def run_test(self, cell):
# run I/V test on cell
V0 = cell.find_i0(showinfo=True)
rmrintau = cell.compute_rmrintau(auto_initialize=False, vrange=None)
iv = IVCurve()
self.iv = iv
iv.run(cell.i_test_range, cell)
if self.audit:
iv.show(cell)
info = dict(
temp=iv.temp,
icmd=iv.current_cmd,
spikes=iv.spike_times(),
rmp=iv.rest_vm(),
rm_taum=iv.input_resistance_tau(),
vpeak=iv.peak_vm(),
vss=iv.steady_vm(),
rmrintau=rmrintau,
)
return info
class Tests():
"""
Class to select cells for tests
"""
def __init__(self):
pass
def selectCell(self, args):
"""
Parameters
----------
args : argparse args from command line
Returns
-------
cell
Instantiated cell of the selected celltype
"""
h.celsius = float(args.temp)
#
# Spiral Ganglion cell tests
#
if args.celltype == 'sgc': # morphology is always "point" for SGCs
cell = cells.SGC.create(debug=debugFlag,
species=args.species,
nach=args.nav,
ttx=args.ttx,
modelType=args.type)
#
# Bushy tests
#
elif args.celltype == 'bushy' and args.morphology == 'point':
cell = cells.Bushy.create(model='RM03',
species=args.species,
modelType=args.type,
ttx=args.ttx,
nach=args.nav,
debug=debugFlag)
# cell.soma().klt.gbar = 0.0003
elif args.celltype == 'bushy' and args.morphology == 'waxon':
cell = cells.Bushy.create(model='RM03',
species=args.species,
modelType=args.type,
nach=args.nav,
ttx=args.ttx,
debug=debugFlag)
cell.add_axon()
elif args.celltype == 'bushy' and args.morphology == 'stick':
cell = cells.Bushy.create(
model='RM03',
species=args.species,
modelType=args.type,
morphology='cnmodel/morphology/bushy_stick.hoc',
decorator=True,
nach=args.nav,
ttx=args.ttx,
debug=debugFlag)
h.topology()
elif args.celltype == 'bushycoop' and args.morphology == 'point':
cell = cells.Bushy.create(model='RM03',
species=args.species,
modelType=args.type,
ttx=args.ttx,
nach=args.nav,
debug=debugFlag)
#
# T-stellate tests
#
elif args.celltype == 'tstellate' and args.morphology == 'point':
cell = cells.TStellate.create(model='RM03',
species=args.species,
modelType=args.type,
nach=args.nav,
ttx=args.ttx,
debug=debugFlag)
elif args.celltype == 'tstellate' and args.morphology == 'stick':
cell = cells.TStellate.create(
model='RM03',
species=args.species,
modelType=args.type,
nach=args.nav,
ttx=args.ttx,
debug=debugFlag,
morphology='cnmodel/morphology/tstellate_stick.hoc',
decorator=True)
elif args.celltype == 'tstellatenav11' and args.morphology == 'point': # note this uses a different model...
print 'test_cells: Stellate NAV11'
cell = cells.TStellateNav11.create(model='Nav11',
species=args.species,
modelType=None,
ttx=args.ttx,
debug=debugFlag)
elif args.celltype == 'tstellatenav11' and args.morphology == 'stick': # note this uses a different model...
cell = cells.TStellateNav11.create(
model='Nav11',
species=args.species,
modelType=None,
morphology='cnmodel/morphology/tstellate_stick.hoc',
decorator=True,
ttx=args.ttx,
debug=debugFlag,
)
h.topology()
#
# Octopus cell tests
#
elif args.celltype == 'octopus' and args.morphology == 'point':
cell = cells.Octopus.create(
species=args.species,
modelType='RM03', # args.type,
nach=args.nav,
ttx=args.ttx,
debug=debugFlag)
elif args.celltype == 'octopus' and args.morphology == 'stick': # Go to spencer et al. model
cell = cells.Octopus.create(
modelType='Spencer',
species=args.species,
morphology='cnmodel/morphology/octopus_spencer_stick.hoc',
decorator=True,
nach=args.nav,
ttx=args.ttx,
debug=debugFlag)
h.topology()
#
# D-stellate tests
#
elif args.celltype == 'dstellate':
cell = cells.DStellate.create(debug=debugFlag,
species=args.species,
ttx=args.ttx,
modelType=args.type)
elif args.celltype == 'dstellateeager':
cell = cells.DStellateEager.create(debug=debugFlag,
ttx=args.ttx,
modelType=args.type)
#
# DCN pyramidal cell tests
#
elif args.celltype == 'pyramidal':
cell = cells.Pyramidal.create(modelType=args.type,
ttx=args.ttx,
debug=debugFlag)
#
# DCN tuberculoventral cell tests
#
elif args.celltype == 'tuberculoventral' and args.morphology == 'point':
cell = cells.Tuberculoventral.create(species='mouse',
modelType='TVmouse',
ttx=args.ttx,
nach=args.nav,
debug=debugFlag)
elif args.celltype == 'tuberculoventral' and args.morphology == 'stick':
cell = cells.Tuberculoventral.create(
species='mouse',
modelType='TVmouse',
morphology='cnmodel/morphology/tv_stick.hoc',
decorator=True,
ttx=args.ttx,
debug=debugFlag)
h.topology()
#
# DCN cartwheel cell tests
#
elif args.celltype == 'cartwheel':
cell = cells.Cartwheel.create(modelType=args.type,
ttx=args.ttx,
debug=debugFlag)
#
# MSO principal neuron tests
#
elif args.celltype == 'mso' and args.morphology == 'point':
cell = cells.MSO.create(model='RM03',
species=args.species,
modelType=args.type,
ttx=args.ttx,
nach=args.nav,
debug=debugFlag)
else:
raise ValueError(
"Cell Type %s and configurations nav=%s or config=%s are not available"
% (args.celltype, args.nav, args.morphology))
print(cell.__doc__)
self.cell = cell
def run_test(self, args):
"""
Run either vc or cc test, and plot the result
Parameters
----------
args : argparse args from command line
"""
self.cell.set_temperature(float(args.temp))
print self.cell.status
V0 = self.cell.find_i0(showinfo=True)
# self.cell.cell_initialize()
print 'Currents at nominal Vrest= %.2f I = 0: I = %g ' % (
V0, self.cell.i_currents(V=V0))
self.cell.print_mechs(self.cell.soma)
instant = self.cell.compute_rmrintau(auto_initialize=False,
vrange=None)
print(
' From Inst: Rin = {:7.1f} Tau = {:7.1f} Vm = {:7.1f}'.format(
instant['Rin'], instant['tau'], instant['v']))
if args.cc is True:
# define the current clamp electrode and default settings
self.iv = IVCurve()
self.iv.run(ccivrange[args.species][args.celltype],
self.cell,
durs=default_durs,
sites=sites,
reppulse=ptype,
temp=float(args.temp))
ret = self.iv.input_resistance_tau()
print(' From IV: Rin = {:7.1f} Tau = {:7.1f} Vm = {:7.1f}'.
format(ret['slope'], ret['tau'], ret['intercept']))
self.iv.show(cell=self.cell)
elif args.rmp is True:
print 'temperature: ', self.cell.status['temperature']
self.iv = IVCurve()
self.iv.run({'pulse': (0, 0, 1)},
self.cell,
durs=default_durs,
sites=sites,
reppulse=ptype,
temp=float(args.temp))
self.iv.show(cell=self.cell, rmponly=True)
elif args.vc is True:
# define the voltage clamp electrode and default settings
self.vc = VCCurve()
self.vc.run((-120, 40, 5), self.cell)
self.vc.show(cell=self.cell)
else:
raise ValueError(
"Nothing to run. Specify one of --cc, --vc, --rmp.")