def loadAndRun(solver=True):
simtime = 500e-3
model = moose.loadModel('../data/h10.CNG.swc', '/cell')
comp = moose.element('/cell/apical_e_177_0')
soma = moose.element('/cell/soma')
for i in range(10):
moose.setClock(i, dt)
if solver:
solver = moose.HSolve('/cell/solver')
solver.target = soma.path
solver.dt = dt
stim = moose.PulseGen('/cell/stim')
stim.delay[0] = 50e-3
stim.delay[1] = 1e9
stim.level[0] = 1e-9
stim.width[0] = 2e-3
moose.connect(stim, 'output', comp, 'injectMsg')
tab = moose.Table('/cell/Vm')
moose.connect(tab, 'requestOut', comp, 'getVm')
tab_soma = moose.Table('/cell/Vm_soma')
moose.connect(tab_soma, 'requestOut', soma, 'getVm')
moose.reinit()
print('[INFO] Running for %s' % simtime)
moose.start(simtime )
vec = tab_soma.vector
moose.delete( '/cell' )
return vec
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 testNeuroMeshMultiscale():
useHsolve = 1
runtime = 0.5
if useHsolve:
elecDt = 50e-6
else:
elecDt = 10e-6
chemDt = 0.005
ePlotDt = 0.5e-3
cPlotDt = 0.005
plotName = 'nm.plot'
makeNeuroMeshModel()
print("after model is completely done")
for i in moose.wildcardFind('/model/chem/#/#/#/transloc#'):
print((i[0].name, i[0].Kf, i[0].Kb, i[0].kf, i[0].kb))
makeChemPlots()
makeElecPlots()
makeCaPlots()
moose.setClock(0, elecDt)
moose.setClock(1, elecDt)
moose.setClock(2, elecDt)
moose.setClock(4, chemDt)
moose.setClock(5, chemDt)
moose.setClock(6, chemDt)
moose.setClock(7, cPlotDt)
moose.setClock(8, ePlotDt)
if useHsolve:
hsolve = moose.HSolve('/model/elec/hsolve')
moose.useClock(1, '/model/elec/hsolve', 'process')
hsolve.dt = elecDt
hsolve.target = '/model/elec/compt'
moose.reinit()
else:
moose.useClock(0, '/model/elec/##[ISA=Compartment]', 'init')
moose.useClock(1, '/model/elec/##[ISA=Compartment]', 'process')
moose.useClock(
2,
'/model/elec/##[ISA=ChanBase],/model/##[ISA=SynBase],/model/##[ISA=CaConc]',
'process')
moose.useClock(1, '/model/elec/##[ISA=SpikeGen]', 'process')
moose.useClock(2, '/model/##[ISA=SynBase],/model/##[ISA=CaConc]',
'process')
moose.useClock(4, '/model/chem/#/dsolve', 'process')
moose.useClock(4, '/model/chem/#/ksolve', 'init')
moose.useClock(5, '/model/chem/#/ksolve', 'process')
moose.useClock(6, '/model/chem/spine/adaptCa', 'process')
moose.useClock(6, '/model/chem/dend/DEND/adaptCa', 'process')
moose.useClock(7, '/graphs/chem/#', 'process')
moose.useClock(8, '/graphs/elec/#,/graphs/ca/#', 'process')
moose.element('/model/elec/soma').inject = 2e-10
moose.element('/model/chem/psd/Ca').concInit = 0.001
moose.element('/model/chem/spine/Ca').concInit = 0.002
moose.element('/model/chem/dend/DEND/Ca').concInit = 0.003
moose.reinit()
moose.start(runtime)
makeGraphics(cPlotDt, ePlotDt)
def main():
"""
A toy compartmental neuronal + chemical model that causes bad things
to happen to the hsolver, as of 28 May 2013. Hopefully this will
become irrelevant soon
"""
fineDt = 1e-5
coarseDt = 5e-5
make_spiny_compt()
make_plots()
for i in range(8):
moose.setClock(i, fineDt)
moose.setClock(8, coarseDt)
moose.reinit()
moose.start(0.1)
display_plots('instab.plot')
# make Hsolver and rerun
hsolve = moose.HSolve('/n/hsolve')
for i in range(8):
moose.setClock(i, coarseDt)
hsolve.dt = coarseDt
hsolve.target = '/n/compt'
moose.reinit()
moose.start(0.1)
display_plots('h_instab.plot')
pylab.show()
def setup_model(model_path, synapse_locations, passive=False, solver='hsolve'):
"""Set up a single cell model under `model_path` with synapses
created in the compartments listed in `synapse_locations`.
`model_path` - location where the model should be created.
`synapse_locations`: compartment names for the synapses.
"""
cell = moose.copy(make_prototype(passive), model_path)
if solver.lower() == 'hsolve':
hsolve = moose.HSolve('%s/solve' % (cell.path))
hsolve.dt = simdt
hsolve.target = cell.path
syninfo_list = []
for compname in synapse_locations:
comppath = '%s/%s' % (cell.path, compname)
print('1111 Creating synapse in', comppath)
compartment = moose.element(comppath)
syninfo = make_synapse(compartment)
syninfo_list.append(syninfo)
# connect pulse stimulus
stim_path = '%s/%s/stim' % (cell.path, compname)
print('2222 Creating stimuls in', stim_path)
stim = moose.PulseGen(stim_path)
moose.connect(stim, 'output', syninfo['spike'], 'Vm')
syninfo['stimulus'] = stim
return {'neuron': cell, 'syninfo': syninfo_list}
def setupSolver(self, path='/hsolve'):
"""Setting up HSolver """
hsolve = moose.HSolve(path)
hsolve.dt = self.simDt
moose.setClock(1, self.simDt)
moose.useClock(1, hsolve.path, 'process')
hsolve.target = self.cablePath
def testNeuroMeshMultiscale():
runtime = 0.5
#elecDt = 0.2e-6
elecDt = 10e-6
chemDt = 0.0025
ePlotDt = 0.5e-3
cPlotDt = 0.0025
plotName = 'nm.plot'
makeNeuroMeshModel()
print("after model is completely done")
for i in moose.wildcardFind('/model/chem/#/#/#/transloc#'):
print((i[0].name, i[0].Kf, i[0].Kb, i[0].kf, i[0].kb))
makeChemPlots()
makeElecPlots()
makeCaPlots()
hsolve = moose.HSolve('/model/elec/hsolve')
hsolve.dt = elecDt
hsolve.target = '/model/elec/compt'
plotlist = makeGraphics()
moose.reinit()
moose.element('/model/elec/soma').inject = 2e-10
moose.element('/model/chem/psd/Ca').concInit = 0.001
moose.element('/model/chem/spine/Ca').concInit = 0.002
moose.element('/model/chem/dend/DEND/Ca').concInit = 0.003
moose.reinit()
numDivs = 200
partialRuntime = runtime / numDivs
for i in range(numDivs):
moose.start(partialRuntime)
updateGraphics(plotlist)
finalizeGraphics(plotlist, cPlotDt, ePlotDt)
def assign_clocks(model_container_list, simdt, plotdt, hsolveYN, name_soma):
log.info('SimDt={}, PlotDt={}', simdt, plotdt)
for tab in moose.wildcardFind(DATA_NAME + '/##[TYPE=Table]'):
moose.setClock(tab.tick, plotdt)
for tick in range(0, 13):
moose.setClock(tick, simdt)
# 1 - CaConc, DifShell, DifBuffer
# 2 — channels and synchans
# 4 — compartments
# 5 - SpikeGen
# 6 — hsolver
# 7 - TimeTables for moose_nerp (see ttables.py)
# 8 - Tables
# 12 - Function
# problem if TimeTable uses plotdt?
moose.setClock(8, plotdt)
# 8 — hdf5datawriter, tables
for path in model_container_list:
if hsolveYN:
hsolve = moose.HSolve(path + '/hsolve')
hsolve.dt = simdt
# Compartment is transformed into zombiecompartment after below statement.
hsolve.target = path + '/' + name_soma
log.info("Using HSOLVE for {} clock {}", hsolve.path, hsolve.tick)
moose.reinit()
def assign_clocks(model_container, data_container, solver='euler'):
"""Assign clockticks to elements.
Parameters
----------
model_container: element
All model components are under this element. The model elements
are assigned clocks as required to maintain the right update
sequence.
INITCLOCK = 0 calls `init` method in Compartments
ELECCLOCK = 1 calls `process` method of Compartments
CHANCLOCK = 2 calls `process` method for HHChannels
POOLCLOCK = 3 is not used in electrical simulation
LOOKUPCLOCK = 6 is not used in these simulations.
STIMCLOCK = 7 calls `process` method in stimulus objects like
PulseGen.
data_container: element
All data recording tables are under this element. They are
assigned PLOTCLOCK, the clock whose update interval is plotdt.
PLOTCLOCK = 8 calls `process` method of Table elements under
data_container
"""
moose.useClock(STIMCLOCK,
model_container.path+'/##[TYPE=PulseGen]',
'process')
moose.useClock(PLOTCLOCK,
data_container.path+'/##[TYPE=Table]',
'process')
if solver == 'hsolve':
for neuron in moose.wildcardFind('%s/##[TYPE=Neuron]'):
solver = moose.HSolve(neuron.path+'/solve')
solver.dt = moose.element('/clock/tick[0]').dt
solver.target = neuron.path
moose.useClock(INITCLOCK,
model_container.path+'/##[TYPE=HSolve]',
'process')
else:
moose.useClock(INITCLOCK,
model_container.path+'/##[TYPE=Compartment]',
'init')
moose.useClock(ELECCLOCK,
model_container.path+'/##[TYPE=Compartment]',
'process')
moose.useClock(CHANCLOCK,
model_container.path+'/##[TYPE=HHChannel]',
'process')
moose.useClock(POOLCLOCK,
model_container.path+'/##[TYPE=CaConc]',
'process')
def __init__(self, path):
if not moose.exists(path):
path_tokens = path.rpartition('/')
moose.copy(self.prototype, path_tokens[0], path_tokens[-1])
moose.Neutral.__init__(self, path)
self.solver = moose.HSolve('{}/solver'.format(path, 'solver'))
self.solver.target = path
self.solver.dt = config.simulationSettings.simulationDt
def testNeuroMeshMultiscale():
runtime = 0.5
#elecDt = 0.2e-6
elecDt = 10e-6
chemDt = 0.0025
ePlotDt = 0.5e-3
cPlotDt = 0.0025
plotName = 'nm.plot'
makeNeuroMeshModel()
print "after model is completely done"
for i in moose.wildcardFind('/model/chem/#/#/#/transloc#'):
print i[0].name, i[0].Kf, i[0].Kb, i[0].kf, i[0].kb
makeChemPlots()
makeElecPlots()
makeCaPlots()
for i in range(10):
moose.setClock(i, elecDt)
for i in range(10, 20):
moose.setClock(i, chemDt)
moose.setClock(8, ePlotDt)
moose.setClock(18, cPlotDt)
moose.useClock(8, '/graphs/elec/#,/graphs/ca/#', 'process')
moose.useClock(18, '/graphs/chem/#', 'process')
hsolve = moose.HSolve('/model/elec/hsolve')
hsolve.dt = elecDt
hsolve.target = '/model/elec/compt'
plotlist = makeGraphics()
moose.reinit()
moose.element('/model/elec/soma').inject = 2e-10
moose.element('/model/chem/psd/Ca').concInit = 0.001
moose.element('/model/chem/spine/Ca').concInit = 0.002
moose.element('/model/chem/dend/DEND/Ca').concInit = 0.003
moose.reinit()
numDivs = 200
partialRuntime = runtime / numDivs
max_voxel = find_max_voxel()
voxel_val_dict = {
'spine': numpy.zeros((max_voxel, numDivs)),
'dend': numpy.zeros((max_voxel, numDivs)),
'elec': numpy.zeros((max_voxel, numDivs)),
'spineCaM': numpy.zeros((max_voxel, numDivs)),
'psdCaM': numpy.zeros((max_voxel, numDivs))
}
for i in range(numDivs):
moose.start(partialRuntime)
voxel_val_dict = updateGraphics(plotlist, voxel_val_dict,
i) #Edited by Chaitanya
# moose.element( '/model/elec/soma' ).inject = 0
# moose.start( 0.25 )
save_NSDF(cPlotDt, ePlotDt, voxel_val_dict,
[max_voxel, numDivs, partialRuntime]) #Edited by Chaitanya
finalizeGraphics(plotlist, cPlotDt, ePlotDt)
def __init__(self, path):
self.path = path
if not moose.exists(self.path):
path_tokens = path.rpartition('/')
moose.copy(self.prototype, path_tokens[0], path_tokens[-1])
self.name = path.split('/')[-1]
self.solver = moose.HSolve('{}/solver'.format(path))
self.solver.target = path
self.solver.dt = config.simulationSettings.simulationDt
def _configureClocks( self ):
for i in range( 0, 8 ):
moose.setClock( i, self.elecDt )
moose.setClock( 10, self.diffDt )
for i in range( 11, 18 ):
moose.setClock( i, self.chemDt )
moose.setClock( 18, self.chemDt * 5.0 )
hsolve = moose.HSolve( self.elecid.path + '/hsolve' )
hsolve.dt = self.elecDt
hsolve.target = self.soma.path
def test_hsolve_calcium():
for tick in range(0, 7):
moose.setClock(tick, 10e-6)
moose.setClock(8, 0.005)
lib = moose.Neutral('/library')
model = moose.loadModel(p_file, 'neuron')
assert model, model
pulse = moose.PulseGen('/neuron/pulse')
inject = 100e-10
chan_proto.chan_proto('/library/SK', param_chan.SK)
chan_proto.chan_proto('/library/CaL12', param_chan.Cal)
pulse.delay[0] = 8.
pulse.width[0] = 500e-12
pulse.level[0] = inject
pulse.delay[1] = 1e9
for comp in moose.wildcardFind('/neuron/#[TYPE=Compartment]'):
new_comp = moose.element(comp)
new_comp.initVm = -.08
difs, difb = td.add_difshells_and_buffers(new_comp, difshell_no,
difbuf_no)
for name in cond:
chan = td.addOneChan(name, cond[name], new_comp)
if 'Ca' in name:
moose.connect(chan, "IkOut", difs[0], "influx")
if 'SK' in name:
moose.connect(difs[0], 'concentrationOut', chan, 'concen')
data = moose.Neutral('/data')
vmtab = moose.Table('/data/Vm')
shelltab = moose.Table('/data/Ca')
caltab = moose.Table('/data/CaL_Gk')
sktab = moose.Table('/data/SK_Gk')
moose.connect(vmtab, 'requestOut', moose.element('/neuron/soma'), 'getVm')
moose.connect(shelltab, 'requestOut', difs[0], 'getC')
moose.connect(caltab, 'requestOut', moose.element('/neuron/soma/CaL12'),
'getGk')
moose.connect(sktab, 'requestOut', moose.element('/neuron/soma/SK'),
'getGk')
hsolve = moose.HSolve('/neuron/hsolve')
hsolve.dt = 10e-6
hsolve.target = ('/neuron/soma')
t_stop = 10.
moose.reinit()
moose.start(t_stop)
vec1 = sktab.vector
vec2 = shelltab.vector
assert_stat(vec1, [0.0, 5.102834e-22, 4.79066e-22, 2.08408e-23])
assert_stat(vec2, [5.0e-5, 5.075007e-5, 5.036985e-5, 2.1950117e-7])
assert len(np.where(sktab.vector < 1e-19)[0]) == 2001
assert len(np.where(shelltab.vector > 50e-6)[0]) == 2000
def schedule(self, simdt, plotdt, solver):
config.logger.info('Scheduling: simdt=%g, plotdt=%g, solver=%s' % (simdt, plotdt, solver))
self.simdt = simdt
self.plotdt = plotdt
self.solver = solver
if self.solver == 'hsolve':
self.hsolve = moose.HSolve('%s/solver' % (self.cell.path))
self.hsolve.dt = simdt
self.hsolve.target = self.cell.path
mutils.setDefaultDt(elecdt=simdt, plotdt2=plotdt)
mutils.assignDefaultTicks(modelRoot=self.model_container.path,
dataRoot=self.data_container.path,
solver=self.solver)
def testNeuroMeshMultiscale():
elecDt = 50e-6
chemDt = 2e-3
plotDt = 5e-4
plotName = 'nm.plot'
makeNeuroMeshModel()
"""
moose.le( '/model/chem/spineMesh/ksolve' )
print 'Neighbors:'
for t in moose.element( '/model/chem/spineMesh/ksolve/junction' ).neighbors['masterJunction']:
print 'masterJunction <-', t.path
for t in moose.wildcardFind( '/model/chem/#Mesh/ksolve' ):
k = moose.element( t[0] )
print k.path + ' localVoxels=', k.numLocalVoxels, ', allVoxels= ', k.numAllVoxels
"""
makeChemPlots()
makeElecPlots()
moose.setClock(0, elecDt)
moose.setClock(1, elecDt)
moose.setClock(2, elecDt)
moose.setClock(5, chemDt)
moose.setClock(6, chemDt)
moose.setClock(7, plotDt)
moose.setClock(8, plotDt)
moose.useClock(0, '/model/elec/##[ISA=Compartment]', 'init')
moose.useClock(1, '/model/elec/##[ISA=SpikeGen]', 'process')
moose.useClock(
2,
'/model/elec/##[ISA=ChanBase],/model/##[ISA=SynBase],/model/##[ISA=CaConc]',
'process')
moose.useClock(
5,
'/model/chem/##[ISA=PoolBase],/model/##[ISA=ReacBase],/model/##[ISA=EnzBase]',
'process')
moose.useClock(6, '/model/chem/##[ISA=Adaptor]', 'process')
moose.useClock(7, '/graphs/#', 'process')
moose.useClock(8, '/graphs/elec/#', 'process')
moose.useClock(5, '/model/chem/#Mesh/ksolve', 'init')
moose.useClock(6, '/model/chem/#Mesh/ksolve', 'process')
hsolve = moose.HSolve('/model/elec/hsolve')
moose.useClock(1, '/model/elec/hsolve', 'process')
hsolve.dt = elecDt
hsolve.target = '/model/elec/compt'
moose.reinit()
moose.reinit()
moose.start(1.0)
dumpPlots(plotName)
def makeSolvers(elecDt):
# Put in the solvers, see how they fare.
# Here we kludge in a single chem solver for the whole system.
ksolve = moose.Ksolve('/model/ksolve')
stoich = moose.Stoich('/model/stoich')
stoich.compartment = moose.element('/model/chem/neuroMesh')
stoich.ksolve = ksolve
stoich.path = '/model/chem/##'
moose.useClock(5, '/model/ksolve', 'init')
moose.useClock(6, '/model/ksolve', 'process')
# Here is the elec solver
hsolve = moose.HSolve('/model/hsolve')
moose.useClock(1, '/model/hsolve', 'process')
hsolve.dt = elecDt
hsolve.target = '/model/elec/compt'
def run_model():
model = moose.Neutral('/model')
data = moose.Neutral('/data')
cell = TuftedIB('/model/TuftedIB')
stim = alpha_stimulus('/model/stim', 1.0e-9, 15e-3, 20e-3, simtime, simdt)
stim.startTime = 1e9
p1 = cell.path + '/' + d1
p2 = cell.path + '/' + d2
comp_d1 = moose.element(p1) if moose.exists(p1) else moose.Compartment(p1)
comp_d2 = moose.element(p2) if moose.exists(p2) else moose.Compartment(p2)
s = '%s/%s' % (cell.path, 'comp_1')
comp_soma = moose.element(s) if moose.exists(s) else moose.Compartment(s)
comp_soma.inject = -0.2e-9
moose.connect(stim, 'output', comp_d1, 'injectMsg')
tab_d1 = moose.Table('%s/d1_Vm' % (data.path))
tab_d2 = moose.Table('%s/d2_Vm' % (data.path))
tab_soma = moose.Table('%s/soma_Vm' % (data.path))
tab_stim = moose.Table('%s/stim' % (data.path))
moose.connect(tab_d1, 'requestOut', comp_d1, 'getVm')
moose.connect(tab_d2, 'requestOut', comp_d2, 'getVm')
moose.connect(tab_soma, 'requestOut', comp_soma, 'getVm')
moose.connect(stim, 'output', tab_stim, 'input')
solver = moose.HSolve('%s/solver' % (cell.path))
solver.dt = simdt
solver.target = cell.path
utils.setDefaultDt(elecdt=simdt, plotdt2=plotdt)
utils.assignDefaultTicks()
moose.reinit()
utils.stepRun(simtime, 1e5 * simdt, logger=config.logger)
pylab.subplot(211)
pylab.plot(np.linspace(0, simtime, len(tab_d1.vector)),
tab_d1.vector * 1e3,
label='D1 Vm (mV)')
pylab.plot(np.linspace(0, simtime, len(tab_d2.vector)),
tab_d2.vector * 1e3,
label='D2 Vm (mV)')
pylab.plot(np.linspace(0, simtime, len(tab_soma.vector)),
tab_soma.vector * 1e3,
label='SOMA Vm (mV)')
pylab.legend()
pylab.subplot(212)
pylab.plot(np.linspace(0, simtime, len(tab_stim.vector)),
tab_stim.vector * 1e9,
label='Stimulus (nA)')
pylab.legend()
pylab.savefig('fig_a4c.png')
pylab.show()
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 testCubeMultiscale(useSolver):
elecDt = 10e-6
chemDt = 1e-4
plotDt = 5e-4
plotName = 'cm.plot'
if (useSolver):
elecDt = 50e-6
chemDt = 2e-3
plotName = 'solve_cm.plot'
makeModelInCubeMesh()
makeChemPlots()
makeElecPlots()
'''
moose.setClock( 0, elecDt )
moose.setClock( 1, elecDt )
moose.setClock( 2, elecDt )
moose.setClock( 5, chemDt )
moose.setClock( 6, chemDt )
moose.setClock( 7, plotDt )
moose.setClock( 8, plotDt )
moose.useClock( 1, '/n/##[ISA=SpikeGen]', 'process' )
moose.useClock( 2, '/n/##[ISA=SynBase]','process')
moose.useClock( 6, '/n/##[ISA=Adaptor]', 'process' )
moose.useClock( 7, '/graphs/#', 'process' )
moose.useClock( 8, '/graphs/elec/#', 'process' )
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]','process')
moose.useClock( 5, '/n/##[ISA=PoolBase],/n/##[ISA=ReacBase],/n/##[ISA=EnzBase]', 'process' )
'''
if (useSolver):
ksolve = moose.Ksolve('/n/ksolve')
stoich = moose.Stoich('/n/stoich')
stoich.compartment = moose.element('/n/chem/neuroMesh')
stoich.ksolve = ksolve
stoich.path = '/n/##'
ksolve.method = 'rk5'
#moose.useClock( 5, '/n/ksolve', 'process' )
hsolve = moose.HSolve('/n/hsolve')
#moose.useClock( 1, '/n/hsolve', 'process' )
hsolve.dt = elecDt
hsolve.target = '/n/compt'
moose.reinit()
moose.start(1)
displayPlots()
def run_current_pulse(amps,
delay=100e-3,
dur=100e-3,
trail=100e-3,
outfile='f_i_curves_data.h5'):
models = []
model = moose.Neutral('/model')
data = moose.Neutral('/data')
ddict = defaultdict(list)
for ii, amp in enumerate(amps):
mc = moose.Neutral('{}/mc_{}'.format(model.path, ii))
models.append(mc)
stim = moose.PulseGen('{}/stim_{}'.format(mc.path, ii))
stim.delay[0] = delay
stim.width[0] = dur
stim.level[0] = amp
stim.delay[
1] = 1e9 # make delay so large that it does not activate again
for celltype in [SpinyStellate, DeepBasket, DeepLTS]:
cell = celltype('{}/{}_{}'.format(mc.path, celltype.__name__, ii))
solver = moose.HSolve('{}/solver'.format(cell.path))
solver.dt = simdt
solver.target = cell.path
stim.connect('output', cell.soma, 'injectMsg')
tab = moose.Table('/data/Vm_{}'.format(cell.name))
ddict[ii].append(tab)
tab.connect('requestOut', cell.soma, 'getVm')
mutils.setDefaultDt(elecdt=simdt, plotdt2=plotdt)
mutils.assignDefaultTicks(modelRoot='/model',
dataRoot='/data',
solver='hsolve')
moose.reinit()
print('Finished scheduling')
moose.start(delay + dur + trail)
print('Finished simulation')
# Save data
fd = h5.File(outfile, 'w')
for ii, tabs in ddict.items():
for tab in tabs:
print('Table', tab.name)
node = fd.create_dataset(tab.name, data=tab.vector)
node.attrs['current'] = amps[ii]
node.attrs['delay'] = delay
node.attrs['width'] = dur
fd.close()
print('Finished saving data in file', outfile)
def _configureClocks(self):
if self.turnOffElec:
elecDt = 1e6
diffDt = 0.1
chemDt = 0.1
else:
elecDt = self.elecDt
diffDt = self.diffDt
chemDt = self.chemDt
for i in range(0, 9):
moose.setClock(i, elecDt)
moose.setClock(10, diffDt)
for i in range(11, 18):
moose.setClock(i, chemDt)
moose.setClock(18, chemDt * 5.0)
hsolve = moose.HSolve(self.elecid.path + '/hsolve')
hsolve.dt = elecDt
hsolve.target = self.soma.path
def setup_model(root='/', hsolve=True):
moose.ce(root)
model = moose.Neutral('model')
data = moose.Neutral('data')
cell = DeepBasket('%s/deepbasket' % (model.path))
soma = moose.Compartment('%s/comp_1' % (cell.path))
if hsolve:
solver = moose.HSolve('%s/solve' % (cell.path))
solver.dt = simdt
solver.target = cell.path
pulse = moose.PulseGen('%s/stimulus' % (model.path))
moose.connect(pulse, 'output', soma, 'injectMsg')
tab_vm = moose.Table('%s/spinystellate_soma_Vm' % (data.path))
moose.connect(tab_vm, 'requestOut', soma, 'getVm')
tab_stim = moose.Table('%s/spinystellate_soma_inject' % (data.path))
moose.connect(tab_stim, 'requestOut', pulse, 'getOutputValue')
utils.setDefaultDt(elecdt=simdt, plotdt2=plotdt)
utils.assignDefaultTicks(model, data)
return {'stimulus': pulse, 'tab_vm': tab_vm, 'tab_stim': tab_stim}
def simulateSelected(self):
cellnames = [str(c.text()) for c in self.cellListWidget.selectedItems()]
assert(len(cellnames) == 1)
name = cellnames[0]
params = self.createCell(name)
print 'Here ......'
hsolve = moose.HSolve('%s/solver' % (params['cell'].path))
hsolve.dt = simdt
hsolve.target = params['cell'].path
mutils.setDefaultDt(elecdt=simdt, plotdt2=plotdt)
mutils.assignDefaultTicks(modelRoot=params['modelRoot'],
dataRoot=params['dataRoot'],
solver='hsolve')
delay = float(str(self.delayText.text()))
width = float(str(self.widthText.text()))
level = float(str(self.ampText.text()))
params['stimulus'].delay[0] = delay * 1e-3
params['stimulus'].width[0] = width * 1e-3
params['stimulus'].level[0] = level * 1e-12
moose.reinit()
simtime = float(str(self.simtimeEdit.text()))*1e-3
ts = datetime.now()
moose.start(simtime)
te = datetime.now()
td = te - ts
print 'Simulating %g s took %g s of computer time' % (simtime, td.days * 86400 + td.seconds + td.microseconds * 1e-6)
ts = np.linspace(0, simtime, len(params['somaVm'].vec))
vm = params['somaVm'].vec
stim = params['injectionCurrent'].vec
self.vmAxes.clear()
self.vmAxes.set_title('membrane potential at soma')
self.vmAxes.set_ylabel('mV')
self.vmAxes.plot(ts * 1e3, vm * 1e3, 'b-', label='Vm (mV)')
self.vmAxes.get_xaxis().set_visible(False)
self.stimAxes.clear()
self.stimAxes.set_title('current injected at soma')
self.stimAxes.set_ylabel('pA')
self.stimAxes.set_xlabel('ms')
self.stimAxes.plot(ts * 1e3, stim * 1e12, 'r-', label='Current (pA)')
self.gs.tight_layout(self.plotFigure)
# self.plotFigure.tight_layout()
self.plotCanvas.draw()
def assign_clocks(model_container_list, simdt, plotdt, hsolveYN, name_soma):
log.info('SimDt={}, PlotDt={}', simdt, plotdt)
for tab in moose.wildcardFind(DATA_NAME + '/##[TYPE=Table]'):
moose.setClock(tab.tick, plotdt)
for tick in range(0, 7):
moose.setClock(tick, simdt)
# 2 — channels
# 4 — compartments
# 6 — hsolver
moose.setClock(8, plotdt)
# 8 — hdf5datawriter
for path in model_container_list:
if hsolveYN:
hsolve = moose.HSolve(path + '/hsolve')
hsolve.dt = simdt
hsolve.target = path + '/' + name_soma
log.info("Using HSOLVE for {} clock {}", hsolve.path, hsolve.tick)
moose.reinit()
def main():
fineDt = 1e-5
coarseDt = 5e-5
make_spiny_compt()
make_plots()
for i in range(8):
moose.setClock(i, fineDt)
moose.setClock(8, coarseDt)
moose.reinit()
moose.start(0.1)
display_plots('instab.plot')
# make Hsolver and rerun
hsolve = moose.HSolve('/n/hsolve')
for i in range(8):
moose.setClock(i, coarseDt)
hsolve.dt = coarseDt
hsolve.target = '/n/compt'
moose.reinit()
moose.start(0.1)
display_plots('h_instab.plot')
pylab.show()
def testNeuroMeshMultiscale():
useHsolve = 0
runtime = 0.5
elecDt = 10e-6
chemDt = 0.005
ePlotDt = 0.5e-3
cPlotDt = 0.005
plotName = 'nm.plot'
makeNeuroMeshModel()
print("after model is completely done")
for i in moose.wildcardFind('/model/chem/#/#/#/transloc#'):
print((i[0].name, i[0].Kf, i[0].Kb, i[0].kf, i[0].kb))
makeChemPlots()
makeElecPlots()
makeCaPlots()
for i in range(10):
moose.setClock(i, elecDt)
for i in range(10, 20):
moose.setClock(i, chemDt)
moose.setClock(8, ePlotDt)
moose.setClock(18, cPlotDt)
if useHsolve:
hsolve = moose.HSolve('/model/elec/hsolve')
#moose.useClock( 1, '/model/elec/hsolve', 'process' )
hsolve.dt = elecDt
hsolve.target = '/model/elec/compt'
moose.reinit()
#soma = moose.element( '/model/elec/soma' )
moose.useClock(18, '/graphs/chem/#', 'process')
moose.useClock(8, '/graphs/elec/#,/graphs/ca/#', 'process')
moose.element('/model/elec/soma').inject = 2e-10
moose.element('/model/chem/psd/Ca').concInit = 0.001
moose.element('/model/chem/spine/Ca').concInit = 0.002
moose.element('/model/chem/dend/DEND/Ca').concInit = 0.003
moose.reinit()
moose.start(runtime)
makeGraphics(cPlotDt, ePlotDt)
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_()
dt = 50e-6 moose.setClock( 0, dt ) moose.setClock( 1, dt ) moose.setClock( 2, dt ) moose.setClock( 3, 2e-4 ) moose.useClock( 0, '/cell/##[ISA=Compartment]', 'init' ) moose.useClock( 1, '/cell/##[ISA=Compartment]', 'process' ) moose.useClock( 2, '/cell/##[ISA!=Compartment]', 'process' ) moose.useClock( 3, '/graphs/soma,/graphs/ca', 'process' ) print 2 moose.reinit() print 3 moose.start( 0.1 ) dumpPlots( '50usec.plot' ) print 4 moose.reinit() hsolve = moose.HSolve( '/cell/hsolve' ) moose.useClock( 1, '/cell/hsolve', 'process' ) hsolve.dt = dt hsolve.target = '/cell/soma' moose.reinit() moose.reinit() print 5 moose.start( 0.1 ) print 6 dumpPlots( 'h50usec.plot' ) print 7
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}