllVoxels = ', pmksolve.numAllVoxels
# Put in junctions between the diffusion solvers
nmdsolve.buildNeuroMeshJunctions(smdsolve, pmdsolve)
"""
CaNpsd = moose.vec( '/model/chem/psdMesh/PSD/PP1_PSD/CaN' )
print 'numCaN in PSD = ', CaNpsd.nInit, ', vol = ', CaNpsd.volume
CaNspine = moose.vec( '/model/chem/spine/SPINE/CaN_BULK/CaN' )
print 'numCaN in spine = ', CaNspine.nInit, ', vol = ', CaNspine.volume
"""
##################################################################
# set up adaptors
aCa = moose.Adaptor('/model/chem/spine/adaptCa', sdc)
adaptCa = moose.vec('/model/chem/spine/adaptCa')
chemCa = moose.vec('/model/chem/spine/Ca')
#print 'aCa = ', aCa, ' foo = ', foo, "len( ChemCa ) = ", len( chemCa ), ", numData = ", chemCa.numData, "len( adaptCa ) = ", len( adaptCa )
assert (len(adaptCa) == sdc)
assert (len(chemCa) == sdc)
for i in range(sdc):
elecCa = moose.element('/model/elec/spine_head_14_' + str(i + 1) +
'/NMDA_Ca_conc')
#print elecCa
moose.connect(elecCa, 'concOut', adaptCa[i], 'input', 'Single')
moose.connect(adaptCa, 'output', chemCa, 'setConc', 'OneToOne')
adaptCa.inputOffset = 0.0 #
adaptCa.outputOffset = 0.00008 # 80 nM offset in chem.
adaptCa.scale = 5e-3 # 520 to 0.0052 mM
#print adaptCa.outputOffset
moose.le('/model/chem/dend/DEND')
compts = neuroCompt.elecComptList
begin = neuroCompt.startVoxelInCompt
end = neuroCompt.endVoxelInCompt
aCa = moose.Adaptor('/model/chem/dend/DEND/adaptCa', len(compts))
adaptCa = moose.vec('/model/chem/dend/DEND/adaptCa')
chemCa = moose.vec('/model/chem/dend/DEND/Ca')
#print 'aCa = ', aCa, ' foo = ', foo, "len( ChemCa ) = ", len( chemCa ), ", numData = ", chemCa.numData, "len( adaptCa ) = ", len( adaptCa )
assert (len(chemCa) == ndc)
for i in zip(compts, adaptCa, begin, end):
name = i[0].path + '/Ca_conc'
if (moose.exists(name)):
elecCa = moose.element(name)
#print i[2], i[3], ' ', elecCa
#print i[1]
moose.connect(elecCa, 'concOut', i[1], 'input', 'Single')
for j in range(i[2], i[3]):
moose.connect(i[1], 'output', chemCa[j], 'setConc', 'Single')
adaptCa.inputOffset = 0.0 #
adaptCa.outputOffset = 0.00008 # 80 nM offset in chem.
adaptCa.scale = 20e-6 # 10 arb units to 2 uM.
viewer.attach_shapes(list(lifs.shapes.values()))
# print "Attached Shapes"
view = moogli.View("view")
viewer.attach_view(view)
# print "Attached View"
return viewer
if __name__=='__main__':
plt.ion()
## ExcInhNetBase has unconnected neurons,
## ExcInhNet connects them
## Instantiate either ExcInhNetBase or ExcInhNet below
#net = ExcInhNetBase(N=N)
net = ExcInhNet(N=N)
print(net)
moose.le( '/' )
moose.le( '/network' )
rdes = buildRdesigneur()
rdes.buildModel( '/model' )
buildNeuronPlots( rdes )
connectDetailedNeuron()
app = QtGui.QApplication(sys.argv)
viewer = create_viewer(rdes)
viewer.showMaximized()
viewer.start()
app.exec_()
## Important to distribute the initial Vm-s
## else weak coupling gives periodic synchronous firing
plotif = True
moose.setCwe( '/library' ) proto18.make_Ca() proto18.make_Ca_conc() proto18.make_K_AHP() proto18.make_K_C() proto18.make_Na() proto18.make_K_DR() proto18.make_K_A() proto18.make_glu() proto18.make_NMDA() proto18.make_Ca_NMDA() proto18.make_NMDA_Ca_conc() proto18.make_axon() cellId = moose.loadModel( 'ca1_asym.p', '/cell', "hsolve" ) moose.le( cellId ) moose.le( '/cell/lat_14_1' ) #le( '/cell' ) graphs = moose.Neutral( '/graphs' ) tab = moose.Table( '/graphs/soma' ) catab = moose.Table( '/graphs/ca' ) soma = moose.element( '/cell/soma' ) soma.inject = 2e-10 moose.connect( tab, 'requestOut', soma, 'getVm' ) capool = moose.element( '/cell/soma/Ca_conc' ) moose.connect( catab, 'requestOut', capool, 'getCa' ) print 1 dt = 50e-6 moose.setClock( 0, dt ) moose.setClock( 1, dt ) moose.setClock( 2, dt )
def make_network():
"""
This snippet sets up a recurrent network of IntFire objects, using
SimpleSynHandlers to deal with spiking events.
It isn't very satisfactory as activity runs down after a while.
It is a good example for using the IntFire, setting up random
connectivity, and using SynHandlers.
"""
global all_done_
done = mp.Value('i', 0)
q = mp.Queue()
th = mp.Process(target=streamer_handler, args=(done, q))
th.start()
size = 1024
dt = 0.2
runsteps = 10
delayMin = 0
delayMax = 4
weightMax = 1
Vmax = 1.0
thresh = 0.4
refractoryPeriod = 0.4
tau = 0.5
connectionProbability = 0.01
random.seed( 123 )
np.random.seed( 456 )
t0 = time.time()
network = moose.IntFire( 'network', size );
syns = moose.SimpleSynHandler( '/network/syns', size );
moose.connect( syns, 'activationOut', network, 'activation', 'OneToOne' )
moose.le( '/network' )
syns.vec.numSynapses = [1] * size
sv = moose.vec( '/network/syns/synapse' )
print('before connect t = %.3f'%(time.time() - t0))
mid = moose.connect( network, 'spikeOut', sv, 'addSpike', 'Sparse')
print('after connect t = %.3f'%(time.time() - t0))
#print mid.destFields
m2 = moose.element( mid )
m2.setRandomConnectivity( connectionProbability, 5489 )
print('after setting connectivity, t=%.3f'%(time.time() - t0))
#network.vec.Vm = [(Vmax*random.random()) for r in range(size)]
network.vec.Vm = np.random.rand( size ) * Vmax
network.vec.thresh = thresh
network.vec.refractoryPeriod = refractoryPeriod
network.vec.tau = tau
numSynVec = syns.vec.numSynapses
print('Middle of setup, t = %.3f'%(time.time() - t0))
numTotSyn = sum( numSynVec )
print((numSynVec.size, ', tot = ', numTotSyn, ', numSynVec = ', numSynVec))
for item in syns.vec:
h = moose.element(item)
h.synapse.delay = delayMin + (delayMax-delayMin) * np.random.rand(len(h.synapse))
h.synapse.weight = np.random.rand(len(h.synapse)) * weightMax
print('After setup, t = %.3f'%(time.time()-t0))
numStats = 100
stats = moose.SpikeStats( '/stats', numStats )
stats.vec.windowLength = 1 # timesteps to put together.
plots = moose.Table( '/plot', numStats )
convergence = size // numStats
for i in range( numStats ):
for j in range( size//numStats ):
k = i * convergence + j
moose.connect( network.vec[k], 'spikeOut', stats.vec[i], 'addSpike' )
moose.connect( plots, 'requestOut', stats, 'getMean', 'OneToOne' )
t1 = time.time()
moose.reinit()
print('reinit time t = %.3f'%(time.time() - t1))
network.vec.Vm = np.random.rand( size ) * Vmax
print('setting Vm , t = %.3f'%(time.time() - t1))
t1 = time.time()
moose.start(runsteps * dt, 1)
time.sleep(0.1)
done.value = 1
print('runtime, t = %.3f'%(time.time() - t1))
print(network.vec.Vm[99:103], network.vec.Vm[900:903])
res = q.get()
for tabPath in res:
aWithTime = res[tabPath]
a = aWithTime[1::2]
b = moose.element(tabPath).vector
print( tabPath, len(a), len(b) )
if len(a) == len(b):
assert np.equal(a, b).all()
else:
print( "Table did not equal size. The last table is allowed to "
" have fewer entries." )
th.join()
print( 'All done' )
