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 F5():
def __init__(self, filename):
# build plotting area
#
self.filename = filename
self.iv = IVCurve() # use standard IVCurve here...
self.temperature = 34
self.initdelay = 150.
def run(self):
self.post_cell = cells.Bushy.create(morphology=self.filename,
decorator=Decorator,
species='mouse',
modelType='XM13')
self.post_cell.set_temperature(float(self.temperature))
self.post_cell.set_d_lambda(
freq=2000.) # necessary to ensure appropriate spatial
self.iv.reset()
irange = self.post_cell.i_test_range
irange = {'pulse': (-0.6, 1.1, 0.2)}
self.durs = (self.initdelay + 20., 100., 50.)
self.iv.run(irange,
self.post_cell,
durs=self.durs,
temp=float(self.temperature),
initdelay=self.initdelay)
def plot(self):
pg.setConfigOption('background', 'w') # set background to white
pg.setConfigOption('foreground', 'k')
self.app = pg.mkQApp()
wintitle = 'test_decorator'
self.view = pg.GraphicsView()
self.layout = pg.GraphicsLayout() #(border=(100,100,100))
self.view.setCentralItem(self.layout)
self.view.resize(800, 600)
self.view.show()
self.plots = {}
nr1 = 6
nc = 10
for i in range(1, nr1):
self.plots['p%d' % i] = None
for i in range(1, nr1 + 1):
self.layout.addLayout(row=i, col=nc)
for i in range(1, nc + 1):
self.layout.addLayout(row=nr1 + 2, col=i)
self.plots['p1'] = self.layout.addPlot(row=1,
col=1,
rowspan=6,
colspan=9,
labels={
'left': 'V (mV)',
'bottom': 'Time (ms)'
})
self.plots['p2'] = self.layout.addPlot(row=7,
col=1,
rowspan=1,
colspan=9,
labels={
'left': 'I (nA)',
'bottom': 'Time (ms)'
})
for k in range(len(self.iv.voltage_traces)):
self.plots['p1'].plot(self.iv.time_values,
np.array(self.iv.voltage_traces[k]),
pen=pg.mkPen('k', width=0.75))
self.plots['p2'].plot(self.iv.time_values,
np.array(self.iv.current_traces[k]),
pen=pg.mkPen('k', width=0.75))
self.plots['p1'].setRange(xRange=(0.,
np.sum(self.durs) - self.initdelay),
yRange=(-160., 40.))
self.plots['p2'].setRange(xRange=(0.,
np.sum(self.durs) - self.initdelay),
yRange=(-1, 1))
PH.noaxes(self.plots['p1'])
PH.calbar(self.plots['p1'],
calbar=[125., -120., 10., 20.],
unitNames={
'x': 'ms',
'y': 'mV'
})
PH.noaxes(self.plots['p2'])
PH.calbar(self.plots['p2'],
calbar=[125, 0.1, 0., 0.5],
unitNames={
'x': 'ms',
'y': 'nA'
})
text = (u"{0:2d}\u00b0C {1:.2f}-{2:.2f} nA".format(
int(self.temperature), np.min(self.iv.current_cmd),
np.max(self.iv.current_cmd)))
ti = pg.TextItem(text, anchor=(1, 0))
ti.setFont(pg.QtGui.QFont('Arial', 9))
ti.setPos(120., -120.)
self.plots['p1'].addItem(ti)
class Toy(Protocol):
"""
Calls to encapsulate the model runs
Run a set of cells with defined parameters to show excitability patterns.
Note that cells from Rothman and Manis are run at 22C; others at various
temperatures depending on how they were initially measured and defined.
"""
def __init__(self):
super(Toy, self).__init__()
def current_name(self, name, n):
"""
From the name of the current model, get the current injection information
Parameters
---------
name : str (no default)
name of the cell type
n : int (no default)
"""
if len(self.celltypes[name][3]) > 2:
injs = self.celltypes[name][3]
injarr = np.linspace(injs[0], injs[1], injs[2], endpoint=True)
return '%.3f' % injarr[n]
else:
return '%.3f' % self.celltypes[name][3][n]
def getname(self, cell, ninj):
name = self.make_name(cell)
iname = self.current_name(name, ninj)
nname = name + ' ' + iname
return name, nname
def make_name(self, cell):
return cell + ', ' + self.celltypes[cell][1] + ':'
def run(self):
sre = re.compile(
'(?P<cell>\w+)(?:[, ]*)(?P<type>[\w-]*)(?:[, ]*)(?P<species>[\w-]*)'
) # regex for keys in cell types
self.celltypes = OrderedDict([
('Bushy, II', (cells.Bushy, "II", 'guineapig', (-0.5, 0.5, 11),
22)),
('Bushy, II-I', (cells.Bushy, "II-I", 'guineapig', (-0.5, 0.5, 11),
22)),
('DStellate, I-II', (cells.DStellate, 'I-II', 'guineapig',
(-0.3, 0.3, 9), 22)),
('TStellate, I-c', (cells.TStellate, "I-c", 'guineapig',
(-0.15, 0.15, 9), 22)),
('TStellate, I-t', (cells.TStellate, "I-t", 'guineapig',
(-0.15, 0.15, 9), 22)),
('Octopus, II-o', (cells.Octopus, 'II-o', 'guineapig', (-2.5, 2.5,
11), 22)),
('Bushy, II, Mouse', (cells.Bushy, "II", 'mouse', (-1, 1.2, 13),
34)),
('TStellate, I-c, Mouse', (cells.TStellate, "I-c", 'mouse',
(-1, 1, 9), 34)),
('DStellate, I-II, Mouse', (cells.DStellate, 'I-II', 'mouse',
(-0.5, 0.5, 9), 34)),
('Pyramidal, I, Rat', (cells.Pyramidal, 'I', 'rat', (-0.3, 0.4,
11), 34)),
('Cartwheel, I, Mouse', (cells.Cartwheel, 'I', 'mouse', (-0.5, 0.5,
9), 34)),
('Tuberculoventral, I, Mouse', (cells.Tuberculoventral, 'I',
'mouse', (-0.35, 1, 11), 34)),
('SGC, bm, Mouse', (cells.SGC, "bm", 'mouse', (-0.2, 0.6, 9), 34)),
('SGC, a, Mouse', (cells.SGC, "a", 'mouse', (-0.2, 0.6, 9), 34)),
])
dt = 0.025
h.dt = dt
h.celsius = 22
stim = {
'NP': 1,
'delay': 10,
'dur': 100,
'amp': 0.,
'dt': h.dt,
}
tend = stim['delay'] + stim['dur'] + 20.
netcells = {}
for c in self.celltypes.keys():
g = sre.match(c)
cellname = g.group('cell')
modelType = g.group('type')
species = self.celltypes[c][2]
if g.group('type') == '':
netcells[c] = self.celltypes[c][0].create()
else:
netcells[c] = self.celltypes[c][0].create(modelType=modelType,
species=species,
debug=False)
# dicts to hold data
pl = OrderedDict([])
pl2 = OrderedDict([])
rvec = OrderedDict([])
vec = OrderedDict([])
istim = OrderedDict([])
ncells = len(self.celltypes.keys())
#
# build plotting area
#
app = pg.mkQApp()
self.win = pg.GraphicsWindow()
self.win.setBackground('w')
self.win.resize(800, 600)
cols, rows = autorowcol(ncells)
row = 0
col = 0
labelStyle = {'color': '#000', 'font-size': '9pt', 'weight': 'normal'}
tickStyle = pg.QtGui.QFont('Arial', 9, pg.QtGui.QFont.Light)
self.iv = IVCurve() # use standard IVCurve here...
for n, name in enumerate(self.celltypes.keys()):
nrn_cell = netcells[
name] # get the Neuron object we are using for this cell class
injcmds = list(self.celltypes[name][3]) # list of injections
injcmds[2] = (injcmds[1] - injcmds[0]) / (
float(injcmds[2] - 1)) # convert to pulse format for IVCurve
temperature = self.celltypes[name][4]
nrn_cell.set_temperature(float(temperature))
ninjs = len(injcmds)
print('cell: ', name)
# print( 'injs: ', injcmds)
pl[name] = self.win.addPlot(labels={
'left': 'V (mV)',
'bottom': 'Time (ms)'
})
PH.nice_plot(pl[name])
pl[name].setTitle(title=name, font=pg.QtGui.QFont('Arial', 10))
col += 1
if col >= cols:
col = 0
self.win.nextRow()
row += 1
self.iv.reset()
self.iv.run({'pulse': [injcmds]},
nrn_cell,
durs=(stim['delay'], stim['dur'], 20.),
sites=None,
reppulse=None,
temp=float(temperature))
for k in range(len(self.iv.voltage_traces)):
pl[name].plot(self.iv.time_values,
self.iv.voltage_traces[k],
pen=pg.mkPen('k', width=0.75))
pl[name].setRange(xRange=(0., 130.), yRange=(-160., 40.))
PH.noaxes(pl[name])
PH.calbar(pl[self.celltypes.keys()[0]],
calbar=[0, -120., 10., 20.],
unitNames={
'x': 'ms',
'y': 'mV'
})
text = (u"{0:2d}\u00b0C {1:.2f}-{2:.2f} nA".format(
int(temperature), np.min(self.iv.current_cmd),
np.max(self.iv.current_cmd)))
ti = pg.TextItem(text, anchor=(1, 0))
ti.setFont(pg.QtGui.QFont('Arial', 9))
ti.setPos(120., -120.)
pl[name].addItem(ti)
# get overall Rin, etc; need to initialize all cells
nrn_cell.cell_initialize()
for n, name in enumerate(self.celltypes.keys()):
nrn_cell = netcells[name]
nrn_cell.vm0 = nrn_cell.soma.v
pars = nrn_cell.compute_rmrintau(auto_initialize=False)
print(
u'{0:>14s} [{1:>24s}] *** Rin = {2:6.1f} M\ohm Tau = {3:6.1f} ms Vm = {4:6.1f} mV'
.format(nrn_cell.status['name'], name, pars['Rin'],
pars['tau'], pars['v']))
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.")